Starting phenix.real_space_refine on Sun Mar 24 23:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kg7_9975/03_2024/6kg7_9975.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kg7_9975/03_2024/6kg7_9975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kg7_9975/03_2024/6kg7_9975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kg7_9975/03_2024/6kg7_9975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kg7_9975/03_2024/6kg7_9975.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kg7_9975/03_2024/6kg7_9975.pdb" } resolution = 3.8 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= 0.078 sd= 1.367 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 303 5.16 5 C 29862 2.51 5 N 7143 2.21 5 O 7584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 598": "NH1" <-> "NH2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1065": "NH1" <-> "NH2" Residue "A ARG 1075": "NH1" <-> "NH2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1092": "NH1" <-> "NH2" Residue "A PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A ARG 1174": "NH1" <-> "NH2" Residue "A PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A TYR 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1269": "NH1" <-> "NH2" Residue "A ASP 1274": "OD1" <-> "OD2" Residue "A TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1361": "NH1" <-> "NH2" Residue "A ASP 1432": "OD1" <-> "OD2" Residue "A ASP 1492": "OD1" <-> "OD2" Residue "A ASP 1499": "OD1" <-> "OD2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "A ARG 1504": "NH1" <-> "NH2" Residue "A GLU 1513": "OE1" <-> "OE2" Residue "A ARG 1514": "NH1" <-> "NH2" Residue "A ASP 1567": "OD1" <-> "OD2" Residue "A TYR 1568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1678": "OD1" <-> "OD2" Residue "A ARG 1689": "NH1" <-> "NH2" Residue "A ASP 1693": "OD1" <-> "OD2" Residue "A ARG 1702": "NH1" <-> "NH2" Residue "A ARG 1717": "NH1" <-> "NH2" Residue "A TYR 1724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1973": "OD1" <-> "OD2" Residue "A PHE 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2032": "NH1" <-> "NH2" Residue "A ARG 2033": "NH1" <-> "NH2" Residue "A TYR 2085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2100": "NH1" <-> "NH2" Residue "A ASP 2110": "OD1" <-> "OD2" Residue "A TYR 2238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2247": "OD1" <-> "OD2" Residue "A PHE 2276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2317": "OD1" <-> "OD2" Residue "A PHE 2345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2353": "OE1" <-> "OE2" Residue "A ARG 2381": "NH1" <-> "NH2" Residue "A PHE 2403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2422": "OD1" <-> "OD2" Residue "A ASP 2427": "OD1" <-> "OD2" Residue "A ARG 2462": "NH1" <-> "NH2" Residue "A TYR 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2508": "OD1" <-> "OD2" Residue "A PHE 2522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2557": "OE1" <-> "OE2" Residue "A GLU 2568": "OE1" <-> "OE2" Residue "A GLU 2570": "OE1" <-> "OE2" Residue "A ARG 2608": "NH1" <-> "NH2" Residue "A ARG 2632": "NH1" <-> "NH2" Residue "A PHE 2681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2690": "NH1" <-> "NH2" Residue "A ARG 2756": "NH1" <-> "NH2" Residue "A PHE 2759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2770": "OE1" <-> "OE2" Residue "A ASP 2783": "OD1" <-> "OD2" Residue "A ASP 2798": "OD1" <-> "OD2" Residue "A PHE 2805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "B PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B ARG 1075": "NH1" <-> "NH2" Residue "B TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1092": "NH1" <-> "NH2" Residue "B PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1173": "NH1" <-> "NH2" Residue "B ARG 1174": "NH1" <-> "NH2" Residue "B PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1210": "NH1" <-> "NH2" Residue "B TYR 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1257": "NH1" <-> "NH2" Residue "B ARG 1269": "NH1" <-> "NH2" Residue "B ASP 1274": "OD1" <-> "OD2" Residue "B TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1361": "NH1" <-> "NH2" Residue "B ASP 1432": "OD1" <-> "OD2" Residue "B ASP 1492": "OD1" <-> "OD2" Residue "B ASP 1499": "OD1" <-> "OD2" Residue "B ARG 1500": "NH1" <-> "NH2" Residue "B ARG 1504": "NH1" <-> "NH2" Residue "B GLU 1513": "OE1" <-> "OE2" Residue "B ARG 1514": "NH1" <-> "NH2" Residue "B ASP 1567": "OD1" <-> "OD2" Residue "B TYR 1568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1678": "OD1" <-> "OD2" Residue "B ARG 1689": "NH1" <-> "NH2" Residue "B ASP 1693": "OD1" <-> "OD2" Residue "B ARG 1702": "NH1" <-> "NH2" Residue "B ARG 1717": "NH1" <-> "NH2" Residue "B TYR 1724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1973": "OD1" <-> "OD2" Residue "B PHE 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2032": "NH1" <-> "NH2" Residue "B ARG 2033": "NH1" <-> "NH2" Residue "B TYR 2085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2100": "NH1" <-> "NH2" Residue "B ASP 2110": "OD1" <-> "OD2" Residue "B TYR 2238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2247": "OD1" <-> "OD2" Residue "B PHE 2276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2317": "OD1" <-> "OD2" Residue "B PHE 2345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2353": "OE1" <-> "OE2" Residue "B ARG 2381": "NH1" <-> "NH2" Residue "B PHE 2403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2422": "OD1" <-> "OD2" Residue "B ASP 2427": "OD1" <-> "OD2" Residue "B ARG 2462": "NH1" <-> "NH2" Residue "B TYR 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2508": "OD1" <-> "OD2" Residue "B PHE 2522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2557": "OE1" <-> "OE2" Residue "B GLU 2568": "OE1" <-> "OE2" Residue "B GLU 2570": "OE1" <-> "OE2" Residue "B ARG 2608": "NH1" <-> "NH2" Residue "B ARG 2632": "NH1" <-> "NH2" Residue "B PHE 2681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2690": "NH1" <-> "NH2" Residue "B ARG 2756": "NH1" <-> "NH2" Residue "B PHE 2759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2770": "OE1" <-> "OE2" Residue "B ASP 2783": "OD1" <-> "OD2" Residue "B ASP 2798": "OD1" <-> "OD2" Residue "B PHE 2805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 942": "OE1" <-> "OE2" Residue "C PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 997": "NH1" <-> "NH2" Residue "C TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1065": "NH1" <-> "NH2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1092": "NH1" <-> "NH2" Residue "C PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1173": "NH1" <-> "NH2" Residue "C ARG 1174": "NH1" <-> "NH2" Residue "C PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1210": "NH1" <-> "NH2" Residue "C TYR 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1257": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "C ASP 1274": "OD1" <-> "OD2" Residue "C TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1361": "NH1" <-> "NH2" Residue "C ASP 1432": "OD1" <-> "OD2" Residue "C ASP 1492": "OD1" <-> "OD2" Residue "C ASP 1499": "OD1" <-> "OD2" Residue "C ARG 1500": "NH1" <-> "NH2" Residue "C ARG 1504": "NH1" <-> "NH2" Residue "C GLU 1513": "OE1" <-> "OE2" Residue "C ARG 1514": "NH1" <-> "NH2" Residue "C ASP 1567": "OD1" <-> "OD2" Residue "C TYR 1568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1678": "OD1" <-> "OD2" Residue "C ARG 1689": "NH1" <-> "NH2" Residue "C ASP 1693": "OD1" <-> "OD2" Residue "C ARG 1702": "NH1" <-> "NH2" Residue "C ARG 1717": "NH1" <-> "NH2" Residue "C TYR 1724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1973": "OD1" <-> "OD2" Residue "C PHE 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2032": "NH1" <-> "NH2" Residue "C ARG 2033": "NH1" <-> "NH2" Residue "C TYR 2085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2100": "NH1" <-> "NH2" Residue "C ASP 2110": "OD1" <-> "OD2" Residue "C TYR 2238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2247": "OD1" <-> "OD2" Residue "C PHE 2276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2317": "OD1" <-> "OD2" Residue "C PHE 2345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2353": "OE1" <-> "OE2" Residue "C ARG 2381": "NH1" <-> "NH2" Residue "C PHE 2403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2422": "OD1" <-> "OD2" Residue "C ASP 2427": "OD1" <-> "OD2" Residue "C ARG 2462": "NH1" <-> "NH2" Residue "C TYR 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2508": "OD1" <-> "OD2" Residue "C PHE 2522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2557": "OE1" <-> "OE2" Residue "C GLU 2568": "OE1" <-> "OE2" Residue "C GLU 2570": "OE1" <-> "OE2" Residue "C ARG 2608": "NH1" <-> "NH2" Residue "C ARG 2632": "NH1" <-> "NH2" Residue "C PHE 2681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2690": "NH1" <-> "NH2" Residue "C ARG 2756": "NH1" <-> "NH2" Residue "C PHE 2759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2770": "OE1" <-> "OE2" Residue "C ASP 2783": "OD1" <-> "OD2" Residue "C ASP 2798": "OD1" <-> "OD2" Residue "C PHE 2805": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44892 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 14908 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 15299 Chain: "B" Number of atoms: 14908 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 15299 Chain: "C" Number of atoms: 14908 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 1817, 14900 Classifications: {'peptide': 1817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 64, 'TRANS': 1752} Chain breaks: 15 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 15299 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 42.06, per 1000 atoms: 0.94 Number of scatterers: 44892 At special positions: 0 Unit cell: (264.789, 250.779, 180.729, 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 303 16.00 O 7584 8.00 N 7143 7.00 C 29862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1031 " - pdb=" SG CYS A1209 " distance=2.03 Simple disulfide: pdb=" SG CYS B1031 " - pdb=" SG CYS B1209 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1209 " distance=2.03 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 Links applied NAG-ASN " NAG A3001 " - " ASN A 769 " " NAG A3002 " - " ASN A1030 " " NAG A3003 " - " ASN A1037 " " NAG A3004 " - " ASN A2642 " " NAG B3001 " - " ASN B 769 " " NAG B3002 " - " ASN B1030 " " NAG B3003 " - " ASN B1037 " " NAG B3004 " - " ASN B2642 " " NAG C3001 " - " ASN C 769 " " NAG C3002 " - " ASN C1030 " " NAG C3003 " - " ASN C1037 " " NAG C3004 " - " ASN C2642 " Time building additional restraints: 17.75 Conformation dependent library (CDL) restraints added in 15.3 seconds 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10464 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 9 sheets defined 68.