Starting phenix.real_space_refine on Tue Mar 12 05:11:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6f_0150/03_2024/6h6f_0150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6f_0150/03_2024/6h6f_0150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6f_0150/03_2024/6h6f_0150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6f_0150/03_2024/6h6f_0150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6f_0150/03_2024/6h6f_0150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h6f_0150/03_2024/6h6f_0150.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 339 5.16 5 C 72261 2.51 5 N 19556 2.21 5 O 22147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1634": "OE1" <-> "OE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1695": "OD1" <-> "OD2" Residue "A TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1227": "OE1" <-> "OE2" Residue "B TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1527": "OE1" <-> "OE2" Residue "B TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2332": "OE1" <-> "OE2" Residue "B TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 901": "OD1" <-> "OD2" Residue "C GLU 1006": "OE1" <-> "OE2" Residue "C PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1227": "OE1" <-> "OE2" Residue "C TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2277": "OE1" <-> "OE2" Residue "C PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "D PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1191": "OE1" <-> "OE2" Residue "D TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1527": "OE1" <-> "OE2" Residue "D PHE 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 351": "OE1" <-> "OE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 545": "OD1" <-> "OD2" Residue "E PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2277": "OE1" <-> "OE2" Residue "E PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 572": "OE1" <-> "OE2" Residue "F TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 785": "OE1" <-> "OE2" Residue "F TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 828": "OD1" <-> "OD2" Residue "F PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 977": "OD1" <-> "OD2" Residue "F TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1033": "OD1" <-> "OD2" Residue "F TYR 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 2064": "OE1" <-> "OE2" Residue "F TYR 2078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 114303 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 19477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19477 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "B" Number of atoms: 19477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19477 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "C" Number of atoms: 19477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19477 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "D" Number of atoms: 19477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19477 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "E" Number of atoms: 19477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19477 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "F" Number of atoms: 16918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2118, 16918 Classifications: {'peptide': 2118} Link IDs: {'PTRANS': 114, 'TRANS': 2003} Chain breaks: 1 Time building chain proxies: 39.88, per 1000 atoms: 0.35 Number of scatterers: 114303 At special positions: 0 Unit cell: (189.2, 190.3, 383.9, 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 339 16.00 O 22147 8.00 N 19556 7.00 C 72261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.70 Conformation dependent library (CDL) restraints added in 14.6 seconds 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 27202 Finding SS restraints... Secondary structure from input PDB file: 552 helices and 0 sheets defined 45.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.83 Creating SS restraints... Processing helix chain 'A' and resid 41 through 70 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 86 through 96 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 142 through 148 removed outlier: 4.109A pdb=" N LYS A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.792A pdb=" N THR A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 232 through 241 removed outlier: 4.491A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 289 through 298 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 471 through 489 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.853A pdb=" N THR A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 545 through 556 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 581 through 598 Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 614 through 617 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 623 through 645 Processing helix chain 'A' and resid 647 through 656 Processing helix chain 'A' and resid 664 through 678 Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 688 through 701 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 Processing helix chain 'A' and resid 726 through 737 Processing helix chain 'A' and resid 748 through 770 removed outlier: 3.558A pdb=" N ILE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 782 Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 797 through 815 Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 839 Processing helix chain 'A' and resid 842 through 856 removed outlier: 3.512A pdb=" N LEU A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 887 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 911 through 924 Processing helix chain 'A' and resid 927 through 954 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 984 through 1002 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1040 Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1070 through 1090 Processing helix chain 'A' and resid 1138 through 1141 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1217 through 1223 Processing helix chain 'A' and resid 1240 through 1243 Processing helix chain 'A' and resid 1255 through 1262 Processing helix chain 'A' and resid 1279 through 1289 Processing helix chain 'A' and resid 1290 through 1294 Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1366 through 1379 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1494 through 1496 No H-bonds generated for 'chain 'A' and resid 1494 through 1496' Processing helix chain 'A' and resid 1513 through 1517 Processing helix chain 'A' and resid 1608 through 1617 removed outlier: 4.284A pdb=" N ALA A1615 " --> pdb=" O ARG A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1625 Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1651 through 1656 Processing helix chain 'A' and resid 1764 through 1773 Processing helix chain 'A' and resid 1773 through 1786 Processing helix chain 'A' and resid 1788 through 1798 Processing helix chain 'A' and resid 1818 through 1824 Processing helix chain 'A' and resid 1836 through 1844 Processing helix chain 'A' and resid 1845 through 1870 Processing helix chain 'A' and resid 1872 through 1891 Processing helix chain 'A' and resid 1906 through 1911 Processing helix chain 'A' and resid 1912 through 1928 Processing helix chain 'A' and resid 1943 through 1947 Processing helix chain 'A' and resid 1953 through 1972 Processing helix chain 'A' and resid 2018 through 2106 removed outlier: 3.592A pdb=" N ASN A2106 " --> pdb=" O LEU A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2123 Processing helix chain 'A' and resid 2124 through 2140 Processing helix chain 'A' and resid 2155 through 2244 Processing helix chain 'A' and resid 2247 through 2284 Processing helix chain 'A' and resid 2298 through 2302 Processing helix chain 'A' and resid 2305 through 2325 Processing helix chain 'A' and resid 2337 through 2343 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2352 through 2363 Processing helix chain 'A' and resid 2394 through 2397 Processing helix chain 'A' and resid 2398 through 2402 Processing helix chain 'A' and resid 2403 through 2407 Processing helix chain 'A' and resid 2496 through 2501 removed outlier: 3.526A pdb=" N MET A2500 " --> pdb=" O LYS A2496 " (cutoff:3.500A) Processing helix chain 'A' and resid 2502 through 2504 No H-bonds generated for 'chain 'A' and resid 2502 through 2504' Processing helix chain 'B' and resid 42 through 70 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 142 through 148 removed outlier: 4.147A pdb=" N LYS B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 181 through 191 removed outlier: 3.829A