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 Processing helix chain 'A' and resid 28 through 41 removed outlier: 4.315A pdb=" N VAL A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 51 through 77 removed outlier: 4.062A pdb=" N PHE A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 removed outlier: 4.161A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 4.020A pdb=" N SER A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 222 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 4.102A pdb=" N TYR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 287 removed outlier: 3.504A pdb=" N PHE A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 356 removed outlier: 3.745A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 515 removed outlier: 3.560A pdb=" N ILE A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 515 " --> pdb=" O TRP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.570A pdb=" N MET A 532 " --> pdb=" O CYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 561 removed outlier: 3.870A pdb=" N TYR A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 583 through 615 removed outlier: 4.040A pdb=" N THR A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 691 Processing helix chain 'A' and resid 691 through 704 removed outlier: 3.684A pdb=" N PHE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 700 " --> pdb=" O GLY A 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 removed outlier: 3.587A pdb=" N MET A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 758 removed outlier: 3.634A pdb=" N PHE A 740 " --> pdb=" O ILE A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 removed outlier: 4.350A pdb=" N GLN A 768 " --> pdb=" O PRO A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 789 through 812 removed outlier: 3.802A pdb=" N THR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Proline residue: A 798 - end of helix removed outlier: 3.520A pdb=" N TYR A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 820 Processing helix chain 'A' and resid 936 through 958 Processing helix chain 'A' and resid 959 through 974 Processing helix chain 'A' and resid 979 through 989 Processing helix chain 'A' and resid 992 through 996 Processing helix chain 'A' and resid 997 through 1017 removed outlier: 3.705A pdb=" N SER A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1100 removed outlier: 3.821A pdb=" N MET A1080 " --> pdb=" O ASN A1076 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1122 removed outlier: 3.909A pdb=" N ASP A1122 " --> pdb=" O HIS A1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1119 through 1122' Processing helix chain 'A' and resid 1123 through 1139 removed outlier: 6.787A pdb=" N PHE A1136 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR A1137 " --> pdb=" O ASN A1133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A1138 " --> pdb=" O TYR A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1156 removed outlier: 3.879A pdb=" N LEU A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1173 removed outlier: 4.213A pdb=" N ARG A1173 " --> pdb=" O GLY A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1180 removed outlier: 3.585A pdb=" N ILE A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 Processing helix chain 'A' and resid 1222 through 1229 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1242 through 1263 removed outlier: 4.085A pdb=" N ASP A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1270 Processing helix chain 'A' and resid 1303 through 1312 Processing helix chain 'A' and resid 1314 through 1325 Processing helix chain 'A' and resid 1333 through 1347 removed outlier: 4.249A pdb=" N TYR A1337 " --> pdb=" O PHE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1354 Processing helix chain 'A' and resid 1355 through 1380 removed outlier: 4.406A pdb=" N ILE A1359 " --> pdb=" O PRO A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1447 removed outlier: 3.550A pdb=" N MET A1447 " --> pdb=" O ARG A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1464 removed outlier: 4.261A pdb=" N HIS A1453 " --> pdb=" O TYR A1449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A1454 " --> pdb=" O TYR A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1513 removed outlier: 4.229A pdb=" N GLY A1468 " --> pdb=" O LEU A1464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1564 removed outlier: 3.948A pdb=" N ARG A1564 " --> pdb=" O ALA A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1571 Processing helix chain 'A' and resid 1669 through 1687 Processing helix chain 'A' and resid 1688 through 1712 Processing helix chain 'A' and resid 1718 through 1725 Processing helix chain 'A' and resid 1961 through 1973 removed outlier: 3.713A pdb=" N GLU A1965 " --> pdb=" O ASP A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1991 Processing helix chain 'A' and resid 1991 through 2007 Processing helix chain 'A' and resid 2010 through 2023 Proline residue: A2016 - end of helix Processing helix chain 'A' and resid 2024 through 2026 No H-bonds generated for 'chain 'A' and resid 2024 through 2026' Processing helix chain 'A' and resid 2031 through 2052 removed outlier: 3.521A pdb=" N TRP A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2086 through 2106 removed outlier: 3.704A pdb=" N HIS A2106 " --> pdb=" O ILE A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2250 removed outlier: 3.925A pdb=" N ILE A2241 " --> pdb=" O ILE A2237 " (cutoff:3.500A) Processing helix chain 'A' and resid 2259 through 2277 Processing helix chain 'A' and resid 2278 through 2280 No H-bonds generated for 'chain 'A' and resid 2278 through 2280' Processing helix chain 'A' and resid 2301 through 2323 removed outlier: 3.871A pdb=" N VAL A2305 " --> pdb=" O GLY A2301 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2347 removed outlier: 3.616A pdb=" N PHE A2338 " --> pdb=" O VAL A2334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A2347 " --> pdb=" O TRP A2343 " (cutoff:3.500A) Processing helix chain 'A' and resid 2355 through 2358 Processing helix chain 'A' and resid 2359 through 2383 Processing helix chain 'A' and resid 2398 through 2410 Processing helix chain 'A' and resid 2414 through 2425 removed outlier: 3.562A pdb=" N TRP A2425 " --> pdb=" O MET A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2431 through 2458 Processing helix chain 'A' and resid 2467 through 2488 removed outlier: 3.663A pdb=" N PHE A2488 " --> pdb=" O CYS A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2491 No H-bonds generated for 'chain 'A' and resid 2489 through 2491' Processing helix chain 'A' and resid 2535 through 2546 removed outlier: 3.751A pdb=" N PHE A2546 " --> pdb=" O PHE A2542 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2557 removed outlier: 3.510A pdb=" N LEU A2556 " --> pdb=" O ALA A2552 " (cutoff:3.500A) Processing helix chain 'A' and resid 2580 through 2593 removed outlier: 3.715A pdb=" N THR A2592 " --> pdb=" O ILE A2588 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A2593 " --> pdb=" O GLN A2589 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2640 Processing helix chain 'A' and resid 2740 through 2761 removed outlier: 3.518A pdb=" N GLU A2757 " --> pdb=" O LYS A2753 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A2758 " --> pdb=" O PHE A2754 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A2759 " --> pdb=" O VAL A2755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A2761 " --> pdb=" O GLU A2757 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2767 removed outlier: 3.647A pdb=" N ILE A2766 " --> pdb=" O SER A2763 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A2767 " --> pdb=" O HIS A2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2763 through 2767' Processing helix chain 'A' and resid 2774 through 2791 Processing helix chain 'A' and resid 2792 through 2808 Processing helix chain 'A' and resid 2809 through 2817 Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 28 through 41 removed outlier: 4.315A pdb=" N VAL B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 51 through 77 removed outlier: 4.062A pdb=" N PHE B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 removed outlier: 4.161A pdb=" N ILE B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 removed outlier: 4.021A pdb=" N SER B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 222 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LYS B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 removed outlier: 4.102A pdb=" N TYR B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 287 removed outlier: 3.505A pdb=" N PHE B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.746A pdb=" N LEU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 515 removed outlier: 3.560A pdb=" N ILE B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 514 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.570A pdb=" N MET B 532 " --> pdb=" O CYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 561 removed outlier: 3.870A pdb=" N TYR B 539 " --> pdb=" O ASN B 535 " (cutoff:3.500A) Proline residue: B 545 - end of helix Processing helix chain 'B' and resid 583 through 615 removed outlier: 4.040A pdb=" N THR B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 691 Processing helix chain 'B' and resid 691 through 704 removed outlier: 3.684A pdb=" N PHE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 700 " --> pdb=" O GLY B 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 701 " --> pdb=" O GLY B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 729 removed outlier: 3.587A pdb=" N MET B 716 " --> pdb=" O LYS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 758 removed outlier: 3.634A pdb=" N PHE B 740 " --> pdb=" O ILE B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 removed outlier: 4.351A pdb=" N GLN B 768 " --> pdb=" O PRO B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 780 Processing helix chain 'B' and resid 789 through 812 removed outlier: 3.802A pdb=" N THR B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Proline residue: B 798 - end of helix removed outlier: 3.520A pdb=" N TYR B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 936 through 958 Processing helix chain 'B' and resid 959 through 974 Processing helix chain 'B' and resid 979 through 989 Processing helix chain 'B' and resid 992 through 996 Processing helix chain 'B' and resid 997 through 1017 removed outlier: 3.706A pdb=" N SER B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS B1008 " --> pdb=" O THR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1100 removed outlier: 3.821A pdb=" N MET B1080 " --> pdb=" O ASN B1076 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B1088 " --> pdb=" O LEU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1122 removed outlier: 3.908A pdb=" N ASP B1122 " --> pdb=" O HIS B1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1119 through 1122' Processing helix chain 'B' and resid 1123 through 1139 removed outlier: 6.788A pdb=" N PHE B1136 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR B1137 " --> pdb=" O ASN B1133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B1138 " --> pdb=" O TYR B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1156 removed outlier: 3.879A pdb=" N LEU B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1157 through 1173 removed outlier: 4.213A pdb=" N ARG B1173 " --> pdb=" O GLY B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1175 through 1180 removed outlier: 3.585A pdb=" N ILE B1179 " --> pdb=" O ARG B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1182 through 1202 Processing helix chain 'B' and resid 1222 through 1229 Processing helix chain 'B' and resid 1239 through 1241 No H-bonds generated for 'chain 'B' and resid 1239 through 1241' Processing helix chain 'B' and resid 1242 through 1263 removed outlier: 4.085A pdb=" N ASP B1246 " --> pdb=" O PHE B1242 