pdb=" N THR B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 232 through 241 removed outlier: 4.297A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 259 through 268 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 433 through 451 Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 471 through 489 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.771A pdb=" N THR B 521 " --> pdb=" O ARG B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 598 Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 623 through 645 Processing helix chain 'B' and resid 647 through 656 Processing helix chain 'B' and resid 664 through 678 Processing helix chain 'B' and resid 688 through 700 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'B' and resid 726 through 737 Processing helix chain 'B' and resid 748 through 770 Processing helix chain 'B' and resid 772 through 782 Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 797 through 814 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 842 through 856 Processing helix chain 'B' and resid 863 through 867 Processing helix chain 'B' and resid 870 through 888 Processing helix chain 'B' and resid 890 through 899 Processing helix chain 'B' and resid 903 through 907 Processing helix chain 'B' and resid 911 through 924 Processing helix chain 'B' and resid 927 through 954 Processing helix chain 'B' and resid 963 through 972 removed outlier: 3.552A pdb=" N TYR B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1002 Processing helix chain 'B' and resid 1011 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1027 through 1037 Processing helix chain 'B' and resid 1038 through 1039 No H-bonds generated for 'chain 'B' and resid 1038 through 1039' Processing helix chain 'B' and resid 1040 through 1044 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1070 through 1090 Processing helix chain 'B' and resid 1138 through 1141 Processing helix chain 'B' and resid 1153 through 1156 removed outlier: 3.984A pdb=" N SER B1156 " --> pdb=" O PRO B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1153 through 1156' Processing helix chain 'B' and resid 1217 through 1223 Processing helix chain 'B' and resid 1240 through 1243 Processing helix chain 'B' and resid 1255 through 1262 removed outlier: 3.583A pdb=" N ASN B1261 " --> pdb=" O SER B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1289 Processing helix chain 'B' and resid 1290 through 1294 Processing helix chain 'B' and resid 1325 through 1329 Processing helix chain 'B' and resid 1366 through 1378 Processing helix chain 'B' and resid 1463 through 1468 Processing helix chain 'B' and resid 1494 through 1496 No H-bonds generated for 'chain 'B' and resid 1494 through 1496' Processing helix chain 'B' and resid 1513 through 1517 Processing helix chain 'B' and resid 1544 through 1546 No H-bonds generated for 'chain 'B' and resid 1544 through 1546' Processing helix chain 'B' and resid 1608 through 1617 removed outlier: 4.323A pdb=" N ALA B1615 " --> pdb=" O ARG B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1628 through 1631 Processing helix chain 'B' and resid 1651 through 1656 Processing helix chain 'B' and resid 1764 through 1773 Processing helix chain 'B' and resid 1773 through 1786 Processing helix chain 'B' and resid 1788 through 1797 Processing helix chain 'B' and resid 1818 through 1824 Processing helix chain 'B' and resid 1836 through 1844 Processing helix chain 'B' and resid 1845 through 1871 removed outlier: 3.633A pdb=" N LEU B1871 " --> pdb=" O ALA B1867 " (cutoff:3.500A) Processing helix chain 'B' and resid 1872 through 1891 Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1912 through 1928 removed outlier: 3.508A pdb=" N GLN B1916 " --> pdb=" O ASP B1912 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1947 Processing helix chain 'B' and resid 1953 through 1972 Processing helix chain 'B' and resid 2018 through 2106 removed outlier: 3.934A pdb=" N GLU B2024 " --> pdb=" O PRO B2020 " (cutoff:3.500A) Processing helix chain 'B' and resid 2108 through 2123 Processing helix chain 'B' and resid 2124 through 2140 Processing helix chain 'B' and resid 2155 through 2244 Processing helix chain 'B' and resid 2247 through 2284 Processing helix chain 'B' and resid 2298 through 2302 Processing helix chain 'B' and resid 2305 through 2325 Processing helix chain 'B' and resid 2337 through 2343 Processing helix chain 'B' and resid 2345 through 2349 Processing helix chain 'B' and resid 2352 through 2363 Processing helix chain 'B' and resid 2380 through 2384 Processing helix chain 'B' and resid 2393 through 2397 Processing helix chain 'B' and resid 2398 through 2402 Processing helix chain 'B' and resid 2403 through 2407 Processing helix chain 'B' and resid 2490 through 2494 Processing helix chain 'B' and resid 2497 through 2504 Processing helix chain 'C' and resid 42 through 70 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 85 through 97 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 181 through 191 removed outlier: 3.937A pdb=" N THR C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.683A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 Processing helix chain 'C' and resid 289 through 298 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 453 through 465 Processing helix chain 'C' and resid 471 through 489 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 523 through 527 Processing helix chain 'C' and resid 545 through 556 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 598 Processing helix chain 'C' and resid 601 through 613 Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 623 through 645 Processing helix chain 'C' and resid 647 through 656 Processing helix chain 'C' and resid 664 through 678 Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 688 through 700 Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 704 through 719 Processing helix chain 'C' and resid 726 through 735 Processing helix chain 'C' and resid 748 through 770 Processing helix chain 'C' and resid 772 through 782 Processing helix chain 'C' and resid 783 through 787 Processing helix chain 'C' and resid 797 through 815 Processing helix chain 'C' and resid 817 through 827 Processing helix chain 'C' and resid 831 through 839 Processing helix chain 'C' and resid 842 through 856 removed outlier: 3.535A pdb=" N LEU C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 867 Processing helix chain 'C' and resid 870 through 888 Processing helix chain 'C' and resid 890 through 899 Processing helix chain 'C' and resid 903 through 907 Processing helix chain 'C' and resid 911 through 924 Processing helix chain 'C' and resid 927 through 954 Processing helix chain 'C' and resid 963 through 972 removed outlier: 3.518A pdb=" N TYR C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1002 Processing helix chain 'C' and resid 1011 through 1014 Processing helix chain 'C' and resid 1015 through 1020 Processing helix chain 'C' and resid 1027 through 1040 Processing helix chain 'C' and resid 1041 through 1044 Processing helix chain 'C' and resid 1054 through 1063 Processing helix chain 'C' and resid 1070 through 1090 Processing helix chain 'C' and resid 1138 through 1141 Processing helix chain 'C' and resid 1153 through 1156 removed outlier: 3.895A pdb=" N SER C1156 " --> pdb=" O PRO C1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1153 through 1156' Processing helix chain 'C' and resid 1217 through 1223 Processing helix chain 'C' and resid 1240 through 1243 Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1279 through 1289 Processing helix chain 'C' and resid 1290 through 1294 Processing helix chain 'C' and resid 1325 through 1329 Processing helix chain 'C' and resid 1366 through 1379 Processing helix chain 'C' and resid 1463 through 1467 Processing helix chain 'C' and resid 1494 through 1496 No H-bonds generated for 'chain 'C' and resid 1494 through 1496' Processing helix chain 'C' and resid 1513 through 1517 Processing helix chain 'C' and resid 1608 through 1617 removed outlier: 4.226A pdb=" N ALA C1615 " --> pdb=" O ARG C1611 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C1616 " --> pdb=" O GLN C1612 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1625 Processing helix chain 'C' and resid 1628 through 1631 Processing helix chain 'C' and resid 1651 through 1656 Processing helix chain 'C' and resid 1764 through 1773 Processing helix chain 'C' and resid 1773 through 1786 Processing helix chain 'C' and resid 1788 through 1798 Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1830 through 1834 