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1270 Processing helix chain 'B' and resid 1303 through 1312 Processing helix chain 'B' and resid 1314 through 1325 Processing helix chain 'B' and resid 1333 through 1347 removed outlier: 4.249A pdb=" N TYR B1337 " --> pdb=" O PHE B1333 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1354 Processing helix chain 'B' and resid 1355 through 1380 removed outlier: 4.406A pdb=" N ILE B1359 " --> pdb=" O PRO B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1430 through 1447 removed outlier: 3.550A pdb=" N MET B1447 " --> pdb=" O ARG B1443 " (cutoff:3.500A) Processing helix chain 'B' and resid 1449 through 1464 removed outlier: 4.262A pdb=" N HIS B1453 " --> pdb=" O TYR B1449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B1454 " --> pdb=" O TYR B1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 1464 through 1513 removed outlier: 4.229A pdb=" N GLY B1468 " --> pdb=" O LEU B1464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B1469 " --> pdb=" O ALA B1465 " (cutoff:3.500A) Processing helix chain 'B' and resid 1558 through 1564 removed outlier: 3.949A pdb=" N ARG B1564 " --> pdb=" O ALA B1560 " (cutoff:3.500A) Processing helix chain 'B' and resid 1567 through 1571 Processing helix chain 'B' and resid 1669 through 1687 Processing helix chain 'B' and resid 1688 through 1712 Processing helix chain 'B' and resid 1718 through 1725 Processing helix chain 'B' and resid 1961 through 1973 removed outlier: 3.713A pdb=" N GLU B1965 " --> pdb=" O ASP B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1991 Processing helix chain 'B' and resid 1991 through 2007 Processing helix chain 'B' and resid 2010 through 2023 Proline residue: B2016 - end of helix Processing helix chain 'B' and resid 2024 through 2026 No H-bonds generated for 'chain 'B' and resid 2024 through 2026' Processing helix chain 'B' and resid 2031 through 2052 removed outlier: 3.521A pdb=" N TRP B2035 " --> pdb=" O SER B2031 " (cutoff:3.500A) Processing helix chain 'B' and resid 2086 through 2106 removed outlier: 3.704A pdb=" N HIS B2106 " --> pdb=" O ILE B2102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2237 through 2250 removed outlier: 3.924A pdb=" N ILE B2241 " --> pdb=" O ILE B2237 " (cutoff:3.500A) Processing helix chain 'B' and resid 2259 through 2277 Processing helix chain 'B' and resid 2278 through 2280 No H-bonds generated for 'chain 'B' and resid 2278 through 2280' Processing helix chain 'B' and resid 2301 through 2323 removed outlier: 3.871A pdb=" N VAL B2305 " --> pdb=" O GLY B2301 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2347 removed outlier: 3.616A pdb=" N PHE B2338 " --> pdb=" O VAL B2334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B2347 " --> pdb=" O TRP B2343 " (cutoff:3.500A) Processing helix chain 'B' and resid 2355 through 2358 Processing helix chain 'B' and resid 2359 through 2383 Processing helix chain 'B' and resid 2398 through 2410 Processing helix chain 'B' and resid 2414 through 2425 removed outlier: 3.561A pdb=" N TRP B2425 " --> pdb=" O MET B2421 " (cutoff:3.500A) Processing helix chain 'B' and resid 2431 through 2458 Processing helix chain 'B' and resid 2467 through 2488 removed outlier: 3.663A pdb=" N PHE B2488 " --> pdb=" O CYS B2484 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2491 No H-bonds generated for 'chain 'B' and resid 2489 through 2491' Processing helix chain 'B' and resid 2535 through 2546 removed outlier: 3.752A pdb=" N PHE B2546 " --> pdb=" O PHE B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2552 through 2557 removed outlier: 3.510A pdb=" N LEU B2556 " --> pdb=" O ALA B2552 " (cutoff:3.500A) Processing helix chain 'B' and resid 2580 through 2593 removed outlier: 3.715A pdb=" N THR B2592 " --> pdb=" O ILE B2588 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP B2593 " --> pdb=" O GLN B2589 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2640 Processing helix chain 'B' and resid 2740 through 2761 removed outlier: 3.518A pdb=" N GLU B2757 " --> pdb=" O LYS B2753 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B2758 " --> pdb=" O PHE B2754 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B2759 " --> pdb=" O VAL B2755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B2761 " --> pdb=" O GLU B2757 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2767 removed outlier: 3.647A pdb=" N ILE B2766 " --> pdb=" O SER B2763 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET B2767 " --> pdb=" O HIS B2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2763 through 2767' Processing helix chain 'B' and resid 2774 through 2791 Processing helix chain 'B' and resid 2792 through 2808 Processing helix chain 'B' and resid 2809 through 2817 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 28 through 41 removed outlier: 4.315A pdb=" N VAL C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 51 through 77 removed outlier: 4.062A pdb=" N PHE C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 142 removed outlier: 4.161A pdb=" N ILE C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 removed outlier: 4.021A pdb=" N SER C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL C 225 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 4.102A pdb=" N TYR C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 287 removed outlier: 3.504A pdb=" N PHE C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 356 removed outlier: 3.745A pdb=" N LEU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 515 removed outlier: 3.560A pdb=" N ILE C 496 " --> pdb=" O VAL C 492 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 515 " --> pdb=" O TRP C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 532 removed outlier: 3.570A pdb=" N MET C 532 " --> pdb=" O CYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 561 removed outlier: 3.870A pdb=" N TYR C 539 " --> pdb=" O ASN C 535 " (cutoff:3.500A) Proline residue: C 545 - end of helix Processing helix chain 'C' and resid 583 through 615 removed outlier: 4.040A pdb=" N THR C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 691 Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.684A pdb=" N PHE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE C 700 " --> pdb=" O GLY C 696 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 701 " --> pdb=" O GLY C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 729 removed outlier: 3.586A pdb=" N MET C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 758 removed outlier: 3.634A pdb=" N PHE C 740 " --> pdb=" O ILE C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 4.351A pdb=" N GLN C 768 " --> pdb=" O PRO C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 789 through 812 removed outlier: 3.802A pdb=" N THR C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Proline residue: C 798 - end of helix removed outlier: 3.520A pdb=" N TYR C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 820 Processing helix chain 'C' and resid 936 through 958 Processing helix chain 'C' and resid 959 through 974 Processing helix chain 'C' and resid 979 through 989 Processing helix chain 'C' and resid 992 through 996 Processing helix chain 'C' and resid 997 through 1017 removed outlier: 3.705A pdb=" N SER C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C1008 " --> pdb=" O THR C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1074 through 1100 removed outlier: 3.821A pdb=" N MET C1080 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C1088 " --> pdb=" O LEU C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1122 removed outlier: 3.909A pdb=" N ASP C1122 " --> pdb=" O HIS C1119 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1119 through 1122' Processing helix chain 'C' and resid 1123 through 1139 removed outlier: 6.787A pdb=" N PHE C1136 " --> pdb=" O VAL C1132 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR C1137 " --> pdb=" O ASN C1133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C1138 " --> pdb=" O TYR C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1156 removed outlier: 3.879A pdb=" N LEU C1146 " --> pdb=" O GLU C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1157 through 1173 removed outlier: 4.213A pdb=" N ARG C1173 " --> pdb=" O GLY C1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 1175 through 1180 removed outlier: 3.585A pdb=" N ILE C1179 " --> pdb=" O ARG C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1182 through 1202 Processing helix chain 'C' and resid 1222 through 1229 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1242 through 1263 removed outlier: 4.085A pdb=" N ASP C1246 " --> pdb=" O PHE C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1265 through 1270 Processing helix chain 'C' and resid 1303 through 1312 Processing helix chain 'C' and resid 1314 through 1325 Processing helix chain 'C' and resid 1333 through 1347 removed outlier: 4.249A pdb=" N TYR C1337 " --> pdb=" O PHE C1333 " (cutoff:3.500A) Processing helix chain 'C' and resid 1350 through 1354 Processing helix chain 'C' and resid 1355 through 1380 removed outlier: 4.406A pdb=" N ILE C1359 " --> pdb=" O PRO C1355 " (cutoff:3.500A) Processing helix chain 'C' and resid 1430 through 1447 removed outlier: 3.549A pdb=" N MET C1447 " --> pdb=" O ARG C1443 " (cutoff:3.500A) Processing helix chain 'C' and resid 1449 through 1464 removed outlier: 4.262A pdb=" N HIS C1453 " --> pdb=" O TYR C1449 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL C1454 " --> pdb=" O TYR C1450 " (cutoff:3.500A) Processing helix chain 'C' and resid 1464 through 1513 removed outlier: 4.229A pdb=" N GLY C1468 " --> pdb=" O LEU C1464 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C1469 " --> pdb=" O ALA C1465 " (cutoff:3.500A) Processing helix chain 'C' and resid 1558 through 1564 removed outlier: 3.949A pdb=" N ARG C1564 " --> pdb=" O ALA C1560 " (cutoff:3.500A) Processing helix chain 'C' and resid 1567 through 1571 Processing helix chain 'C' and resid 1669 through 1687 Processing helix chain 'C' and resid 1688 through 1712 Processing helix chain 'C' and resid 1718 through 1725 Processing helix chain 'C' and resid 1961 through 1973 removed outlier: 3.714A pdb=" N GLU C1965 " --> pdb=" O ASP C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1991 Processing helix chain 'C' and resid 1991 through 2007 Processing helix chain 'C' and resid 2010 through 2023 Proline residue: C2016 - end of helix Processing helix chain 'C' and resid 2024 through 2026 No H-bonds generated for 'chain 'C' and resid 2024 through 2026' Processing helix chain 'C' and resid 2031 through 2052 removed outlier: 3.521A pdb=" N TRP C2035 " --> pdb=" O SER C2031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2086 through 2106 removed outlier: 3.704A pdb=" N HIS C2106 " --> pdb=" O ILE C2102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2250 removed outlier: 3.925A pdb=" N ILE C2241 " --> pdb=" O ILE C2237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2259 through 2277 Processing helix chain 'C' and resid 2278 through 2280 No H-bonds generated for 'chain 'C' and resid 2278 through 2280' Processing helix chain 'C' and resid 2301 through 2323 removed outlier: 3.871A pdb=" N VAL C2305 " --> pdb=" O GLY C2301 " (cutoff:3.500A) Processing helix chain 'C' and resid 2326 through 2347 removed outlier: 3.616A pdb=" N PHE C2338 " --> pdb=" O VAL