removed outlier: 4.201A pdb=" N ASP C1833 " --> pdb=" O ASP C1830 " (cutoff:3.500A) Processing helix chain 'C' and resid 1836 through 1844 Processing helix chain 'C' and resid 1845 through 1869 Processing helix chain 'C' and resid 1872 through 1891 Processing helix chain 'C' and resid 1906 through 1911 Processing helix chain 'C' and resid 1912 through 1929 Processing helix chain 'C' and resid 1943 through 1947 Processing helix chain 'C' and resid 1953 through 1972 Processing helix chain 'C' and resid 2018 through 2105 Processing helix chain 'C' and resid 2108 through 2123 Processing helix chain 'C' and resid 2124 through 2139 Processing helix chain 'C' and resid 2155 through 2244 Processing helix chain 'C' and resid 2247 through 2285 Processing helix chain 'C' and resid 2298 through 2302 Processing helix chain 'C' and resid 2305 through 2325 Processing helix chain 'C' and resid 2337 through 2343 Processing helix chain 'C' and resid 2345 through 2349 Processing helix chain 'C' and resid 2352 through 2363 Processing helix chain 'C' and resid 2394 through 2397 Processing helix chain 'C' and resid 2398 through 2402 Processing helix chain 'C' and resid 2403 through 2407 Processing helix chain 'C' and resid 2437 through 2441 removed outlier: 3.635A pdb=" N GLY C2440 " --> pdb=" O ASP C2437 " (cutoff:3.500A) Processing helix chain 'C' and resid 2490 through 2494 Processing helix chain 'C' and resid 2500 through 2504 Processing helix chain 'D' and resid 42 through 70 Processing helix chain 'D' and resid 71 through 78 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 143 through 148 removed outlier: 3.526A pdb=" N SER D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 161 through 177 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.959A pdb=" N THR D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 241 removed outlier: 4.261A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 272 through 278 Processing helix chain 'D' and resid 278 through 286 Processing helix chain 'D' and resid 289 through 298 removed outlier: 3.814A pdb=" N PHE D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 434 through 451 Processing helix chain 'D' and resid 453 through 465 Processing helix chain 'D' and resid 471 through 489 Processing helix chain 'D' and resid 491 through 498 Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'D' and resid 545 through 556 Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 581 through 598 Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 623 through 645 Processing helix chain 'D' and resid 647 through 656 Processing helix chain 'D' and resid 664 through 678 Processing helix chain 'D' and resid 688 through 701 Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 704 through 719 Processing helix chain 'D' and resid 726 through 737 Processing helix chain 'D' and resid 748 through 770 Processing helix chain 'D' and resid 772 through 782 Processing helix chain 'D' and resid 783 through 787 Processing helix chain 'D' and resid 797 through 814 Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 839 Processing helix chain 'D' and resid 842 through 856 removed outlier: 3.554A pdb=" N LEU D 846 " --> pdb=" O ASP D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 867 Processing helix chain 'D' and resid 870 through 887 Processing helix chain 'D' and resid 890 through 899 Processing helix chain 'D' and resid 903 through 907 Processing helix chain 'D' and resid 911 through 924 Processing helix chain 'D' and resid 927 through 954 Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 984 through 1002 Processing helix chain 'D' and resid 1009 through 1014 Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1027 through 1040 Processing helix chain 'D' and resid 1041 through 1044 Processing helix chain 'D' and resid 1054 through 1064 Processing helix chain 'D' and resid 1070 through 1090 Processing helix chain 'D' and resid 1129 through 1131 No H-bonds generated for 'chain 'D' and resid 1129 through 1131' Processing helix chain 'D' and resid 1137 through 1141 Processing helix chain 'D' and resid 1153 through 1156 removed outlier: 4.169A pdb=" N SER D1156 " --> pdb=" O PRO D1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1153 through 1156' Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1240 through 1243 Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1279 through 1289 Processing helix chain 'D' and resid 1290 through 1294 Processing helix chain 'D' and resid 1325 through 1329 Processing helix chain 'D' and resid 1366 through 1378 Processing helix chain 'D' and resid 1463 through 1468 Processing helix chain 'D' and resid 1494 through 1496 No H-bonds generated for 'chain 'D' and resid 1494 through 1496' Processing helix chain 'D' and resid 1513 through 1517 Processing helix chain 'D' and resid 1544 through 1546 No H-bonds generated for 'chain 'D' and resid 1544 through 1546' Processing helix chain 'D' and resid 1608 through 1617 removed outlier: 4.557A pdb=" N ALA D1615 " --> pdb=" O ARG D1611 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D1616 " --> pdb=" O GLN D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1625 Processing helix chain 'D' and resid 1628 through 1631 Processing helix chain 'D' and resid 1651 through 1656 Processing helix chain 'D' and resid 1764 through 1773 Processing helix chain 'D' and resid 1773 through 1786 Processing helix chain 'D' and resid 1788 through 1798 Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1830 through 1834 removed outlier: 3.515A pdb=" N ASP D1833 " --> pdb=" O ASP D1830 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D1834 " --> pdb=" O PRO D1831 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1830 through 1834' Processing helix chain 'D' and resid 1836 through 1844 Processing helix chain 'D' and resid 1845 through 1871 removed outlier: 3.891A pdb=" N LEU D1871 " --> pdb=" O ALA D1867 " (cutoff:3.500A) Processing helix chain 'D' and resid 1872 through 1891 Processing helix chain 'D' and resid 1906 through 1911 Processing helix chain 'D' and resid 1912 through 1928 Processing helix chain 'D' and resid 1943 through 1947 Processing helix chain 'D' and resid 1953 through 1972 Processing helix chain 'D' and resid 2018 through 2106 Processing helix chain 'D' and resid 2108 through 2123 Processing helix chain 'D' and resid 2124 through 2139 Processing helix chain 'D' and resid 2155 through 2244 Processing helix chain 'D' and resid 2247 through 2285 Processing helix chain 'D' and resid 2298 through 2302 Processing helix chain 'D' and resid 2305 through 2324 Processing helix chain 'D' and resid 2337 through 2343 Processing helix chain 'D' and resid 2345 through 2349 Processing helix chain 'D' and resid 2352 through 2363 Processing helix chain 'D' and resid 2393 through 2397 Processing helix chain 'D' and resid 2398 through 2402 Processing helix chain 'D' and resid 2403 through 2407 Processing helix chain 'D' and resid 2437 through 2441 Processing helix chain 'D' and resid 2490 through 2494 Processing helix chain 'D' and resid 2496 through 2501 Processing helix chain 'D' and resid 2502 through 2504 No H-bonds generated for 'chain 'D' and resid 2502 through 2504' Processing helix chain 'E' and resid 42 through 70 Processing helix chain 'E' and resid 71 through 78 Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.874A pdb=" N THR E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 218 through 223 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 232 through 241 removed outlier: 4.273A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 259 through 268 Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 Processing helix chain 'E' and resid 289 through 298 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 453 through 465 Processing helix chain 'E' and resid 471 through 489 Processing helix chain 'E' and resid 491 through 498 Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 545 through 556 Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 598 Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 623 through 645 Processing helix chain 'E' and resid 647 through 656 Processing helix chain 'E' and resid 664 through 678 Processing helix chain 'E' and resid 682 through 686 Processing helix chain 'E' and resid 688 through 701 Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 704 through 719 Processing helix chain 'E' and resid 726 through 737 Processing helix chain 'E' and resid 748 through 770 Processing helix chain 'E' and resid 772 through 782 Processing helix chain 'E' and resid 783 through 787 Processing helix chain 'E' and resid 788 through 792 Processing helix chain 'E' and resid 797 through 815 Processing helix chain 'E' and resid 817 through 827 Processing helix chain 'E' and resid 831 through 839 Processing helix chain 'E' and resid 842 through 856 Processing helix chain 'E' and resid 870 through 888 Processing helix chain 'E' and resid 890 through 899 Processing helix chain 'E' and resid 904 through 909 Processing helix chain 'E' and resid 911 through 924 Processing helix chain 'E' and resid 927 through 954 Processing helix chain 'E' and resid 963 through 972 Processing helix chain 'E' and resid 984 through 1002 Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1027 through 1040 removed outlier: 4.009A pdb=" N VAL E1038 " --> pdb=" O VAL E1034 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR E1039 " --> pdb=" O SER E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1063 Processing helix chain 'E' and resid 1070 through 1090 Processing helix chain 'E' and resid 1138 through 1141 Processing helix chain 'E' and resid 1153 through 1156 removed outlier: 4.015A pdb=" N SER E1156 " --> pdb=" O PRO E1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1153 through 1156' Processing helix chain 'E' and resid 1217 through 1224 Processing helix chain 'E' and resid 1240 through 1243 Processing helix chain 'E' and resid 1255 through 1260 removed outlier: 3.533A pdb=" N TYR E1259 " --> pdb=" O THR E1255 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1289 Processing helix chain 'E' and resid 1290 through 1294 Processing helix chain 'E' and resid 1325 through 1329 Processing helix chain 'E' and resid 1366 through 1378 Processing helix chain 'E' and resid 1463 through 1468 Processing helix chain 'E' and resid 1494 through 1496 No H-bonds generated for 'chain 'E' and resid 1494 through 1496' Processing helix chain 'E' and resid 1513 through 1517 Processing helix chain 'E' and resid 1608 through 1617 removed outlier: 4.482A pdb=" N ALA E1615 " --> pdb=" O ARG E1611 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E1616 " --> pdb=" O GLN E1612 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1625 Processing helix chain 'E' and resid 1628 through 1631 Processing helix chain 'E' and resid 1651 through 1656 Processing helix chain 'E' and resid 1764 through 1773 Processing helix chain 'E' and resid 1773 through 1786 Processing helix chain 'E' and resid 1788 through 1798 Processing helix chain 'E' and resid 1818 through 1824 Processing helix chain 'E' and resid 1830 through 1834 removed outlier: 3.569A pdb=" N ASP E1833 " --> pdb=" O ASP E1830 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER E1834 " --> pdb=" O PRO E1831 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1830 through 1834' Processing helix chain 'E' and resid 1836 through 1844 Processing helix chain 'E' and resid 1845 through 1870 Processing helix chain 'E' and resid 1872 through 1891 Processing helix chain 'E' and resid 1906 through 1911 Processing helix chain 'E' and resid 1912 through 1928 Processing helix chain 'E' and resid 1943 through 1947 Processing helix chain 'E' and resid 1953 through 1972 Processing helix chain 'E' and resid 2018 through 2105 removed outlier: 3.655A pdb=" N GLU E2024 " --> pdb=" O PRO E2020 " (cutoff:3.500A) Processing helix chain 'E' and resid 2108 through 2123 Processing helix chain 'E' and resid 2124 through 2140 Processing helix chain 'E' and resid 2155 through 2244 Processing helix chain 'E' and resid 2247 through 2285 Processing helix chain 'E' and resid 2298 through 2302 Processing helix chain 'E' and resid 2305 through 2324 Processing helix chain 'E' and resid 2337 through 2343 Processing helix chain 'E' and resid 2345 through 2349 Processing helix chain 'E' and resid 2352 through 2362 Processing helix chain 'E' and resid 2394 through 2402 removed outlier: 6.255A pdb=" N ILE E2398 " --> pdb=" O ASP E2395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ARG E2399 " --> pdb=" O LEU E2396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR E2402 " --> pdb=" O ARG E2399 " (cutoff:3.500A) Processing helix chain 'E' and resid 2403 through 2407 Processing helix chain 'E' and resid 2490 through 2494 Processing helix chain 'E' and resid 2499 through 2504 Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 495 through 498 Processing helix chain 'F' and resid 606 through 608 No H-bonds generated for 'chain 'F' and resid 606 through 608' Processing helix chain 'F' and resid 717 through 732 removed outlier: 5.071A pdb=" N THR F 730 " --> pdb=" O ALA F 726 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR F 731 " --> pdb=" O ALA F 727 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 821 Processing helix chain 'F' and resid 822 through 824 No H-bonds generated for 'chain 'F' and resid 822 through 824' Processing helix chain 'F' and resid 854 through 864 Processing helix chain 'F' and resid 963 through 967 removed outlier: 3.568A pdb=" N THR F 966 " --> pdb=" O TYR F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 968 through 974 removed outlier: 4.022A pdb=" N LEU F 972 " --> pdb=" O PRO F 968 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 981 Processing helix chain 'F' and resid 1017 through 1021 Processing helix chain 'F' and resid 1027 through 1033 Processing helix chain 'F' and resid 1081 through 1086 Processing helix chain 'F' and resid 1087 through 1089 No H-bonds generated for 'chain 'F' and resid 1087 through 1089' Processing helix chain 'F' and resid 1093 through 1104 Processing helix chain 'F' and resid 1133 through 1137 Processing helix chain 'F' and resid 1224 through 1228 Processing helix chain 'F' and resid 1235 through 1241 Processing helix chain 'F' and resid 1264 through 1271 Processing helix chain 'F' and resid 1271 through 1282 removed outlier: 6.595A pdb=" N GLN F1277 " --> pdb=" O GLU F1273 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS F1278 " --> pdb=" O GLN F1274 " (cutoff:3.500A) Processing helix chain 'F' and resid 1293 through 1302 Processing helix chain 'F' and resid 1306 through 1315 Processing helix chain 'F' and resid 1414 through 1421 Processing helix chain 'F' and resid 1461 through 1470 removed outlier: 3.919A pdb=" N ALA F1467 " --> pdb=" O ASN F1463 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU F1468 " --> pdb=" O ASP F1464 " (cutoff:3.500A) Processing helix chain 'F' and resid 1484 through 1489 Processing helix chain 'F' and resid 1538 through 1548 removed outlier: 3.640A pdb=" N THR F1547 " --> pdb=" O GLU F1543 " (cutoff:3.500A) Processing helix chain 'F' and resid 1635 through 1641 Processing helix chain 'F' and resid 1688 through 1695 removed outlier: 3.564A pdb=" N TRP F1692 " --> pdb=" O ASN F1688 " (cutoff:3.500A) Processing helix chain 'F' and resid 1791 through 1794 Processing helix chain 'F' and resid 1865 through 1869 Processing helix chain 'F' and resid 1925 through 1930 Processing helix chain 'F' and resid 2090 through 2095 Processing helix chain 'F' and resid 2100 through 2104 removed outlier: 3.509A pdb=" N GLY F2103 " --> pdb=" O ARG F2100 " (cutoff:3.500A) Processing helix chain 'F' and resid 2143 through 2147 4447 hydrogen bonds defined for protein. 12648 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: 37.28 Time building geometry restraints manager: 36.