C2334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C2347 " --> pdb=" O TRP C2343 " (cutoff:3.500A) Processing helix chain 'C' and resid 2355 through 2358 Processing helix chain 'C' and resid 2359 through 2383 Processing helix chain 'C' and resid 2398 through 2410 Processing helix chain 'C' and resid 2414 through 2425 removed outlier: 3.561A pdb=" N TRP C2425 " --> pdb=" O MET C2421 " (cutoff:3.500A) Processing helix chain 'C' and resid 2431 through 2458 Processing helix chain 'C' and resid 2467 through 2488 removed outlier: 3.663A pdb=" N PHE C2488 " --> pdb=" O CYS C2484 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2491 No H-bonds generated for 'chain 'C' and resid 2489 through 2491' Processing helix chain 'C' and resid 2535 through 2546 removed outlier: 3.751A pdb=" N PHE C2546 " --> pdb=" O PHE C2542 " (cutoff:3.500A) Processing helix chain 'C' and resid 2552 through 2557 removed outlier: 3.511A pdb=" N LEU C2556 " --> pdb=" O ALA C2552 " (cutoff:3.500A) Processing helix chain 'C' and resid 2580 through 2593 removed outlier: 3.715A pdb=" N THR C2592 " --> pdb=" O ILE C2588 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP C2593 " --> pdb=" O GLN C2589 " (cutoff:3.500A) Processing helix chain 'C' and resid 2628 through 2640 Processing helix chain 'C' and resid 2740 through 2761 removed outlier: 3.518A pdb=" N GLU C2757 " --> pdb=" O LYS C2753 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C2758 " --> pdb=" O PHE C2754 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C2759 " --> pdb=" O VAL C2755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C2761 " --> pdb=" O GLU C2757 " (cutoff:3.500A) Processing helix chain 'C' and resid 2763 through 2767 removed outlier: 3.647A pdb=" N ILE C2766 " --> pdb=" O SER C2763 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET C2767 " --> pdb=" O HIS C2764 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2763 through 2767' Processing helix chain 'C' and resid 2774 through 2791 Processing helix chain 'C' and resid 2792 through 2808 Processing helix chain 'C' and resid 2809 through 2817 Processing sheet with id=AA1, first strand: chain 'A' and resid 2522 through 2526 Processing sheet with id=AA2, first strand: chain 'A' and resid 2531 through 2533 Processing sheet with id=AA3, first strand: chain 'A' and resid 2651 through 2654 Processing sheet with id=AA4, first strand: chain 'B' and resid 2522 through 2526 Processing sheet with id=AA5, first strand: chain 'B' and resid 2531 through 2533 Processing sheet with id=AA6, first strand: chain 'B' and resid 2651 through 2654 Processing sheet with id=AA7, first strand: chain 'C' and resid 2522 through 2526 Processing sheet with id=AA8, first strand: chain 'C' and resid 2531 through 2533 Processing sheet with id=AA9, first strand: chain 'C' and resid 2651 through 2654 2721 hydrogen bonds defined for protein. 8052 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: 16.60 Time building geometry restraints manager: 19.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13255 1.34 - 1.46: 8465 1.46 - 1.58: 23919 1.58 - 1.69: 0 1.69 - 1.81: 486 Bond restraints: 46125 Sorted by residual: bond pdb=" C1 NAG A3004 " pdb=" O5 NAG A3004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG C3004 " pdb=" O5 NAG C3004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C1 NAG B3004 " pdb=" O5 NAG B3004 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C1 NAG B3003 " pdb=" O5 NAG B3003 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C1 NAG B3002 " pdb=" O5 NAG B3002 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 ... (remaining 46120 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 1206 106.72 - 113.55: 25269 113.55 - 120.38: 18231 120.38 - 127.21: 17311 127.21 - 134.04: 566 Bond angle restraints: 62583 Sorted by residual: angle pdb=" O LEU C 773 " pdb=" C LEU C 773 " pdb=" N LYS C 774 " ideal model delta sigma weight residual 123.27 127.38 -4.11 1.16e+00 7.43e-01 1.26e+01 angle pdb=" O LEU A 773 " pdb=" C LEU A 773 " pdb=" N LYS A 774 " ideal model delta sigma weight residual 123.27 127.36 -4.09 1.16e+00 7.43e-01 1.25e+01 angle pdb=" O LEU B 773 " pdb=" C LEU B 773 " pdb=" N LYS B 774 " ideal model delta sigma weight residual 123.27 127.35 -4.08 1.16e+00 7.43e-01 1.24e+01 angle pdb=" CA ASN B1047 " pdb=" C ASN B1047 " pdb=" N LYS B1048 " ideal model delta sigma weight residual 117.96 113.63 4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" CA ASN A1047 " pdb=" C ASN A1047 " pdb=" N LYS A1048 " ideal model delta sigma weight residual 117.96 113.64 4.32 1.23e+00 6.61e-01 1.23e+01 ... (remaining 62578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 25754 23.82 - 47.64: 1153 47.64 - 71.46: 93 71.46 - 95.27: 54 95.27 - 119.09: 12 Dihedral angle restraints: 27066 sinusoidal: 10923 harmonic: 16143 Sorted by residual: dihedral pdb=" CA PRO C 299 " pdb=" C PRO C 299 " pdb=" N PRO C 300 " pdb=" CA PRO C 300 " ideal model delta harmonic sigma weight residual -180.00 -152.90 -27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PRO B 299 " pdb=" C PRO B 299 " pdb=" N PRO B 300 " pdb=" CA PRO B 300 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N PRO A 300 " pdb=" CA PRO A 300 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 27063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 7081 0.137 - 0.274: 26 0.274 - 0.411: 0 0.411 - 0.548: 0 0.548 - 0.685: 3 Chirality restraints: 7110 Sorted by residual: chirality pdb=" C1 NAG C3001 " pdb=" ND2 ASN C 769 " pdb=" C2 NAG C3001 " pdb=" O5 NAG C3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C1 NAG A3001 " pdb=" ND2 ASN A 769 " pdb=" C2 NAG A3001 " pdb=" O5 NAG A3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C1 NAG B3001 " pdb=" ND2 ASN B 769 " pdb=" C2 NAG B3001 " pdb=" O5 NAG B3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.17e+01 ... (remaining 7107 not shown) Planarity restraints: 7581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C3002 " -0.113 2.00e-02 2.50e+03 9.58e-02 1.15e+02 pdb=" C7 NAG C3002 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG C3002 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG C3002 " 0.153 2.00e-02 2.50e+03 pdb=" O7 NAG C3002 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3002 " 0.113 2.00e-02 2.50e+03 9.57e-02 1.14e+02 pdb=" C7 NAG A3002 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG A3002 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A3002 " -0.152 2.00e-02 2.50e+03 pdb=" O7 NAG A3002 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B3002 " 0.113 2.00e-02 2.50e+03 9.54e-02 1.14e+02 pdb=" C7 NAG B3002 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B3002 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG B3002 " -0.152 2.00e-02 2.50e+03 pdb=" O7 NAG B3002 " 0.091 2.00e-02 2.50e+03 ... (remaining 7578 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8138 2.76 - 3.29: 46016 3.29 - 3.83: 73982 3.83 - 4.36: 81153 4.36 - 4.90: 138137 Nonbonded interactions: 347426 Sorted by model distance: nonbonded pdb=" O GLY A2517 " pdb=" OG SER B2525 " model vdw 2.223 2.440 nonbonded pdb=" O GLY B2517 " pdb=" OG SER C2525 " model vdw 2.227 2.440 nonbonded pdb=" OG SER A2525 " pdb=" O GLY C2517 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR C2518 " pdb=" OE1 GLU C2590 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR A2518 " pdb=" OE1 GLU A2590 " model vdw 2.248 2.440 ... (remaining 347421 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' and (resid 8 through 2341 or resid 2343 through 2822 or resid 3001 th \ rough 3004)) selection = (chain 'B' and (resid 8 through 2341 or resid 2343 through 2822 or resid 3001 th \ rough 3004)) selection = (chain 'C' and (resid 8 through 2341 or resid 2343 through 2822 or resid 3001 th \ rough 3004)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 9.280 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 141.420 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.004 0.098 46125 Z= 0.227 Angle : 0.596 6.599 62583 Z= 0.338 Chirality : 0.042 0.685 7110 Planarity : 0.004 0.096 7569 Dihedral : 13.563 119.094 16593 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.77 (0.11), residues: 5358 helix: 0.06 (0.08), residues: 3426 sheet: -1.92 (0.28), residues: 216 loop : -3.67 (0.13), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 986 HIS 0.010 0.001 HIS A1727 PHE 0.012 0.001 PHE A2602 TYR 0.014 0.001 TYR B2050 ARG 0.007 0.000 ARG C2608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 ILE cc_start: 0.8812 (mm) cc_final: 0.8557 (mm) REVERT: A 532 MET cc_start: 0.8833 (ptm) cc_final: 0.8606 (ptm) REVERT: A 698 MET cc_start: 0.9255 (tpp) cc_final: 0.9053 (tpp) REVERT: A 983 LEU cc_start: 0.8747 (tt) cc_final: 0.8482 (tt) REVERT: A 1147 MET cc_start: 0.9521 (tpp) cc_final: 0.9304 (mmp) REVERT: A 1202 ILE cc_start: 0.9234 (tp) cc_final: 0.8991 (tt) REVERT: A 1271 MET cc_start: 0.8410 (ptm) cc_final: 0.7952 (ptp) REVERT: A 1462 GLN cc_start: 0.8952 (tp40) cc_final: 0.8679 (tt0) REVERT: A 1704 MET cc_start: 0.8924 (ttm) cc_final: 0.8447 (tmm) REVERT: A 1716 THR cc_start: 0.7169 (m) cc_final: 0.6881 (p) REVERT: A 2039 ILE cc_start: 0.9418 (mt) cc_final: 0.9174 (mt) REVERT: A 2331 ILE cc_start: 0.9209 (mm) cc_final: 0.9008 (mm) REVERT: A 2344 MET cc_start: 0.9210 (mmm) cc_final: 0.8743 (tpt) REVERT: A 2513 ILE cc_start: 0.9486 (mp) cc_final: 0.9212 (tp) REVERT: A 2655 LYS cc_start: 0.7258 (mttt) cc_final: 0.6861 (mmtt) REVERT: A 2690 ARG cc_start: 0.8323 (ptm160) cc_final: 0.7974 (ptt90) REVERT: A 2807 TYR cc_start: 0.9353 (m-80) cc_final: 0.9118 (m-10) REVERT: B 218 MET cc_start: 0.8810 (tpt) cc_final: 0.8442 (tpp) REVERT: B 698 MET cc_start: 0.9289 (tpp) cc_final: 0.9024 (tpp) REVERT: B 749 MET cc_start: 0.7838 (ttp) cc_final: 0.7598 (ttp) REVERT: B 1376 MET cc_start: 0.8457 (mmm) cc_final: 0.8008 (mpp) REVERT: B 1716 THR cc_start: 0.7569 (m) cc_final: 0.7235 (p) REVERT: B 2317 ASP cc_start: 0.9298 (t0) cc_final: 0.9084 (t0) REVERT: B 2344 MET cc_start: 0.9263 (mmm) cc_final: 0.8866 (mmm) REVERT: B 2485 ILE cc_start: 0.9179 (mt) cc_final: 0.8893 (mt) REVERT: B 2553 MET cc_start: 0.8551 (mtp) cc_final: 0.8177 (mpp) REVERT: B 2682 MET cc_start: 0.2922 (tpp) cc_final: 0.2513 (tpp) REVERT: B 2690 ARG cc_start: 0.8332 (ptm160) cc_final: 0.7896 (ttp80) REVERT: B 2716 GLN cc_start: 0.8698 (tt0) cc_final: 0.8236 (mp10) REVERT: C 218 MET cc_start: 0.8818 (tpt) cc_final: 0.8562 (tpt) REVERT: C 698 MET cc_start: 0.9296 (tpp) cc_final: 0.9064 (tpp) REVERT: C 1147 MET cc_start: 0.9605 (tpp) cc_final: 0.9370 (mmt) REVERT: C 1376 MET cc_start: 0.8653 (mmm) cc_final: 0.8282 (mpp) REVERT: C 1491 MET cc_start: 0.8969 (mmp) cc_final: 0.8754 (mmp) REVERT: C 1716 THR cc_start: 0.7544 (m) cc_final: 0.7285 (p) REVERT: C 2344 MET cc_start: 0.9218 (mmm) cc_final: 0.8767 (tpt) REVERT: C 2481 LEU cc_start: 0.9323 (tp) cc_final: 0.9111 (tt) REVERT: C 2485 ILE cc_start: 0.8960 (mt) cc_final: 0.8614 (mp) REVERT: C 2513 ILE cc_start: 0.9528 (mp) cc_final: 0.9288 (tp) REVERT: C 2553 MET cc_start: 0.8525 (mtp) cc_final: 0.8042 (mpp) REVERT: C 2590 GLU cc_start: 0.8748 (pt0) cc_final: 0.8536 (pt0) REVERT: C 2741 MET cc_start: 0.7238 (tpp) cc_final: 0.6974 (mmp) REVERT: C 2769 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8856 (mm-30) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.4958 time to fit residues: 468.5877 Evaluate side-chains 379 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 5.