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 20213 1.30 - 1.44: 34320 1.44 - 1.57: 61519 1.57 - 1.71: 146 1.71 - 1.85: 619 Bond restraints: 116817 Sorted by residual: bond pdb=" CB HIS A1724 " pdb=" CG HIS A1724 " ideal model delta sigma weight residual 1.497 1.392 0.105 1.40e-02 5.10e+03 5.58e+01 bond pdb=" CD ARG C 141 " pdb=" NE ARG C 141 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.08e+01 bond pdb=" CB HIS C1145 " pdb=" CG HIS C1145 " ideal model delta sigma weight residual 1.497 1.401 0.096 1.40e-02 5.10e+03 4.72e+01 bond pdb=" CB HIS E1847 " pdb=" CG HIS E1847 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.54e+01 bond pdb=" CD ARG C1819 " pdb=" NE ARG C1819 " ideal model delta sigma weight residual 1.458 1.365 0.093 1.40e-02 5.10e+03 4.43e+01 ... (remaining 116812 not shown) Histogram of bond angle deviations from ideal: 94.04 - 102.14: 498 102.14 - 110.24: 32278 110.24 - 118.34: 59323 118.34 - 126.45: 65231 126.45 - 134.55: 1428 Bond angle restraints: 158758 Sorted by residual: angle pdb=" N LYS F1395 " pdb=" CA LYS F1395 " pdb=" C LYS F1395 " ideal model delta sigma weight residual 113.97 101.57 12.40 1.28e+00 6.10e-01 9.38e+01 angle pdb=" N LYS E1477 " pdb=" CA LYS E1477 " pdb=" C LYS E1477 " ideal model delta sigma weight residual 114.04 102.82 11.22 1.24e+00 6.50e-01 8.19e+01 angle pdb=" C ASP D1844 " pdb=" N PRO D1845 " pdb=" CA PRO D1845 " ideal model delta sigma weight residual 119.56 128.79 -9.23 1.02e+00 9.61e-01 8.19e+01 angle pdb=" N VAL D1004 " pdb=" CA VAL D1004 " pdb=" C VAL D1004 " ideal model delta sigma weight residual 110.72 101.74 8.98 1.01e+00 9.80e-01 7.90e+01 angle pdb=" C SER E1354 " pdb=" N PRO E1355 " pdb=" CA PRO E1355 " ideal model delta sigma weight residual 120.03 128.79 -8.76 9.90e-01 1.02e+00 7.83e+01 ... (remaining 158753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 67383 17.89 - 35.77: 1725 35.77 - 53.66: 411 53.66 - 71.54: 341 71.54 - 89.43: 70 Dihedral angle restraints: 69930 sinusoidal: 27636 harmonic: 42294 Sorted by residual: dihedral pdb=" C ARG F 196 " pdb=" N ARG F 196 " pdb=" CA ARG F 196 " pdb=" CB ARG F 196 " ideal model delta harmonic sigma weight residual -122.60 -132.91 10.31 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C THR C 521 " pdb=" N THR C 521 " pdb=" CA THR C 521 " pdb=" CB THR C 521 " ideal model delta harmonic sigma weight residual -122.00 -131.54 9.54 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" N ARG F2106 " pdb=" C ARG F2106 " pdb=" CA ARG F2106 " pdb=" CB ARG F2106 " ideal model delta harmonic sigma weight residual 122.80 132.31 -9.51 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 69927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 11786 0.088 - 0.177: 4740 0.177 - 0.265: 867 0.265 - 0.353: 116 0.353 - 0.442: 14 Chirality restraints: 17523 Sorted by residual: chirality pdb=" CA TRP E 731 " pdb=" N TRP E 731 " pdb=" C TRP E 731 " pdb=" CB TRP E 731 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA ARG F 196 " pdb=" N ARG F 196 " pdb=" C ARG F 196 " pdb=" CB ARG F 196 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA ARG F2106 " pdb=" N ARG F2106 " pdb=" C ARG F2106 " pdb=" CB ARG F2106 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 17520 not shown) Planarity restraints: 20695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 521 " 0.097 5.00e-02 4.00e+02 1.48e-01 3.52e+01 pdb=" N PRO E 522 " -0.257 5.00e-02 4.00e+02 pdb=" CA PRO E 522 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO E 522 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 521 " 0.094 5.00e-02 4.00e+02 1.45e-01 3.34e+01 pdb=" N PRO D 522 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO D 522 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO D 522 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 810 " 0.073 2.00e-02 2.50e+03 3.63e-02 3.29e+01 pdb=" CG TRP B 810 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 810 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 810 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 810 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 810 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP B 810 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 810 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 810 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 810 " 0.038 2.00e-02 2.50e+03 ... (remaining 20692 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 15556 2.73 - 3.27: 119136 3.27 - 3.81: 203421 3.81 - 4.36: 258267 4.36 - 4.90: 409732 Nonbonded interactions: 1006112 Sorted by model distance: nonbonded pdb=" OH TYR F 228 " pdb=" OG1 THR F 301 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR E1868 " pdb=" O LEU E1974 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR C1868 " pdb=" O LEU C1974 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR A1868 " pdb=" O LEU A1974 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR D 92 " pdb=" NH1 ARG D 99 " model vdw 2.257 2.520 ... (remaining 1006107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 23.620 Check model and map are aligned: 1.170 Set scattering table: 0.720 Process input model: 210.660 Find NCS groups from input model: 5.580 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 249.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.020 0.162 116817 Z= 1.327 Angle : 1.678 12.667 158758 Z= 1.140 Chirality : 0.093 0.442 17523 Planarity : 0.010 0.148 20695 Dihedral : 10.879 89.431 42728 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.65 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.01 % 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: 0.96 (0.06), residues: 14354 helix: 0.58 (0.06), residues: 5739 sheet: 1.15 (0.10), residues: 2531 loop : 0.69 (0.08), residues: 6084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.011 TRP B 810 HIS 0.016 0.003 HIS B1724 PHE 0.042 0.006 PHE F1014 TYR 0.072 0.009 TYR A1205 ARG 0.013 0.001 ARG D2018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3420 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3420 time to evaluate : 9.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7093 (t0) cc_final: 0.6861 (t0) REVERT: A 136 TYR cc_start: 0.7274 (m-80) cc_final: 0.6700 (m-80) REVERT: A 159 LEU cc_start: 0.8278 (pt) cc_final: 0.7864 (pt) REVERT: A 164 LEU cc_start: 0.8576 (mt) cc_final: 0.8164 (mp) REVERT: A 195 SER cc_start: 0.7560 (m) cc_final: 0.7189 (p) REVERT: A 255 ILE cc_start: 0.8426 (mt) cc_final: 0.7942 (mp) REVERT: A 546 TRP cc_start: 0.8275 (p-90) cc_final: 0.8009 (p-90) REVERT: A 658 SER cc_start: 0.8359 (m) cc_final: 0.7755 (p) REVERT: A 916 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 1015 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7462 (mtp180) REVERT: A 1039 TYR cc_start: 0.7144 (m-80) cc_final: 0.6835 (m-10) REVERT: A 1049 MET cc_start: 0.7559 (ppp) cc_final: 0.7164 (ptm) REVERT: A 1103 ASN cc_start: 0.7028 (m-40) cc_final: 0.6625 (t0) REVERT: A 1115 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6505 (tp30) REVERT: A 1214 THR cc_start: 0.8162 (m) cc_final: 0.7936 (t) REVERT: A 1288 ASP cc_start: 0.8544 (m-30) cc_final: 0.8033 (t70) REVERT: A 1310 TYR cc_start: 0.7876 (m-80) cc_final: 0.7570 (m-80) REVERT: A 1324 TRP cc_start: 0.8273 (m100) cc_final: 0.8045 (m100) REVERT: A 1333 TYR cc_start: 0.7092 (t80) cc_final: 0.6626 (t80) REVERT: A 1397 ASN cc_start: 0.6897 (m-40) cc_final: 0.6279 (t0) REVERT: A 1490 ASN cc_start: 0.8316 (t0) cc_final: 0.7660 (p0) REVERT: A 1544 PHE cc_start: 0.8112 (m-80) cc_final: 0.7766 (m-80) REVERT: A 1676 ILE cc_start: 0.8973 (pt) cc_final: 0.8684 (tp) REVERT: A 1733 VAL cc_start: 0.7802 (t) cc_final: 0.7589 (t) REVERT: A 1791 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7034 (mm-30) REVERT: A 1794 ARG cc_start: 0.7020 (ttt180) cc_final: 0.6804 (ttm170) REVERT: A 1871 LEU cc_start: 0.7847 (mt) cc_final: 0.7459 (tp) REVERT: A 1904 ASP cc_start: 0.6772 (m-30) cc_final: 0.6538 (m-30) REVERT: A 2019 PHE cc_start: 0.8532 (t80) cc_final: 0.8251 (t80) REVERT: A 2053 ASN cc_start: 0.8008 (m-40) cc_final: 0.7618 (t0) REVERT: A 2124 LEU cc_start: 0.8433 (mm) cc_final: 0.7879 (mm) REVERT: A 2159 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 2330 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 2504 LEU cc_start: 0.8985 (tp) cc_final: 0.8586 (tt) REVERT: B 67 LEU cc_start: 0.8290 (mt) cc_final: 0.7680 (mp) REVERT: B 75 GLN cc_start: 0.6458 (mt0) cc_final: 0.5871 (mm110) REVERT: B 83 LEU cc_start: 0.7408 (mt) cc_final: 0.7147 (pp) REVERT: B 93 ASN cc_start: 0.7465 (m-40) cc_final: 0.7187 (m-40) REVERT: B 134 SER cc_start: 0.7628 (t) cc_final: 0.7170 (m) REVERT: B 170 LEU cc_start: 0.8957 (tp) cc_final: 0.8543 (mt) REVERT: B 242 SER cc_start: 0.8786 (m) cc_final: 0.8422 (p) REVERT: B 404 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7855 (pm20) REVERT: B 583 LYS cc_start: 0.9058 (tttt) cc_final: 0.8575 (tppt) REVERT: B 606 ASP cc_start: 0.7968 (t70) cc_final: 0.7442 (t0) REVERT: B 804 LEU cc_start: 0.8630 (mt) cc_final: 0.8411 (mm) REVERT: B 1023 LYS cc_start: 0.7368 (tttt) cc_final: 0.5968 (ttmt) REVERT: B 1028 TYR cc_start: 0.7181 (t80) cc_final: 0.6451 (t80) REVERT: B 1170 LEU cc_start: 0.8811 (tp) cc_final: 0.8286 (mt) REVERT: B 1194 TYR cc_start: 0.8248 (m-80) cc_final: 0.7897 (m-10) REVERT: B 1275 SER cc_start: 0.9158 (t) cc_final: 0.8836 (p) REVERT: B 1362 ASN cc_start: 0.7956 (t0) cc_final: 0.7714 (p0) REVERT: B 1397 ASN cc_start: 0.8624 (m-40) cc_final: 0.8127 (m-40) REVERT: B 1424 PHE cc_start: 0.7723 (p90) cc_final: 0.7457 (p90) REVERT: B 1456 TYR cc_start: 0.8763 (p90) cc_final: 0.8295 (p90) REVERT: B 1575 THR cc_start: 0.8049 (m) cc_final: 0.7794 (t) REVERT: B 1854 MET cc_start: 0.8002 (mtm) cc_final: 0.7709 (mmp) REVERT: B 1878 GLU cc_start: 0.8581 (tt0) cc_final: 0.8212 (mm-30) REVERT: B 1884 MET cc_start: 0.7536 (mmm) cc_final: 0.7221 (mmm) REVERT: B 2081 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7776 (tp30) REVERT: B 2103 TYR cc_start: 0.8540 (t80) cc_final: 0.7675 (t80) REVERT: B 2128 VAL cc_start: 0.6369 (t) cc_final: 0.6103 (p) REVERT: B 2164 VAL cc_start: 0.7157 (t) cc_final: 0.6734 (m) REVERT: B 2167 PHE cc_start: 0.6880 (t80) cc_final: 0.6635 (t80) REVERT: B 2168 SER cc_start: 0.7810 (t) cc_final: 0.6413 (p) REVERT: B 2414 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6678 (tm-30) REVERT: C 95 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8167 (mm-40) REVERT: C 170 LEU cc_start: 0.8903 (tp) cc_final: 0.8686 (tp) REVERT: C 189 LEU cc_start: 0.8376 (mt) cc_final: 0.8103 (mt) REVERT: C 218 LEU cc_start: 0.8377 (mt) cc_final: 0.8039 (tt) REVERT: C 622 ILE cc_start: 0.7903 (tt) cc_final: 0.7573 (mt) REVERT: C 632 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8051 (ptp-110) REVERT: C 647 SER cc_start: 0.7736 (p) cc_final: 0.7254 (m) REVERT: C 804 LEU cc_start: 0.8750 (mt) cc_final: 0.8224 (mt) REVERT: C 972 LEU cc_start: 0.6843 (mt) cc_final: 0.6440 (mt) REVERT: C 1023 LYS cc_start: 0.6814 (tttt) cc_final: 0.6126 (ptpt) REVERT: C 1031 TRP cc_start: 0.6953 (t60) cc_final: 0.6366 (t-100) REVERT: C 1051 ILE cc_start: 0.8484 (mt) cc_final: 0.8242 (mt) REVERT: C 1070 ASN cc_start: 0.7771 (p0) cc_final: 0.7433 (p0) REVERT: C 1080 SER cc_start: 0.8627 (t) cc_final: 0.8424 (t) REVERT: C 1090 ASN cc_start: 0.7824 (m-40) cc_final: 0.7431 (m110) REVERT: C 1147 ILE cc_start: 0.7201 (mt) cc_final: 0.6919 (mt) REVERT: C 1170 LEU cc_start: 0.8970 (tp) cc_final: 0.8699 (tt) REVERT: C 1215 PHE cc_start: 0.7610 (m-80) cc_final: 0.7236 (m-10) REVERT: C 1272 ASP cc_start: 0.6976 (p0) cc_final: 0.5488 (t70) REVERT: C 1310 TYR cc_start: 0.7643 (m-80) cc_final: 0.7054 (m-80) REVERT: C 1388 TYR cc_start: 0.6885 (m-80) cc_final: 0.6625 (m-80) REVERT: C 1407 VAL cc_start: 0.8553 (t) cc_final: 0.8068 (m) REVERT: C 1645 PHE cc_start: 0.8705 (m-80) cc_final: 0.8290 (m-10) REVERT: C 1681 LEU cc_start: 0.8473 (mt) cc_final: 0.7810 (tp) REVERT: C 1771 LEU cc_start: 0.8698 (tp) cc_final: 0.8240 (tp) REVERT: C 1793 ASN cc_start: 0.8916 (t0) cc_final: 0.8386 (t0) REVERT: C 1901 THR cc_start: 0.7416 (p) cc_final: 0.7068 (t) REVERT: C 1947 LEU cc_start: 0.7704 (mt) cc_final: 0.7412 (tp) REVERT: C 1957 MET cc_start: 0.8413 (mmm) cc_final: 0.7827 (tpt) REVERT: C 1965 GLN cc_start: 0.7392 (tp40) cc_final: 0.7175 (tt0) REVERT: C 1983 LEU cc_start: 0.8261 (mt) cc_final: 0.7464 (pp) REVERT: C 2077 GLU cc_start: 0.7882 (tt0) cc_final: 0.6843 (tt0) REVERT: C 2099 TYR cc_start: 0.7671 (m-80) cc_final: 0.7471 (m-80) REVERT: C 2102 LEU cc_start: 0.8352 (mt) cc_final: 0.8040 (mp) REVERT: C 2103 TYR cc_start: 0.7740 (t80) cc_final: 0.6462 (t80) REVERT: C 2124 LEU cc_start: 0.7751 (mt) cc_final: 0.7531 (mt) REVERT: C 2132 ARG cc_start: 0.5771 (mmt180) cc_final: 0.5092 (mmm160) REVERT: C 2142 PRO cc_start: 0.7230 (Cg_exo) cc_final: 0.7020 (Cg_endo) REVERT: C 2183 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6797 (mm-30) REVERT: C 2264 GLN cc_start: 0.8482 (mt0) cc_final: 0.7998 (mp10) REVERT: C 2317 MET cc_start: 0.8570 (ttm) cc_final: 0.8303 (ttm) REVERT: C 2334 THR cc_start: 0.8177 (m) cc_final: 0.7582 (p) REVERT: C 2438 LYS cc_start: 0.7608 (pttt) cc_final: 0.7221 (tttp) REVERT: C 2503 THR cc_start: 0.8527 (p) cc_final: 0.8242 (t) REVERT: D 67 LEU cc_start: 0.7705 (mt) cc_final: 0.7373 (mt) REVERT: D 80 LEU cc_start: 0.7867 (mt) cc_final: 0.7653 (mt) REVERT: D 90 ILE cc_start: 0.7109 (mt) cc_final: 0.6488 (tt) REVERT: D 93 ASN cc_start: 0.7203 (m-40) cc_final: 0.6839 (p0) REVERT: D 138 LEU cc_start: 0.8068 (tp) cc_final: 0.7799 (tp) REVERT: D 175 THR cc_start: 0.8459 (m) cc_final: 0.8099 (p) REVERT: D 242 SER cc_start: 0.8706 (m) cc_final: 0.8390 (p) REVERT: D 339 TYR cc_start: 0.6030 (p90) cc_final: 0.5688 (p90) REVERT: D 355 LEU cc_start: 0.9087 (tp) cc_final: 0.8859 (tt) REVERT: D 524 LEU cc_start: 0.8265 (tp) cc_final: 0.7720 (tt) REVERT: D 619 LEU cc_start: 0.8742 (mt) cc_final: 0.8515 (mt) REVERT: D 654 MET cc_start: 0.8874 (mtp) cc_final: 0.8641 (mtp) REVERT: D 774 ASN cc_start: 0.7747 (m-40) cc_final: 0.7545 (t0) REVERT: D 937 PHE cc_start: 0.8252 (t80) cc_final: 0.7116 (t80) REVERT: D 1035 SER cc_start: 0.9420 (m) cc_final: 0.9134 (t) REVERT: D 1086 GLU cc_start: 0.6322 (tt0) cc_final: 0.6069 (tm-30) REVERT: D 1324 TRP cc_start: 0.7361 (m100) cc_final: 0.6838 (m100) REVERT: D 1677 TYR cc_start: 0.8323 (t80) cc_final: 0.7946 (t80) REVERT: D 1680 GLN cc_start: 0.5521 (mm-40) cc_final: 0.5217 (mp10) REVERT: D 1858 ASP cc_start: 0.7662 (m-30) cc_final: 0.7356 (m-30) REVERT: D 1913 ILE cc_start: 0.6298 (tt) cc_final: 0.6076 (mt) REVERT: D 1973 ASN cc_start: 0.8713 (t0) cc_final: 0.8168 (t0) REVERT: D 2170 ASN cc_start: 0.8082 (m-40) cc_final: 0.7815 (m110) REVERT: E 90 ILE cc_start: 0.8594 (mt) cc_final: 0.8258 (tt) REVERT: E 101 SER cc_start: 0.8741 (m) cc_final: 0.8485 (p) REVERT: E 129 LEU cc_start: 0.8293 (mt) cc_final: 0.8006 (mt) REVERT: E 188 MET cc_start: 0.8958 (tmm) cc_final: 0.8734 (tmm) REVERT: E 510 ASN cc_start: 0.6732 (p0) cc_final: 0.6193 (p0) REVERT: E 810 TRP cc_start: 0.8708 (t60) cc_final: 0.8432 (t60) REVERT: E 954 VAL cc_start: 0.9146 (t) cc_final: 0.8839 (t) REVERT: E 1021 TRP cc_start: 0.6634 (t-100) cc_final: 0.6062 (t-100) REVERT: E 1051 ILE cc_start: 0.7824 (mt) cc_final: 0.7432 (tp) REVERT: E 1079 MET cc_start: 0.7958 (mmt) cc_final: 0.7553 (mmt) REVERT: E 1141 TRP cc_start: 0.7978 (m100) cc_final: 0.7517 (m100) REVERT: E 1166 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7680 (tpp80) REVERT: E 1203 ILE cc_start: 0.8193 (mt) cc_final: 0.7959 (tt) REVERT: E 1205 TYR cc_start: 0.8184 (m-80) cc_final: 0.7706 (m-80) REVERT: E 1272 ASP cc_start: 0.8312 (p0) cc_final: 0.7275 (t0) REVERT: E 1609 PHE cc_start: 0.7397 (t80) cc_final: 0.7165 (t80) REVERT: E 1637 LEU cc_start: 0.7976 (mt) cc_final: 0.7466 (mp) REVERT: E 1770 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7373 (mt-10) REVERT: E 1859 LEU cc_start: 0.7106 (tp) cc_final: 0.6821 (tp) REVERT: E 1860 LEU cc_start: 0.8588 (mt) cc_final: 0.8247 (mt) REVERT: E 1907 LEU cc_start: 0.8162 (tp) cc_final: 0.7887 (tp) REVERT: E 1916 GLN cc_start: 0.7169 (tt0) cc_final: 0.6603 (tm-30) REVERT: E 1956 MET cc_start: 0.8190 (mmm) cc_final: 0.7637 (mmt) REVERT: E 1958 ASN cc_start: 0.8853 (m-40) cc_final: 0.8235 (m-40) REVERT: E 1992 PRO cc_start: 0.8657 (Cg_exo) cc_final: 0.8007 (Cg_endo) REVERT: E 2094 SER cc_start: 0.8984 (t) cc_final: 0.8361 (p) REVERT: E 2170 ASN cc_start: 0.7381 (m-40) cc_final: 0.6709 (m-40) REVERT: E 2459 GLN cc_start: 0.6536 (mt0) cc_final: 0.6011 (mt0) REVERT: E 2462 LEU cc_start: 0.7743 (tp) cc_final: 0.6959 (pt) REVERT: F 36 MET cc_start: 0.8729 (mmp) cc_final: 0.8504 (mmt) REVERT: F 159 SER cc_start: 0.8652 (t) cc_final: 0.8286 (p) REVERT: F 430 SER cc_start: 0.7175 (t) cc_final: 0.6926 (p) REVERT: F 454 VAL cc_start: 0.8562 (t) cc_final: 0.8146 (m) REVERT: F 675 LEU cc_start: 0.8487 (mt) cc_final: 0.7987 (mp) REVERT: F 706 MET cc_start: 0.8681 (mtp) cc_final: 0.8391 (mtp) REVERT: F 854 ASP cc_start: 0.7400 (p0) cc_final: 0.7039 (p0) REVERT: F 967 LEU cc_start: 0.8065 (mp) cc_final: 0.7569 (mp) REVERT: F 1555 PHE cc_start: 0.8377 (m-80) cc_final: 0.8174 (m-80) REVERT: F 1769 ASP cc_start: 0.8846 (t0) cc_final: 0.8632 (t70) REVERT: F 1883 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8456 (tpt170) REVERT: F 2001 LEU cc_start: 0.3631 (mp) cc_final: 0.3312 (mp) REVERT: F 2111 LEU cc_start: 0.8955 (mt) cc_final: 0.8685 (mt) outliers start: 0 outliers final: 0 residues processed: 3420 average time/residue: 1.0980 time to fit residues: 6409.7187 Evaluate side-chains 1627 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1627 time to evaluate : 9.