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 458 optimal weight: 0.8980 chunk 411 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 425 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 258 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 493 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 357 GLN A 558 GLN A 600 HIS ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 GLN A1076 ASN A1094 GLN A1150 ASN A1370 ASN A1727 HIS A2310 GLN A2460 GLN A2528 GLN A2674 GLN B 53 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 357 GLN B 558 GLN B 600 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 GLN B1076 ASN B1094 GLN B1154 GLN B1370 ASN B1727 HIS ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2460 GLN B2528 GLN C 53 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 357 GLN C 558 GLN C 600 HIS ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 GLN C1018 GLN C1076 ASN C1094 GLN ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1154 GLN C1370 ASN C1727 HIS C2460 GLN C2528 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 46125 Z= 0.187 Angle : 0.582 9.294 62583 Z= 0.290 Chirality : 0.040 0.217 7110 Planarity : 0.004 0.062 7569 Dihedral : 7.079 82.564 6162 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.92 % Allowed : 9.04 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.40 (0.12), residues: 5358 helix: 1.12 (0.09), residues: 3489 sheet: -1.32 (0.30), residues: 216 loop : -3.27 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2604 HIS 0.007 0.001 HIS C1727 PHE 0.033 0.001 PHE A1977 TYR 0.021 0.001 TYR B 501 ARG 0.008 0.000 ARG A2462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 425 time to evaluate : 5.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 TRP cc_start: 0.7251 (OUTLIER) cc_final: 0.6402 (t60) REVERT: A 698 MET cc_start: 0.9205 (tpp) cc_final: 0.8994 (tpp) REVERT: A 1147 MET cc_start: 0.9487 (tpp) cc_final: 0.9244 (mmp) REVERT: A 1202 ILE cc_start: 0.9189 (tp) cc_final: 0.8943 (tt) REVERT: A 1271 MET cc_start: 0.8423 (ptm) cc_final: 0.7962 (ptp) REVERT: A 1462 GLN cc_start: 0.8821 (tp40) cc_final: 0.8589 (tt0) REVERT: A 1704 MET cc_start: 0.9020 (ttm) cc_final: 0.8728 (tmm) REVERT: A 1716 THR cc_start: 0.7248 (m) cc_final: 0.6972 (p) REVERT: A 2513 ILE cc_start: 0.9478 (mp) cc_final: 0.9243 (tp) REVERT: A 2655 LYS cc_start: 0.7381 (mttt) cc_final: 0.7158 (mttp) REVERT: A 2690 ARG cc_start: 0.8302 (ptm160) cc_final: 0.7939 (ptt90) REVERT: B 218 MET cc_start: 0.8800 (tpt) cc_final: 0.8419 (tpp) REVERT: B 532 MET cc_start: 0.8866 (ptp) cc_final: 0.8615 (ptm) REVERT: B 698 MET cc_start: 0.9299 (tpp) cc_final: 0.8998 (tpp) REVERT: B 749 MET cc_start: 0.7984 (ttp) cc_final: 0.7697 (ttp) REVERT: B 1376 MET cc_start: 0.8475 (mmm) cc_final: 0.8056 (mpp) REVERT: B 1704 MET cc_start: 0.8687 (ppp) cc_final: 0.8481 (ppp) REVERT: B 1716 THR cc_start: 0.7383 (m) cc_final: 0.7093 (p) REVERT: B 2485 ILE cc_start: 0.9182 (mt) cc_final: 0.8881 (mp) REVERT: B 2553 MET cc_start: 0.8565 (mtp) cc_final: 0.8261 (mpp) REVERT: B 2682 MET cc_start: 0.3202 (tpp) cc_final: 0.2837 (tpp) REVERT: B 2716 GLN cc_start: 0.8633 (tt0) cc_final: 0.8207 (mp10) REVERT: C 218 MET cc_start: 0.8881 (tpt) cc_final: 0.8547 (tpt) REVERT: C 698 MET cc_start: 0.9285 (tpp) cc_final: 0.9023 (tpp) REVERT: C 980 TYR cc_start: 0.8561 (t80) cc_final: 0.8136 (t80) REVERT: C 1147 MET cc_start: 0.9568 (tpp) cc_final: 0.9336 (mmt) REVERT: C 1376 MET cc_start: 0.8644 (mmm) cc_final: 0.8309 (mpp) REVERT: C 1716 THR cc_start: 0.7481 (m) cc_final: 0.7272 (p) REVERT: C 2314 MET cc_start: 0.8822 (mtm) cc_final: 0.8465 (mtt) REVERT: C 2344 MET cc_start: 0.9178 (mmm) cc_final: 0.8690 (tpt) REVERT: C 2481 LEU cc_start: 0.9219 (tp) cc_final: 0.9019 (tt) REVERT: C 2485 ILE cc_start: 0.8932 (mt) cc_final: 0.8579 (mt) REVERT: C 2513 ILE cc_start: 0.9527 (mp) cc_final: 0.9269 (tp) REVERT: C 2553 MET cc_start: 0.8527 (mtp) cc_final: 0.8037 (mpp) REVERT: C 2590 GLU cc_start: 0.8788 (pt0) cc_final: 0.8293 (pt0) REVERT: C 2690 ARG cc_start: 0.7209 (ptm-80) cc_final: 0.6778 (ptm-80) REVERT: C 2741 MET cc_start: 0.7247 (tpp) cc_final: 0.7012 (mmp) REVERT: C 2769 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8790 (mm-30) outliers start: 45 outliers final: 22 residues processed: 443 average time/residue: 0.4955 time to fit residues: 385.0564 Evaluate side-chains 420 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 397 time to evaluate : 4.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 2019 ILE Chi-restraints excluded: chain A residue 2310 GLN Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 2019 ILE Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2013 LEU Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2272 ILE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 274 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 410 optimal weight: 1.9990 chunk 335 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 493 optimal weight: 2.9990 chunk 533 optimal weight: 0.6980 chunk 439 optimal weight: 10.0000 chunk 489 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 396 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN A2398 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1222 ASN ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 46125 Z= 0.172 Angle : 0.563 9.552 62583 Z= 0.278 Chirality : 0.040 0.275 7110 Planarity : 0.004 0.064 7569 Dihedral : 5.928 56.536 6162 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.98 % Allowed : 11.36 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.08 (0.12), residues: 5358 helix: 1.48 (0.09), residues: 3519 sheet: -1.02 (0.31), residues: 216 loop : -3.18 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 986 HIS 0.005 0.001 HIS A1559 PHE 0.030 0.001 PHE A1977 TYR 0.022 0.001 TYR A 501 ARG 0.007 0.000 ARG C2690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 430 time to evaluate : 5.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6492 (t60) REVERT: A 698 MET cc_start: 0.9182 (tpp) cc_final: 0.8979 (tpp) REVERT: A 1147 MET cc_start: 0.9448 (tpp) cc_final: 0.9203 (mmp) REVERT: A 1271 MET cc_start: 0.8487 (ptm) cc_final: 0.8068 (ptp) REVERT: A 1704 MET cc_start: 0.8965 (ttm) cc_final: 0.8665 (tmm) REVERT: A 1716 THR cc_start: 0.7342 (m) cc_final: 0.7066 (p) REVERT: A 2421 MET cc_start: 0.8802 (mmp) cc_final: 0.8554 (mmp) REVERT: A 2513 ILE cc_start: 0.9489 (mp) cc_final: 0.9246 (tp) REVERT: A 2690 ARG cc_start: 0.8296 (ptm160) cc_final: 0.8007 (tmm-80) REVERT: A 2813 MET cc_start: 0.9228 (ttp) cc_final: 0.8985 (ttt) REVERT: B 218 MET cc_start: 0.8823 (tpt) cc_final: 0.8459 (tpp) REVERT: B 342 LEU cc_start: 0.9558 (tt) cc_final: 0.9302 (pp) REVERT: B 698 MET cc_start: 0.9299 (tpp) cc_final: 0.8972 (tpp) REVERT: B 749 MET cc_start: 0.7927 (ttp) cc_final: 0.7718 (ttp) REVERT: B 1156 MET cc_start: 0.8807 (tpt) cc_final: 0.8408 (tpt) REVERT: B 1246 ASP cc_start: 0.8505 (m-30) cc_final: 0.8143 (t70) REVERT: B 1376 MET cc_start: 0.8404 (mmm) cc_final: 0.8004 (mpp) REVERT: B 1704 MET cc_start: 0.8743 (ppp) cc_final: 0.8481 (ppp) REVERT: B 1716 THR cc_start: 0.7311 (m) cc_final: 0.7031 (p) REVERT: B 2485 ILE cc_start: 0.9217 (mt) cc_final: 0.8903 (mp) REVERT: B 2553 MET cc_start: 0.8590 (mtp) cc_final: 0.8203 (mpp) REVERT: B 2656 ILE cc_start: 0.8856 (mm) cc_final: 0.8647 (mp) REVERT: B 2716 GLN cc_start: 0.8630 (tt0) cc_final: 0.8217 (mp10) REVERT: C 237 MET cc_start: 0.8330 (tpp) cc_final: 0.8063 (tpt) REVERT: C 698 MET cc_start: 0.9279 (tpp) cc_final: 0.9013 (tpp) REVERT: C 716 MET cc_start: 0.8938 (tpp) cc_final: 0.8568 (tpp) REVERT: C 1147 MET cc_start: 0.9542 (tpp) cc_final: 0.9302 (mmt) REVERT: C 1161 MET cc_start: 0.8695 (ttp) cc_final: 0.8351 (tmm) REVERT: C 1704 MET cc_start: 0.8988 (ptm) cc_final: 0.8650 (ppp) REVERT: C 2013 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8904 (tp) REVERT: C 2314 MET cc_start: 0.8854 (mtm) cc_final: 0.8502 (mtt) REVERT: C 2344 MET cc_start: 0.9150 (mmm) cc_final: 0.8925 (mmm) REVERT: C 2481 LEU cc_start: 0.9212 (tp) cc_final: 0.8974 (tt) REVERT: C 2485 ILE cc_start: 0.8898 (mt) cc_final: 0.8538 (mt) REVERT: C 2513 ILE cc_start: 0.9535 (mp) cc_final: 0.9295 (tp) REVERT: C 2553 MET cc_start: 0.8658 (mtp) cc_final: 0.8214 (mpp) REVERT: C 2690 ARG cc_start: 0.7231 (ptm-80) cc_final: 0.6798 (ptm-80) REVERT: C 2741 MET cc_start: 0.7250 (tpp) cc_final: 0.7009 (mmp) REVERT: C 2769 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8717 (mm-30) outliers start: 48 outliers final: 23 residues processed: 454 average time/residue: 0.4931 time to fit residues: 394.3983 Evaluate side-chains 419 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 394 time to evaluate : 5.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2019 ILE Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 2019 ILE Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain B residue 2784 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2013 LEU Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 488 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 331 optimal weight: 0.8980 chunk 495 optimal weight: 4.9990 chunk 524 optimal weight: 7.9990 chunk 259 optimal weight: 0.0170 chunk 469 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1133 ASN C2607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 46125 Z= 0.163 Angle : 0.556 11.756 62583 Z= 0.274 Chirality : 0.039 0.239 7110 Planarity : 0.004 0.064 7569 Dihedral : 5.336 55.472 6162 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.21 % Allowed : 12.77 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.12), residues: 5358 helix: 1.70 (0.09), residues: 3507 sheet: -0.90 (0.32), residues: 216 loop : -2.99 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 561 HIS 0.004 0.001 HIS A1559 PHE 0.032 0.001 PHE C1372 TYR 0.018 0.001 TYR B 501 ARG 0.006 0.000 ARG C2690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 428 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9200 (mm) REVERT: A 214 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.9246 (p90) REVERT: A 237 MET cc_start: 0.8328 (tpp) cc_final: 0.7930 (tpt) REVERT: A 518 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6541 (t60) REVERT: A 554 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9349 (pp) REVERT: A 698 MET cc_start: 0.9164 (tpp) cc_final: 0.8961 (tpp) REVERT: A 1147 MET cc_start: 0.9450 (tpp) cc_final: 0.9189 (mmp) REVERT: A 1271 MET cc_start: 0.8504 (ptm) cc_final: 0.8177 (ptp) REVERT: A 1562 MET cc_start: 0.9100 (ttm) cc_final: 0.8664 (ptp) REVERT: A 1704 MET cc_start: 0.8956 (ttm) cc_final: 0.8646 (tmm) REVERT: A 1716 THR cc_start: 0.7364 (m) cc_final: 0.7111 (p) REVERT: A 2470 VAL cc_start: 0.9534 (m) cc_final: 0.9324 (p) REVERT: A 2610 MET cc_start: 0.5071 (mmm) cc_final: 0.4826 (mmm) REVERT: A 2690 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7914 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8567 (tmmm) REVERT: A 2813 MET cc_start: 0.9216 (ttp) cc_final: 0.8950 (ttt) REVERT: B 342 LEU cc_start: 0.9555 (tt) cc_final: 0.9297 (pp) REVERT: B 698 MET cc_start: 0.9291 (tpp) cc_final: 0.8961 (tpp) REVERT: B 749 MET cc_start: 0.7992 (ttp) cc_final: 0.7644 (ttp) REVERT: B 980 TYR cc_start: 0.8515 (t80) cc_final: 0.8094 (t80) REVERT: B 1246 ASP cc_start: 0.8528 (m-30) cc_final: 0.8227 (t70) REVERT: B 1376 MET cc_start: 0.8387 (mmm) cc_final: 0.7998 (mpp) REVERT: B 1704 MET cc_start: 0.8779 (ppp) cc_final: 0.8536 (ppp) REVERT: B 1716 THR cc_start: 0.7224 (m) cc_final: 0.6948 (p) REVERT: B 2485 ILE cc_start: 0.9194 (mt) cc_final: 0.8875 (mp) REVERT: B 2508 ASP cc_start: 0.8526 (t0) cc_final: 0.8313 (t0) REVERT: B 2553 MET cc_start: 0.8658 (mtp) cc_final: 0.8294 (mpp) REVERT: B 2621 ASP cc_start: 0.8286 (t70) cc_final: 0.7895 (t70) REVERT: B 2716 GLN cc_start: 0.8624 (tt0) cc_final: 0.8223 (mp10) REVERT: C 40 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9328 (mm) REVERT: C 237 MET cc_start: 0.8318 (tpp) cc_final: 0.8081 (tpt) REVERT: C 676 MET cc_start: 0.8126 (mmm) cc_final: 0.7864 (mmt) REVERT: C 698 MET cc_start: 0.9269 (tpp) cc_final: 0.9014 (tpp) REVERT: C 1147 MET cc_start: 0.9529 (tpp) cc_final: 0.9146 (mmt) REVERT: C 1161 MET cc_start: 0.8644 (ttp) cc_final: 0.8283 (tmm) REVERT: C 1704 MET cc_start: 0.8995 (ptm) cc_final: 0.8626 (ppp) REVERT: C 2314 MET cc_start: 0.8854 (mtm) cc_final: 0.8502 (mtt) REVERT: C 2344 MET cc_start: 0.9129 (mmm) cc_final: 0.8904 (mmm) REVERT: C 2470 VAL cc_start: 0.9551 (m) cc_final: 0.9207 (p) REVERT: C 2485 ILE cc_start: 0.8856 (mt) cc_final: 0.8572 (mt) REVERT: C 2513 ILE cc_start: 0.9591 (mp) cc_final: 0.9340 (tp) REVERT: C 2553 MET cc_start: 0.8739 (mtp) cc_final: 0.8326 (mpp) REVERT: C 2690 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.6801 (ptm-80) REVERT: C 2716 GLN cc_start: 0.8896 (tt0) cc_final: 0.8346 (mp10) REVERT: C 2741 MET cc_start: 0.7200 (tpp) cc_final: 0.6927 (mmp) REVERT: C 2769 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8701 (mm-30) outliers start: 59 outliers final: 29 residues processed: 464 average time/residue: 0.4837 time to fit residues: 396.5601 Evaluate side-chains 434 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 399 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1200 VAL Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 437 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 390 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 447 optimal weight: 3.9990 chunk 362 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 268 optimal weight: 0.7980 chunk 471 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46125 Z= 0.220 Angle : 0.571 10.496 62583 Z= 0.284 Chirality : 0.040 0.328 7110 Planarity : 0.004 0.063 7569 Dihedral : 5.115 56.225 6162 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.27 % Allowed : 13.63 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.46 (0.12), residues: 5358 helix: 1.73 (0.09), residues: 3540 sheet: -0.86 (0.32), residues: 216 loop : -2.96 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C2604 HIS 0.004 0.001 HIS C1559 PHE 0.032 0.001 PHE A1977 TYR 0.020 0.001 TYR B 501 ARG 0.006 0.000 ARG C2690 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 397 time to evaluate : 5.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9203 (mm) REVERT: A 214 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.9236 (p90) REVERT: A 237 MET cc_start: 0.8436 (tpp) cc_final: 0.8027 (tpt) REVERT: A 518 TRP cc_start: 0.7241 (OUTLIER) cc_final: 0.6508 (t60) REVERT: A 554 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9398 (pp) REVERT: A 698 MET cc_start: 0.9192 (tpp) cc_final: 0.8951 (tpp) REVERT: A 1147 MET cc_start: 0.9445 (tpp) cc_final: 0.9160 (mmp) REVERT: A 1271 MET cc_start: 0.8564 (ptm) cc_final: 0.8245 (ptp) REVERT: A 1704 MET cc_start: 0.8976 (ttm) cc_final: 0.8654 (tmm) REVERT: A 1716 THR cc_start: 0.7307 (m) cc_final: 0.7089 (p) REVERT: A 2587 MET cc_start: 0.9403 (ttm) cc_final: 0.9001 (tpp) REVERT: A 2610 MET cc_start: 0.4996 (mmm) cc_final: 0.4718 (mmm) REVERT: A 2690 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7934 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8572 (tmmm) REVERT: A 2813 MET cc_start: 0.9240 (ttp) cc_final: 0.8966 (ttt) REVERT: B 698 MET cc_start: 0.9323 (tpp) cc_final: 0.8967 (tpp) REVERT: B 749 MET cc_start: 0.7934 (ttp) cc_final: 0.7554 (ttp) REVERT: B 1156 MET cc_start: 0.8829 (tpt) cc_final: 0.8482 (tpt) REVERT: B 1376 MET cc_start: 0.8426 (mmm) cc_final: 0.8014 (mpp) REVERT: B 1704 MET cc_start: 0.8832 (ppp) cc_final: 0.8574 (ppp) REVERT: B 1716 THR cc_start: 0.7443 (m) cc_final: 0.7145 (p) REVERT: B 2485 ILE cc_start: 0.9223 (mt) cc_final: 0.8939 (mp) REVERT: B 2553 MET cc_start: 0.8699 (mtp) cc_final: 0.8313 (mpp) REVERT: B 2621 ASP cc_start: 0.8304 (t70) cc_final: 0.7889 (t70) REVERT: B 2638 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8618 (tpp) REVERT: B 2716 GLN cc_start: 0.8649 (tt0) cc_final: 0.8235 (mp10) REVERT: C 40 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9329 (mm) REVERT: C 237 MET cc_start: 0.8334 (tpp) cc_final: 0.8090 (tpt) REVERT: C 497 MET cc_start: 0.8080 (mmm) cc_final: 0.7704 (ptt) REVERT: C 676 MET cc_start: 0.8172 (mmm) cc_final: 0.7897 (mmt) REVERT: C 698 MET cc_start: 0.9287 (tpp) cc_final: 0.8999 (tpp) REVERT: C 1161 MET cc_start: 0.8662 (ttp) cc_final: 0.8321 (tmm) REVERT: C 1704 MET cc_start: 0.9019 (ptm) cc_final: 0.8642 (ppp) REVERT: C 2314 MET cc_start: 0.8865 (mtm) cc_final: 0.8506 (mtt) REVERT: C 2344 MET cc_start: 0.9120 (mmm) cc_final: 0.8851 (mmm) REVERT: C 2485 ILE cc_start: 0.8931 (mt) cc_final: 0.8664 (mp) REVERT: C 2513 ILE cc_start: 0.9627 (mp) cc_final: 0.9377 (tp) REVERT: C 2553 MET cc_start: 0.8772 (mtp) cc_final: 0.8335 (mpp) REVERT: C 2741 MET cc_start: 0.7186 (tpp) cc_final: 0.6870 (mmp) REVERT: C 2769 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8775 (mm-30) outliers start: 62 outliers final: 37 residues processed: 434 average time/residue: 0.4693 time to fit residues: 358.3852 Evaluate side-chains 437 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 393 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2019 ILE Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2275 VAL Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 2019 ILE Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 176 optimal weight: 0.9990 chunk 472 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 308 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 525 optimal weight: 5.9990 chunk 436 optimal weight: 0.0170 chunk 243 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 173 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B2310 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2607 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46125 Z= 0.166 Angle : 0.556 10.920 62583 Z= 0.273 Chirality : 0.039 0.269 7110 Planarity : 0.004 0.063 7569 Dihedral : 4.880 55.532 6162 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.23 % Allowed : 14.45 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.59 (0.12), residues: 5358 helix: 1.80 (0.09), residues: 3543 sheet: -0.74 (0.32), residues: 216 loop : -2.86 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C2604 HIS 0.004 0.001 HIS A1559 PHE 0.030 0.001 PHE A1977 TYR 0.026 0.001 TYR A 34 ARG 0.004 0.000 ARG C2690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 424 time to evaluate : 4.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9215 (mm) REVERT: A 214 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9203 (p90) REVERT: A 237 MET cc_start: 0.8370 (tpp) cc_final: 0.7919 (tpt) REVERT: A 518 TRP cc_start: 0.7160 (OUTLIER) cc_final: 0.6533 (t60) REVERT: A 554 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9386 (pp) REVERT: A 698 MET cc_start: 0.9163 (tpp) cc_final: 0.8924 (tpp) REVERT: A 980 TYR cc_start: 0.8599 (t80) cc_final: 0.8263 (t80) REVERT: A 1147 MET cc_start: 0.9443 (tpp) cc_final: 0.9145 (mmp) REVERT: A 1235 ILE cc_start: 0.8878 (tp) cc_final: 0.8634 (mm) REVERT: A 1271 MET cc_start: 0.8522 (ptm) cc_final: 0.8206 (ptp) REVERT: A 1562 MET cc_start: 0.9094 (ttm) cc_final: 0.8534 (ptp) REVERT: A 1704 MET cc_start: 0.8971 (ttm) cc_final: 0.8662 (tmm) REVERT: A 2587 MET cc_start: 0.9353 (ttm) cc_final: 0.8953 (tpp) REVERT: A 2610 MET cc_start: 0.4910 (mmm) cc_final: 0.4650 (mmm) REVERT: A 2690 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7923 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8565 (tmmm) REVERT: A 2813 MET cc_start: 0.9243 (ttp) cc_final: 0.8943 (ttt) REVERT: B 698 MET cc_start: 0.9305 (tpp) cc_final: 0.8949 (tpp) REVERT: B 749 MET cc_start: 0.7844 (ttp) cc_final: 0.7510 (ttp) REVERT: B 1156 MET cc_start: 0.8808 (tpt) cc_final: 0.8493 (tpt) REVERT: B 1562 MET cc_start: 0.8928 (ttm) cc_final: 0.8676 (ptp) REVERT: B 1704 MET cc_start: 0.8846 (ppp) cc_final: 0.8571 (ppp) REVERT: B 1716 THR cc_start: 0.7243 (m) cc_final: 0.6989 (p) REVERT: B 1984 MET cc_start: 0.9102 (mtm) cc_final: 0.8661 (mmt) REVERT: B 2485 ILE cc_start: 0.9209 (mt) cc_final: 0.8929 (mp) REVERT: B 2508 ASP cc_start: 0.8480 (t0) cc_final: 0.8242 (t0) REVERT: B 2553 MET cc_start: 0.8703 (mtp) cc_final: 0.8321 (mpp) REVERT: B 2621 ASP cc_start: 0.8304 (t70) cc_final: 0.7838 (t70) REVERT: B 2638 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8660 (tpp) REVERT: B 2716 GLN cc_start: 0.8682 (tt0) cc_final: 0.8279 (mp10) REVERT: C 40 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9331 (mm) REVERT: C 237 MET cc_start: 0.8282 (tpp) cc_final: 0.8043 (tpt) REVERT: C 676 MET cc_start: 0.8177 (mmm) cc_final: 0.7908 (mmt) REVERT: C 698 MET cc_start: 0.9273 (tpp) cc_final: 0.8988 (tpp) REVERT: C 980 TYR cc_start: 0.8473 (t80) cc_final: 0.8026 (t80) REVERT: C 1161 MET cc_start: 0.8652 (ttp) cc_final: 0.8302 (tmm) REVERT: C 1704 MET cc_start: 0.8987 (ptm) cc_final: 0.8591 (ppp) REVERT: C 2314 MET cc_start: 0.8861 (mtm) cc_final: 0.8498 (mtt) REVERT: C 2344 MET cc_start: 0.9104 (mmm) cc_final: 0.8856 (mmm) REVERT: C 2470 VAL cc_start: 0.9544 (m) cc_final: 0.9216 (p) REVERT: C 2485 ILE cc_start: 0.8945 (mt) cc_final: 0.8688 (mp) REVERT: C 2513 ILE cc_start: 0.9617 (mp) cc_final: 0.9370 (tp) REVERT: C 2553 MET cc_start: 0.8772 (mtp) cc_final: 0.8334 (mpp) REVERT: C 2587 MET cc_start: 0.9404 (ttm) cc_final: 0.9107 (tpp) REVERT: C 2716 GLN cc_start: 0.8924 (tt0) cc_final: 0.8391 (mp10) REVERT: C 2741 MET cc_start: 0.7128 (tpp) cc_final: 0.6890 (mmp) REVERT: C 2769 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8688 (mm-30) outliers start: 60 outliers final: 39 residues processed: 461 average time/residue: 0.4845 time to fit residues: 392.6126 Evaluate side-chains 451 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 405 time to evaluate : 5.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2087 LEU Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1320 THR Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2310 GLN Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1713 ASN Chi-restraints excluded: chain C residue 1724 TYR Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 506 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 299 optimal weight: 0.7980 chunk 383 optimal weight: 0.9980 chunk 297 optimal weight: 0.6980 chunk 442 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 chunk 523 optimal weight: 20.0000 chunk 327 optimal weight: 0.0870 chunk 319 optimal weight: 0.6980 chunk 241 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 46125 Z= 0.150 Angle : 0.554 11.405 62583 Z= 0.270 Chirality : 0.039 0.259 7110 Planarity : 0.004 0.063 7569 Dihedral : 4.723 55.521 6162 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.29 % Allowed : 14.68 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.69 (0.12), residues: 5358 helix: 1.87 (0.09), residues: 3543 sheet: -0.67 (0.32), residues: 216 loop : -2.81 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C2604 HIS 0.003 0.001 HIS C 334 PHE 0.030 0.001 PHE A1977 TYR 0.032 0.001 TYR A 34 ARG 0.003 0.000 ARG C2608 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 428 time to evaluate : 5.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9208 (mm) REVERT: A 214 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9206 (p90) REVERT: A 237 MET cc_start: 0.8288 (tpp) cc_final: 0.7859 (tpt) REVERT: A 518 TRP cc_start: 0.7104 (OUTLIER) cc_final: 0.6587 (t60) REVERT: A 554 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9317 (pp) REVERT: A 698 MET cc_start: 0.9168 (tpp) cc_final: 0.8954 (tpp) REVERT: A 980 TYR cc_start: 0.8532 (t80) cc_final: 0.8250 (t80) REVERT: A 1147 MET cc_start: 0.9461 (tpp) cc_final: 0.9165 (mmp) REVERT: A 1235 ILE cc_start: 0.8910 (tp) cc_final: 0.8688 (mm) REVERT: A 1271 MET cc_start: 0.8560 (ptm) cc_final: 0.8279 (ptp) REVERT: A 1562 MET cc_start: 0.9082 (ttm) cc_final: 0.8524 (ptp) REVERT: A 1704 MET cc_start: 0.8952 (ttm) cc_final: 0.8615 (tmm) REVERT: A 2587 MET cc_start: 0.9331 (ttm) cc_final: 0.8933 (tpp) REVERT: A 2610 MET cc_start: 0.4975 (mmm) cc_final: 0.4733 (mmm) REVERT: A 2690 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7887 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8566 (tmmm) REVERT: A 2813 MET cc_start: 0.9231 (ttp) cc_final: 0.8913 (ttt) REVERT: B 342 LEU cc_start: 0.9562 (tt) cc_final: 0.9303 (pp) REVERT: B 698 MET cc_start: 0.9296 (tpp) cc_final: 0.8951 (tpp) REVERT: B 710 MET cc_start: 0.8649 (tpp) cc_final: 0.8421 (tpp) REVERT: B 749 MET cc_start: 0.7887 (ttp) cc_final: 0.7684 (ttp) REVERT: B 1156 MET cc_start: 0.8760 (tpt) cc_final: 0.8476 (tpt) REVERT: B 1562 MET cc_start: 0.8933 (ttm) cc_final: 0.8662 (ptp) REVERT: B 1704 MET cc_start: 0.8843 (ppp) cc_final: 0.8562 (ppp) REVERT: B 1716 THR cc_start: 0.6840 (m) cc_final: 0.6559 (p) REVERT: B 1984 MET cc_start: 0.9094 (mtm) cc_final: 0.8657 (mmt) REVERT: B 2485 ILE cc_start: 0.9207 (mt) cc_final: 0.8912 (mp) REVERT: B 2508 ASP cc_start: 0.8453 (t0) cc_final: 0.8206 (t0) REVERT: B 2553 MET cc_start: 0.8707 (mtp) cc_final: 0.8325 (mpp) REVERT: B 2587 MET cc_start: 0.9202 (ttm) cc_final: 0.8998 (tpp) REVERT: B 2604 TRP cc_start: 0.8332 (p90) cc_final: 0.7164 (p90) REVERT: B 2621 ASP cc_start: 0.8296 (t70) cc_final: 0.7482 (t70) REVERT: B 2638 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8688 (tpp) REVERT: B 2716 GLN cc_start: 0.8692 (tt0) cc_final: 0.8287 (mp10) REVERT: C 40 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9295 (mm) REVERT: C 218 MET cc_start: 0.8955 (tpt) cc_final: 0.8613 (tpt) REVERT: C 237 MET cc_start: 0.8208 (tpp) cc_final: 0.7956 (tpt) REVERT: C 497 MET cc_start: 0.8034 (mmm) cc_final: 0.7685 (ptt) REVERT: C 676 MET cc_start: 0.8271 (mmm) cc_final: 0.8009 (mmt) REVERT: C 698 MET cc_start: 0.9266 (tpp) cc_final: 0.8985 (tpp) REVERT: C 980 TYR cc_start: 0.8485 (t80) cc_final: 0.8205 (t80) REVERT: C 1161 MET cc_start: 0.8646 (ttp) cc_final: 0.8294 (tmm) REVERT: C 1704 MET cc_start: 0.8984 (ptm) cc_final: 0.8609 (ppp) REVERT: C 2314 MET cc_start: 0.8861 (mtm) cc_final: 0.8493 (mtt) REVERT: C 2344 MET cc_start: 0.9096 (mmm) cc_final: 0.8830 (mmm) REVERT: C 2470 VAL cc_start: 0.9527 (m) cc_final: 0.9202 (p) REVERT: C 2485 ILE cc_start: 0.8994 (mt) cc_final: 0.8782 (mp) REVERT: C 2508 ASP cc_start: 0.8418 (t0) cc_final: 0.8090 (t0) REVERT: C 2513 ILE cc_start: 0.9619 (mp) cc_final: 0.9379 (tp) REVERT: C 2553 MET cc_start: 0.8713 (mtp) cc_final: 0.8267 (mpp) REVERT: C 2587 MET cc_start: 0.9367 (ttm) cc_final: 0.9116 (tpp) REVERT: C 2716 GLN cc_start: 0.8865 (tt0) cc_final: 0.8366 (mp10) REVERT: C 2741 MET cc_start: 0.7126 (tpp) cc_final: 0.6852 (mmp) REVERT: C 2769 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8678 (mm-30) outliers start: 63 outliers final: 38 residues processed: 470 average time/residue: 0.4811 time to fit residues: 398.7529 Evaluate side-chains 459 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 414 time to evaluate : 4.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 1724 TYR Chi-restraints excluded: chain A residue 2400 VAL Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2533 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1713 ASN Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 1994 MET Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 323 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 312 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 258 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 411 optimal weight: 7.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1126 ASN C1370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 46125 Z= 0.160 Angle : 0.554 11.384 62583 Z= 0.271 Chirality : 0.039 0.240 7110 Planarity : 0.004 0.062 7569 Dihedral : 4.612 55.822 6162 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.23 % Allowed : 14.99 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.73 (0.12), residues: 5358 helix: 1.91 (0.09), residues: 3537 sheet: -0.65 (0.32), residues: 216 loop : -2.81 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C2604 HIS 0.004 0.001 HIS C 334 PHE 0.031 0.001 PHE A1977 TYR 0.041 0.001 TYR C1724 ARG 0.003 0.000 ARG C2608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 422 time to evaluate : 5.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9204 (mm) REVERT: A 214 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.9192 (p90) REVERT: A 237 MET cc_start: 0.8186 (tpp) cc_final: 0.7736 (tpt) REVERT: A 342 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9257 (pp) REVERT: A 518 TRP cc_start: 0.7081 (OUTLIER) cc_final: 0.6564 (t60) REVERT: A 554 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9326 (pp) REVERT: A 698 MET cc_start: 0.9163 (tpp) cc_final: 0.8962 (tpp) REVERT: A 980 TYR cc_start: 0.8532 (t80) cc_final: 0.8263 (t80) REVERT: A 1147 MET cc_start: 0.9456 (tpp) cc_final: 0.9160 (mmp) REVERT: A 1235 ILE cc_start: 0.8898 (tp) cc_final: 0.8678 (mm) REVERT: A 1246 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8289 (t70) REVERT: A 1271 MET cc_start: 0.8606 (ptm) cc_final: 0.8352 (ptp) REVERT: A 1562 MET cc_start: 0.9101 (ttm) cc_final: 0.8537 (ptp) REVERT: A 1704 MET cc_start: 0.8945 (ttm) cc_final: 0.8621 (tmm) REVERT: A 2610 MET cc_start: 0.4967 (mmm) cc_final: 0.4723 (mmm) REVERT: A 2690 ARG cc_start: 0.8179 (ptm160) cc_final: 0.7857 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8560 (tmmm) REVERT: A 2813 MET cc_start: 0.9238 (ttp) cc_final: 0.8920 (ttt) REVERT: B 342 LEU cc_start: 0.9565 (tt) cc_final: 0.9304 (pp) REVERT: B 698 MET cc_start: 0.9299 (tpp) cc_final: 0.8954 (tpp) REVERT: B 710 MET cc_start: 0.8659 (tpp) cc_final: 0.8435 (tpp) REVERT: B 749 MET cc_start: 0.7914 (ttp) cc_final: 0.7642 (ttp) REVERT: B 980 TYR cc_start: 0.8547 (t80) cc_final: 0.8109 (t80) REVERT: B 984 ILE cc_start: 0.9356 (mt) cc_final: 0.9088 (mm) REVERT: B 1704 MET cc_start: 0.8855 (ppp) cc_final: 0.8563 (ppp) REVERT: B 1716 THR cc_start: 0.6786 (m) cc_final: 0.6509 (p) REVERT: B 1984 MET cc_start: 0.9094 (mtm) cc_final: 0.8657 (mmt) REVERT: B 2485 ILE cc_start: 0.9205 (mt) cc_final: 0.8907 (mp) REVERT: B 2508 ASP cc_start: 0.8449 (t0) cc_final: 0.8177 (t0) REVERT: B 2553 MET cc_start: 0.8720 (mtp) cc_final: 0.8335 (mpp) REVERT: B 2604 TRP cc_start: 0.8341 (p90) cc_final: 0.7174 (p90) REVERT: B 2621 ASP cc_start: 0.8290 (t70) cc_final: 0.7488 (t70) REVERT: B 2638 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8711 (tpp) REVERT: B 2716 GLN cc_start: 0.8693 (tt0) cc_final: 0.8296 (mp10) REVERT: C 237 MET cc_start: 0.8259 (tpp) cc_final: 0.8003 (tpt) REVERT: C 497 MET cc_start: 0.7966 (mmm) cc_final: 0.7719 (ptt) REVERT: C 676 MET cc_start: 0.8298 (mmm) cc_final: 0.8029 (mmt) REVERT: C 698 MET cc_start: 0.9315 (tpp) cc_final: 0.9050 (tpp) REVERT: C 980 TYR cc_start: 0.8486 (t80) cc_final: 0.8229 (t80) REVERT: C 1161 MET cc_start: 0.8651 (ttp) cc_final: 0.8304 (tmm) REVERT: C 2314 MET cc_start: 0.8855 (mtm) cc_final: 0.8558 (mtt) REVERT: C 2344 MET cc_start: 0.9079 (mmm) cc_final: 0.8829 (mmm) REVERT: C 2470 VAL cc_start: 0.9530 (m) cc_final: 0.9211 (p) REVERT: C 2485 ILE cc_start: 0.8936 (mt) cc_final: 0.8680 (mp) REVERT: C 2553 MET cc_start: 0.8525 (mtp) cc_final: 0.8096 (mpp) REVERT: C 2587 MET cc_start: 0.9379 (ttm) cc_final: 0.9110 (tpp) REVERT: C 2638 MET cc_start: 0.8635 (tmm) cc_final: 0.7786 (tmm) REVERT: C 2691 ASP cc_start: 0.8737 (p0) cc_final: 0.8468 (p0) REVERT: C 2716 GLN cc_start: 0.8862 (tt0) cc_final: 0.8367 (mp10) REVERT: C 2769 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8687 (mm-30) outliers start: 60 outliers final: 38 residues processed: 457 average time/residue: 0.4856 time to fit residues: 391.5915 Evaluate side-chains 457 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 411 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2533 VAL Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 1724 TYR Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1713 ASN Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 1994 MET Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 476 optimal weight: 1.9990 chunk 501 optimal weight: 6.9990 chunk 457 optimal weight: 3.9990 chunk 487 optimal weight: 0.6980 chunk 293 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 382 optimal weight: 0.6980 chunk 149 optimal weight: 0.0040 chunk 440 optimal weight: 1.9990 chunk 461 optimal weight: 0.9990 chunk 486 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1370 ASN ** C2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 46125 Z= 0.149 Angle : 0.557 11.815 62583 Z= 0.270 Chirality : 0.039 0.324 7110 Planarity : 0.004 0.062 7569 Dihedral : 4.527 55.637 6162 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.15 % Allowed : 15.13 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.80 (0.12), residues: 5358 helix: 1.97 (0.09), residues: 3525 sheet: -0.60 (0.32), residues: 216 loop : -2.77 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 561 HIS 0.004 0.001 HIS C 334 PHE 0.031 0.001 PHE A1977 TYR 0.030 0.001 TYR C1724 ARG 0.003 0.000 ARG C2608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 423 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9195 (mm) REVERT: A 214 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.9186 (p90) REVERT: A 237 MET cc_start: 0.8118 (tpp) cc_final: 0.7749 (tpt) REVERT: A 342 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9294 (pp) REVERT: A 497 MET cc_start: 0.8204 (mmt) cc_final: 0.7888 (ptt) REVERT: A 518 TRP cc_start: 0.7036 (OUTLIER) cc_final: 0.6516 (t60) REVERT: A 554 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9315 (pp) REVERT: A 980 TYR cc_start: 0.8496 (t80) cc_final: 0.8255 (t80) REVERT: A 1147 MET cc_start: 0.9452 (tpp) cc_final: 0.9160 (mmp) REVERT: A 1235 ILE cc_start: 0.8878 (tp) cc_final: 0.8661 (mm) REVERT: A 1246 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8287 (t70) REVERT: A 1271 MET cc_start: 0.8598 (ptm) cc_final: 0.8361 (ptp) REVERT: A 1562 MET cc_start: 0.9094 (ttm) cc_final: 0.8516 (ptp) REVERT: A 1704 MET cc_start: 0.8940 (ttm) cc_final: 0.8623 (tmm) REVERT: A 1969 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8803 (ttmm) REVERT: A 2587 MET cc_start: 0.9213 (ttm) cc_final: 0.8944 (tpp) REVERT: A 2589 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8430 (mm-40) REVERT: A 2610 MET cc_start: 0.4699 (mmm) cc_final: 0.4465 (mmm) REVERT: A 2690 ARG cc_start: 0.8150 (ptm160) cc_final: 0.7822 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8554 (tmmm) REVERT: A 2813 MET cc_start: 0.9223 (ttp) cc_final: 0.8896 (ttt) REVERT: B 40 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9258 (mm) REVERT: B 43 LEU cc_start: 0.8733 (tt) cc_final: 0.8436 (tt) REVERT: B 342 LEU cc_start: 0.9566 (tt) cc_final: 0.9304 (pp) REVERT: B 698 MET cc_start: 0.9313 (tpp) cc_final: 0.8999 (tpp) REVERT: B 710 MET cc_start: 0.8656 (tpp) cc_final: 0.8418 (tpp) REVERT: B 749 MET cc_start: 0.7879 (ttp) cc_final: 0.7670 (ttp) REVERT: B 980 TYR cc_start: 0.8505 (t80) cc_final: 0.8172 (t80) REVERT: B 1562 MET cc_start: 0.8991 (ttm) cc_final: 0.8711 (ptp) REVERT: B 1704 MET cc_start: 0.8856 (ppp) cc_final: 0.8561 (ppp) REVERT: B 1716 THR cc_start: 0.6898 (m) cc_final: 0.6654 (p) REVERT: B 1984 MET cc_start: 0.9088 (mtm) cc_final: 0.8650 (mmt) REVERT: B 2485 ILE cc_start: 0.9203 (mt) cc_final: 0.8903 (mp) REVERT: B 2508 ASP cc_start: 0.8417 (t0) cc_final: 0.8106 (t0) REVERT: B 2553 MET cc_start: 0.8722 (mtp) cc_final: 0.8338 (mpp) REVERT: B 2604 TRP cc_start: 0.8301 (p90) cc_final: 0.7147 (p90) REVERT: B 2621 ASP cc_start: 0.8289 (t70) cc_final: 0.7480 (t70) REVERT: B 2638 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8725 (tpp) REVERT: B 2716 GLN cc_start: 0.8678 (tt0) cc_final: 0.8278 (mp10) REVERT: C 237 MET cc_start: 0.8184 (tpp) cc_final: 0.7922 (tpt) REVERT: C 497 MET cc_start: 0.7965 (mmm) cc_final: 0.7732 (ptt) REVERT: C 676 MET cc_start: 0.8303 (mmm) cc_final: 0.8034 (mmt) REVERT: C 698 MET cc_start: 0.9311 (tpp) cc_final: 0.9064 (tpp) REVERT: C 980 TYR cc_start: 0.8471 (t80) cc_final: 0.8266 (t80) REVERT: C 1156 MET cc_start: 0.8715 (tpt) cc_final: 0.8496 (tpt) REVERT: C 1161 MET cc_start: 0.8642 (ttp) cc_final: 0.8297 (tmm) REVERT: C 2314 MET cc_start: 0.8885 (mtm) cc_final: 0.8584 (mtt) REVERT: C 2344 MET cc_start: 0.9104 (mmm) cc_final: 0.8860 (mmm) REVERT: C 2470 VAL cc_start: 0.9532 (m) cc_final: 0.9307 (p) REVERT: C 2485 ILE cc_start: 0.8927 (mt) cc_final: 0.8667 (mp) REVERT: C 2553 MET cc_start: 0.8526 (mtp) cc_final: 0.8100 (mpp) REVERT: C 2587 MET cc_start: 0.9370 (ttm) cc_final: 0.9135 (tpp) REVERT: C 2691 ASP cc_start: 0.8651 (p0) cc_final: 0.8425 (p0) REVERT: C 2716 GLN cc_start: 0.8856 (tt0) cc_final: 0.8372 (mp10) REVERT: C 2769 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8679 (mm-30) outliers start: 56 outliers final: 42 residues processed: 460 average time/residue: 0.4931 time to fit residues: 399.1577 Evaluate side-chains 469 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 418 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1678 ASP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2400 VAL Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2533 VAL Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1271 MET Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 1724 TYR Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 1977 PHE Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1713 ASN Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 320 optimal weight: 5.9990 chunk 515 optimal weight: 0.0570 chunk 314 optimal weight: 0.7980 chunk 244 optimal weight: 0.1980 chunk 358 optimal weight: 0.9980 chunk 540 optimal weight: 3.9990 chunk 497 optimal weight: 2.9990 chunk 430 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 332 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1370 ASN B2003 ASN ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1721 HIS ** C2464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 46125 Z= 0.138 Angle : 0.559 11.759 62583 Z= 0.269 Chirality : 0.039 0.315 7110 Planarity : 0.004 0.062 7569 Dihedral : 4.437 55.544 6162 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.11 % Allowed : 15.38 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.86 (0.12), residues: 5358 helix: 1.99 (0.09), residues: 3540 sheet: -0.56 (0.32), residues: 216 loop : -2.73 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C2604 HIS 0.004 0.001 HIS B2004 PHE 0.033 0.001 PHE A 70 TYR 0.024 0.001 TYR A 34 ARG 0.003 0.000 ARG C1707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10716 Ramachandran restraints generated. 5358 Oldfield, 0 Emsley, 5358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 448 time to evaluate : 4.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9176 (mm) REVERT: A 214 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9191 (p90) REVERT: A 237 MET cc_start: 0.8162 (tpp) cc_final: 0.7694 (tpt) REVERT: A 497 MET cc_start: 0.8101 (mmt) cc_final: 0.7823 (ptt) REVERT: A 1147 MET cc_start: 0.9447 (tpp) cc_final: 0.9155 (mmp) REVERT: A 1235 ILE cc_start: 0.8874 (tp) cc_final: 0.8670 (mm) REVERT: A 1246 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8277 (t70) REVERT: A 1562 MET cc_start: 0.9086 (ttm) cc_final: 0.8488 (ptp) REVERT: A 1704 MET cc_start: 0.8936 (ttm) cc_final: 0.8622 (tmm) REVERT: A 1969 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8805 (ttmm) REVERT: A 2344 MET cc_start: 0.9187 (mmm) cc_final: 0.8718 (tpt) REVERT: A 2587 MET cc_start: 0.9182 (ttm) cc_final: 0.8951 (tpp) REVERT: A 2589 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8419 (mm-40) REVERT: A 2610 MET cc_start: 0.4676 (mmm) cc_final: 0.4431 (tpt) REVERT: A 2690 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7794 (tmm-80) REVERT: A 2753 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8551 (tmmm) REVERT: A 2813 MET cc_start: 0.9204 (ttp) cc_final: 0.8853 (ttt) REVERT: B 231 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9313 (mt) REVERT: B 342 LEU cc_start: 0.9565 (tt) cc_final: 0.9306 (pp) REVERT: B 532 MET cc_start: 0.8572 (ptm) cc_final: 0.8166 (ptm) REVERT: B 698 MET cc_start: 0.9304 (tpp) cc_final: 0.9015 (tpp) REVERT: B 710 MET cc_start: 0.8605 (tpp) cc_final: 0.8351 (tpp) REVERT: B 749 MET cc_start: 0.7897 (ttp) cc_final: 0.7628 (ttp) REVERT: B 980 TYR cc_start: 0.8450 (t80) cc_final: 0.8244 (t80) REVERT: B 1562 MET cc_start: 0.9019 (ttm) cc_final: 0.8714 (ptp) REVERT: B 1704 MET cc_start: 0.8851 (ppp) cc_final: 0.8549 (ppp) REVERT: B 1716 THR cc_start: 0.6778 (m) cc_final: 0.6540 (p) REVERT: B 1984 MET cc_start: 0.9074 (mtm) cc_final: 0.8645 (mmt) REVERT: B 2485 ILE cc_start: 0.9198 (mt) cc_final: 0.8920 (mt) REVERT: B 2508 ASP cc_start: 0.8436 (t0) cc_final: 0.8138 (t0) REVERT: B 2553 MET cc_start: 0.8717 (mtp) cc_final: 0.8338 (mpp) REVERT: B 2589 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8490 (mm-40) REVERT: B 2604 TRP cc_start: 0.8245 (p90) cc_final: 0.7292 (p90) REVERT: B 2638 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8626 (tpp) REVERT: B 2716 GLN cc_start: 0.8670 (tt0) cc_final: 0.8288 (mp10) REVERT: C 39 LEU cc_start: 0.9146 (tt) cc_final: 0.8767 (tp) REVERT: C 237 MET cc_start: 0.8136 (tpp) cc_final: 0.7924 (tpt) REVERT: C 676 MET cc_start: 0.8318 (mmm) cc_final: 0.8056 (mmt) REVERT: C 1156 MET cc_start: 0.8661 (tpt) cc_final: 0.8441 (tpt) REVERT: C 1161 MET cc_start: 0.8627 (ttp) cc_final: 0.8274 (tmm) REVERT: C 2314 MET cc_start: 0.8883 (mtm) cc_final: 0.8606 (mtt) REVERT: C 2344 MET cc_start: 0.9102 (mmm) cc_final: 0.8882 (mmm) REVERT: C 2470 VAL cc_start: 0.9515 (m) cc_final: 0.9296 (p) REVERT: C 2485 ILE cc_start: 0.8914 (mt) cc_final: 0.8702 (mp) REVERT: C 2508 ASP cc_start: 0.8434 (t0) cc_final: 0.8099 (t0) REVERT: C 2553 MET cc_start: 0.8523 (mtp) cc_final: 0.8101 (mpp) REVERT: C 2587 MET cc_start: 0.9358 (ttm) cc_final: 0.9140 (tpp) REVERT: C 2691 ASP cc_start: 0.8616 (p0) cc_final: 0.8385 (p0) REVERT: C 2716 GLN cc_start: 0.8851 (tt0) cc_final: 0.8378 (mp10) REVERT: C 2769 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8679 (mm-30) outliers start: 54 outliers final: 39 residues processed: 482 average time/residue: 0.4843 time to fit residues: 412.4972 Evaluate side-chains 473 residues out of total 4944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 428 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 1193 ILE Chi-restraints excluded: chain A residue 1246 ASP Chi-restraints excluded: chain A residue 1670 TRP Chi-restraints excluded: chain A residue 1671 VAL Chi-restraints excluded: chain A residue 1678 ASP Chi-restraints excluded: chain A residue 1713 ASN Chi-restraints excluded: chain A residue 2400 VAL Chi-restraints excluded: chain A residue 2481 LEU Chi-restraints excluded: chain A residue 2533 VAL Chi-restraints excluded: chain A residue 2644 THR Chi-restraints excluded: chain A residue 2753 LYS Chi-restraints excluded: chain A residue 2760 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 1193 ILE Chi-restraints excluded: chain B residue 1373 VAL Chi-restraints excluded: chain B residue 1670 TRP Chi-restraints excluded: chain B residue 1671 VAL Chi-restraints excluded: chain B residue 1713 ASN Chi-restraints excluded: chain B residue 1724 TYR Chi-restraints excluded: chain B residue 1955 MET Chi-restraints excluded: chain B residue 2303 PHE Chi-restraints excluded: chain B residue 2400 VAL Chi-restraints excluded: chain B residue 2601 VAL Chi-restraints excluded: chain B residue 2638 MET Chi-restraints excluded: chain B residue 2760 SER Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 518 TRP Chi-restraints excluded: chain C residue 1193 ILE Chi-restraints excluded: chain C residue 1671 VAL Chi-restraints excluded: chain C residue 1713 ASN Chi-restraints excluded: chain C residue 1977 PHE Chi-restraints excluded: chain C residue 2303 PHE Chi-restraints excluded: chain C residue 2304 LEU Chi-restraints excluded: chain C residue 2400 VAL Chi-restraints excluded: chain C residue 2601 VAL Chi-restraints excluded: chain C residue 2685 THR Chi-restraints excluded: chain C residue 2767 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 342 optimal weight: 0.9980 chunk 458 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 397 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 431 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 443 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2528 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1370 ASN ** B2310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.077260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.060043 restraints weight = 233585.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.062273 restraints weight = 103854.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.063759 restraints weight = 57164.566| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 46125 Z= 0.144 Angle : 0.558 11.916 62583 Z= 0.269 Chirality : 0.039 0.273 7110 Planarity : 0.004 0.061 7569 Dihedral : 4.401 55.774 6162 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.07 % Allowed : 15.76 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.91 (0.12), residues: 5358 helix: 2.03 (0.09), residues: 3540 sheet: -0.50 (0.32), residues: 216 loop : -2.68 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2604 HIS 0.004 0.001 HIS B2004 PHE 0.038 0.001 PHE B2625 TYR 0.031 0.001 TYR B 34 ARG 0.003 0.000 ARG C2608 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8871.21 seconds wall clock time: 166 minutes 16.42 seconds (9976.42 seconds total)