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 1212 optimal weight: 2.9990 chunk 1088 optimal weight: 0.9980 chunk 603 optimal weight: 0.9990 chunk 371 optimal weight: 3.9990 chunk 734 optimal weight: 0.9980 chunk 581 optimal weight: 3.9990 chunk 1125 optimal weight: 2.9990 chunk 435 optimal weight: 0.7980 chunk 684 optimal weight: 5.9990 chunk 837 optimal weight: 0.7980 chunk 1304 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 767 HIS A 892 GLN A 953 GLN A1261 ASN A1334 ASN ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 ASN A1793 ASN ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1885 GLN A1972 HIS ** A2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 222 ASN B 599 GLN B 953 GLN B1090 ASN B1303 ASN B1671 ASN B1785 HIS B1866 HIS B2173 ASN B2427 GLN B2452 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 240 ASN C 581 ASN C 767 HIS C 854 GLN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1743 HIS C1793 ASN C2004 GLN C2053 ASN ** C2173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2209 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN D 337 ASN D 525 ASN D 527 GLN D 660 ASN D 929 GLN D1053 GLN D1174 GLN D1304 ASN ** D1448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1671 ASN D1752 ASN D1808 HIS ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2430 GLN ** D2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 701 GLN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1043 ASN E1152 ASN ** E1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1531 GLN E1671 ASN E1810 GLN ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2113 GLN E2129 GLN E2430 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN F 461 GLN F 663 GLN ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 882 ASN F 947 GLN F 988 GLN F1125 HIS F1187 GLN F1252 GLN F1303 GLN F1564 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 116817 Z= 0.235 Angle : 0.654 12.420 158758 Z= 0.349 Chirality : 0.043 0.255 17523 Planarity : 0.005 0.068 20695 Dihedral : 4.760 35.948 15727 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Rotamer: Outliers : 2.19 % Allowed : 8.43 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.45 (0.07), residues: 14354 helix: 1.78 (0.07), residues: 5749 sheet: 0.80 (0.10), residues: 2668 loop : 0.36 (0.08), residues: 5937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 810 HIS 0.011 0.001 HIS B1888 PHE 0.025 0.002 PHE E 192 TYR 0.037 0.002 TYR B1024 ARG 0.013 0.001 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2227 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1957 time to evaluate : 9.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 HIS cc_start: 0.7584 (t70) cc_final: 0.7035 (m-70) REVERT: A 94 ASN cc_start: 0.7700 (m110) cc_final: 0.7292 (t0) REVERT: A 148 MET cc_start: 0.8249 (ttp) cc_final: 0.7925 (ptm) REVERT: A 187 GLU cc_start: 0.7896 (tp30) cc_final: 0.7576 (tp30) REVERT: A 220 GLN cc_start: 0.7447 (tp-100) cc_final: 0.7167 (mm-40) REVERT: A 604 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 658 SER cc_start: 0.8060 (m) cc_final: 0.7679 (p) REVERT: A 675 TYR cc_start: 0.8974 (t80) cc_final: 0.8741 (t80) REVERT: A 908 GLU cc_start: 0.8351 (tp30) cc_final: 0.8145 (pt0) REVERT: A 1049 MET cc_start: 0.7711 (ppp) cc_final: 0.7191 (ptp) REVERT: A 1205 TYR cc_start: 0.7506 (m-80) cc_final: 0.6997 (m-80) REVERT: A 1210 ASN cc_start: 0.8576 (t0) cc_final: 0.8143 (t0) REVERT: A 1295 ASP cc_start: 0.6163 (m-30) cc_final: 0.5832 (t0) REVERT: A 1403 MET cc_start: 0.6985 (mtm) cc_final: 0.6597 (ptt) REVERT: A 1490 ASN cc_start: 0.8296 (t0) cc_final: 0.7451 (p0) REVERT: A 1625 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 1676 ILE cc_start: 0.9164 (pt) cc_final: 0.8810 (tp) REVERT: A 1764 ASN cc_start: 0.8368 (m-40) cc_final: 0.8157 (m110) REVERT: A 1783 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 1791 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6564 (mm-30) REVERT: A 1814 TYR cc_start: 0.7546 (p90) cc_final: 0.7113 (p90) REVERT: A 1854 MET cc_start: 0.7316 (mtt) cc_final: 0.7015 (mtt) REVERT: A 1871 LEU cc_start: 0.7903 (mt) cc_final: 0.7495 (tp) REVERT: A 1878 GLU cc_start: 0.7241 (tp30) cc_final: 0.6934 (tp30) REVERT: A 1895 TYR cc_start: 0.8450 (t80) cc_final: 0.8215 (t80) REVERT: A 2048 ASP cc_start: 0.6553 (m-30) cc_final: 0.6143 (m-30) REVERT: A 2050 GLU cc_start: 0.7561 (tp30) cc_final: 0.7281 (tp30) REVERT: A 2055 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8692 (tp) REVERT: A 2317 MET cc_start: 0.9265 (ttp) cc_final: 0.8765 (ttm) REVERT: A 2340 VAL cc_start: 0.9247 (t) cc_final: 0.8672 (t) REVERT: B 75 GLN cc_start: 0.6570 (mt0) cc_final: 0.5959 (pp30) REVERT: B 83 LEU cc_start: 0.7474 (mt) cc_final: 0.7147 (pp) REVERT: B 93 ASN cc_start: 0.7707 (m-40) cc_final: 0.7484 (m-40) REVERT: B 134 SER cc_start: 0.7362 (t) cc_final: 0.7056 (m) REVERT: B 170 LEU cc_start: 0.8854 (tp) cc_final: 0.8532 (mt) REVERT: B 583 LYS cc_start: 0.9038 (tttt) cc_final: 0.8566 (tppt) REVERT: B 763 GLU cc_start: 0.7840 (tp30) cc_final: 0.7621 (tm-30) REVERT: B 804 LEU cc_start: 0.8575 (mt) cc_final: 0.8190 (tp) REVERT: B 914 GLN cc_start: 0.8620 (mt0) cc_final: 0.8374 (mp10) REVERT: B 1028 TYR cc_start: 0.7017 (t80) cc_final: 0.6144 (t80) REVERT: B 1611 ARG cc_start: 0.7299 (tpp-160) cc_final: 0.7071 (mmt180) REVERT: B 1627 MET cc_start: 0.6695 (mmm) cc_final: 0.6369 (mmm) REVERT: B 1854 MET cc_start: 0.8089 (mtm) cc_final: 0.7771 (mmp) REVERT: B 1878 GLU cc_start: 0.8398 (tt0) cc_final: 0.8020 (mm-30) REVERT: B 1883 TYR cc_start: 0.6791 (m-80) cc_final: 0.6550 (m-80) REVERT: B 1924 VAL cc_start: 0.8010 (p) cc_final: 0.7699 (m) REVERT: B 1959 TYR cc_start: 0.7456 (m-80) cc_final: 0.6990 (m-80) REVERT: B 1993 LYS cc_start: 0.6436 (ttpp) cc_final: 0.6001 (tptp) REVERT: B 2022 MET cc_start: 0.8669 (tpp) cc_final: 0.8410 (tmm) REVERT: B 2103 TYR cc_start: 0.8340 (t80) cc_final: 0.8128 (t80) REVERT: B 2164 VAL cc_start: 0.7005 (t) cc_final: 0.6771 (m) REVERT: B 2168 SER cc_start: 0.7594 (t) cc_final: 0.7364 (p) REVERT: B 2193 GLU cc_start: 0.7032 (tt0) cc_final: 0.6563 (mt-10) REVERT: B 2285 ASN cc_start: 0.8343 (t0) cc_final: 0.7900 (t0) REVERT: C 95 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8054 (mm-40) REVERT: C 218 LEU cc_start: 0.8382 (mt) cc_final: 0.7965 (tp) REVERT: C 219 GLU cc_start: 0.6473 (tp30) cc_final: 0.6256 (tp30) REVERT: C 220 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7666 (tp-100) REVERT: C 402 ILE cc_start: 0.8084 (mm) cc_final: 0.7868 (pt) REVERT: C 622 ILE cc_start: 0.7777 (tt) cc_final: 0.7513 (mt) REVERT: C 632 ARG cc_start: 0.8444 (ttm110) cc_final: 0.7999 (ptp-110) REVERT: C 683 LYS cc_start: 0.7869 (pttt) cc_final: 0.7612 (pptt) REVERT: C 811 VAL cc_start: 0.7879 (t) cc_final: 0.7601 (p) REVERT: C 839 MET cc_start: 0.8795 (mtp) cc_final: 0.8434 (mtp) REVERT: C 939 ASP cc_start: 0.7657 (m-30) cc_final: 0.7398 (m-30) REVERT: C 1023 LYS cc_start: 0.6789 (tttt) cc_final: 0.6474 (ptpt) REVERT: C 1056 MET cc_start: 0.7770 (mtm) cc_final: 0.7529 (mtm) REVERT: C 1170 LEU cc_start: 0.8598 (tp) cc_final: 0.8369 (tt) REVERT: C 1178 THR cc_start: 0.8745 (m) cc_final: 0.8288 (p) REVERT: C 1210 ASN cc_start: 0.8234 (t0) cc_final: 0.7972 (m-40) REVERT: C 1272 ASP cc_start: 0.6817 (p0) cc_final: 0.5665 (t70) REVERT: C 1388 TYR cc_start: 0.6941 (m-80) cc_final: 0.6660 (m-80) REVERT: C 1429 THR cc_start: 0.7389 (p) cc_final: 0.7061 (p) REVERT: C 1482 ASP cc_start: 0.6920 (m-30) cc_final: 0.6326 (m-30) REVERT: C 1645 PHE cc_start: 0.8408 (m-80) cc_final: 0.7952 (m-10) REVERT: C 1663 LEU cc_start: 0.8284 (mt) cc_final: 0.7973 (mt) REVERT: C 1681 LEU cc_start: 0.8526 (mt) cc_final: 0.7857 (tp) REVERT: C 1965 GLN cc_start: 0.7563 (tp40) cc_final: 0.7292 (tt0) REVERT: C 2102 LEU cc_start: 0.8389 (mt) cc_final: 0.8157 (mt) REVERT: C 2103 TYR cc_start: 0.7113 (t80) cc_final: 0.6531 (t80) REVERT: C 2163 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.6176 (t80) REVERT: C 2185 TYR cc_start: 0.8122 (m-10) cc_final: 0.7879 (m-10) REVERT: C 2438 LYS cc_start: 0.7486 (pttt) cc_final: 0.7189 (ptmm) REVERT: C 2482 LEU cc_start: 0.9253 (tp) cc_final: 0.9021 (tt) REVERT: D 49 TYR cc_start: 0.4611 (t80) cc_final: 0.4211 (t80) REVERT: D 133 ASP cc_start: 0.7308 (p0) cc_final: 0.6983 (p0) REVERT: D 404 GLN cc_start: 0.8754 (mm-40) cc_final: 0.7921 (pm20) REVERT: D 619 LEU cc_start: 0.8633 (mt) cc_final: 0.8366 (mt) REVERT: D 785 MET cc_start: 0.8494 (mmm) cc_final: 0.8279 (mtp) REVERT: D 869 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7551 (t) REVERT: D 999 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7367 (mtp85) REVERT: D 1028 TYR cc_start: 0.7867 (t80) cc_final: 0.7582 (t80) REVERT: D 1035 SER cc_start: 0.9351 (m) cc_final: 0.9121 (p) REVERT: D 1039 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6141 (t80) REVERT: D 1324 TRP cc_start: 0.7464 (m100) cc_final: 0.6511 (m-90) REVERT: D 1336 ASP cc_start: 0.7110 (p0) cc_final: 0.6759 (m-30) REVERT: D 1364 TYR cc_start: 0.7257 (t80) cc_final: 0.6730 (t80) REVERT: D 1399 SER cc_start: 0.8581 (p) cc_final: 0.8086 (t) REVERT: D 1419 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5774 (mp10) REVERT: D 1422 LEU cc_start: 0.8495 (tp) cc_final: 0.8065 (tt) REVERT: D 1455 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: D 1657 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6740 (t70) REVERT: D 1677 TYR cc_start: 0.8241 (t80) cc_final: 0.7719 (t80) REVERT: D 1680 GLN cc_start: 0.5491 (mm-40) cc_final: 0.5150 (mp10) REVERT: D 1956 MET cc_start: 0.8347 (mmp) cc_final: 0.8113 (mmp) REVERT: D 1973 ASN cc_start: 0.8516 (t0) cc_final: 0.7774 (t0) REVERT: D 2022 MET cc_start: 0.8761 (tpp) cc_final: 0.8505 (tpp) REVERT: D 2170 ASN cc_start: 0.8079 (m-40) cc_final: 0.7654 (m110) REVERT: D 2459 GLN cc_start: 0.7114 (pt0) cc_final: 0.6893 (mm110) REVERT: E 73 GLN cc_start: 0.7057 (mt0) cc_final: 0.6658 (mt0) REVERT: E 101 SER cc_start: 0.8439 (m) cc_final: 0.8211 (t) REVERT: E 206 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8228 (t0) REVERT: E 510 ASN cc_start: 0.6363 (p0) cc_final: 0.6039 (t0) REVERT: E 592 LYS cc_start: 0.9006 (tptp) cc_final: 0.8768 (tttp) REVERT: E 764 MET cc_start: 0.7907 (ttm) cc_final: 0.7665 (ttp) REVERT: E 802 ILE cc_start: 0.9302 (tt) cc_final: 0.9100 (pt) REVERT: E 928 SER cc_start: 0.7494 (p) cc_final: 0.7269 (t) REVERT: E 1012 VAL cc_start: 0.8622 (t) cc_final: 0.8401 (t) REVERT: E 1021 TRP cc_start: 0.6446 (t-100) cc_final: 0.5972 (t-100) REVERT: E 1141 TRP cc_start: 0.7895 (m100) cc_final: 0.7343 (m100) REVERT: E 1272 ASP cc_start: 0.8207 (p0) cc_final: 0.7245 (t0) REVERT: E 1402 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8676 (tp) REVERT: E 1833 ASP cc_start: 0.6342 (p0) cc_final: 0.6038 (t0) REVERT: E 1979 GLN cc_start: 0.6782 (mm-40) cc_final: 0.6579 (mt0) REVERT: E 1983 LEU cc_start: 0.7978 (tp) cc_final: 0.7655 (pt) REVERT: E 2094 SER cc_start: 0.9014 (t) cc_final: 0.8808 (p) REVERT: E 2129 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7466 (pp30) REVERT: F 454 VAL cc_start: 0.8195 (t) cc_final: 0.7957 (m) REVERT: F 465 VAL cc_start: 0.9076 (t) cc_final: 0.8799 (m) REVERT: F 706 MET cc_start: 0.8471 (mtp) cc_final: 0.8161 (mtp) REVERT: F 854 ASP cc_start: 0.7263 (p0) cc_final: 0.6896 (p0) REVERT: F 1555 PHE cc_start: 0.8315 (m-80) cc_final: 0.8067 (m-80) REVERT: F 1674 GLN cc_start: 0.8359 (tt0) cc_final: 0.7985 (tt0) REVERT: F 1769 ASP cc_start: 0.8767 (t0) cc_final: 0.8559 (t0) REVERT: F 1883 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8420 (tpt170) outliers start: 270 outliers final: 151 residues processed: 2148 average time/residue: 1.0175 time to fit residues: 3822.1226 Evaluate side-chains 1520 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1357 time to evaluate : 9.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1783 LEU Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1846 MET Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2064 ILE Chi-restraints excluded: chain A residue 2094 SER Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1331 MET Chi-restraints excluded: chain B residue 1493 ILE Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1851 SER Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2283 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 553 ARG Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1514 ASP Chi-restraints excluded: chain C residue 1607 THR Chi-restraints excluded: chain C residue 1618 THR Chi-restraints excluded: chain C residue 1652 LEU Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1766 LEU Chi-restraints excluded: chain C residue 1856 THR Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1981 LEU Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2070 ILE Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2131 SER Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain C residue 2428 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 689 LEU Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 966 ASP Chi-restraints excluded: chain D residue 1010 SER Chi-restraints excluded: chain D residue 1039 TYR Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1063 SER Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1143 GLU Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1362 ASN Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1465 ASP Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1981 LEU Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2052 LEU Chi-restraints excluded: chain D residue 2064 ILE Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2309 THR Chi-restraints excluded: chain D residue 2494 LYS Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1176 GLU Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1622 ASP Chi-restraints excluded: chain E residue 1684 THR Chi-restraints excluded: chain E residue 1742 THR Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1888 HIS Chi-restraints excluded: chain E residue 1962 THR Chi-restraints excluded: chain E residue 2129 GLN Chi-restraints excluded: chain E residue 2246 SER Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 882 ASN Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1263 LEU Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1588 LEU Chi-restraints excluded: chain F residue 1871 THR Chi-restraints excluded: chain F residue 2143 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 724 optimal weight: 7.9990 chunk 404 optimal weight: 5.9990 chunk 1085 optimal weight: 0.8980 chunk 887 optimal weight: 0.7980 chunk 359 optimal weight: 7.9990 chunk 1306 optimal weight: 6.9990 chunk 1411 optimal weight: 20.0000 chunk 1163 optimal weight: 0.9980 chunk 1295 optimal weight: 0.9980 chunk 445 optimal weight: 0.9980 chunk 1048 optimal weight: 0.0970 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 929 GLN A1448 GLN ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 HIS ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1965 GLN ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN B 295 GLN B 626 GLN B 650 GLN ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN B1252 GLN B1533 ASN B1961 GLN ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2173 ASN B2181 GLN B2197 ASN B2237 GLN B2252 ASN C 86 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 854 GLN C1090 ASN C1304 ASN C1418 ASN C1531 GLN C1533 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2059 GLN C2252 ASN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 HIS D 295 GLN D 854 GLN D1448 GLN ** D1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1589 ASN D1591 ASN D1612 GLN D1764 ASN D1961 GLN D1973 ASN D2113 GLN ** D2452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2497 GLN E 75 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 676 HIS ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 HIS E1362 ASN E1651 ASN E1785 HIS E1808 HIS ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2032 GLN E2129 GLN E2252 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1420 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 116817 Z= 0.188 Angle : 0.569 11.831 158758 Z= 0.298 Chirality : 0.041 0.251 17523 Planarity : 0.004 0.060 20695 Dihedral : 4.459 35.210 15727 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.01 % Rotamer: Outliers : 2.40 % Allowed : 10.62 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.45 (0.07), residues: 14354 helix: 1.95 (0.07), residues: 5761 sheet: 0.76 (0.10), residues: 2658 loop : 0.17 (0.08), residues: 5935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 731 HIS 0.010 0.001 HIS B1888 PHE 0.028 0.002 PHE F 138 TYR 0.038 0.002 TYR B1024 ARG 0.013 0.000 ARG F1789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1849 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1553 time to evaluate : 9.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 HIS cc_start: 0.7635 (t70) cc_final: 0.7134 (m90) REVERT: A 68 LYS cc_start: 0.6458 (pttt) cc_final: 0.5705 (pttt) REVERT: A 94 ASN cc_start: 0.7850 (m110) cc_final: 0.7563 (t0) REVERT: A 148 MET cc_start: 0.8277 (ttp) cc_final: 0.7788 (ptm) REVERT: A 220 GLN cc_start: 0.7301 (tp-100) cc_final: 0.7041 (mm-40) REVERT: A 253 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 658 SER cc_start: 0.8113 (m) cc_final: 0.7733 (p) REVERT: A 675 TYR cc_start: 0.8995 (t80) cc_final: 0.8771 (t80) REVERT: A 804 LEU cc_start: 0.9060 (mt) cc_final: 0.8797 (mt) REVERT: A 1049 MET cc_start: 0.7812 (ppp) cc_final: 0.7233 (ptp) REVERT: A 1205 TYR cc_start: 0.7486 (m-80) cc_final: 0.7031 (m-80) REVERT: A 1295 ASP cc_start: 0.6271 (m-30) cc_final: 0.5897 (t0) REVERT: A 1300 ARG cc_start: 0.5813 (mtm110) cc_final: 0.4816 (mtp85) REVERT: A 1490 ASN cc_start: 0.8311 (t0) cc_final: 0.7666 (p0) REVERT: A 1625 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 1676 ILE cc_start: 0.9092 (pt) cc_final: 0.8656 (tp) REVERT: A 1764 ASN cc_start: 0.8412 (m-40) cc_final: 0.8159 (m110) REVERT: A 1777 MET cc_start: 0.8324 (mmm) cc_final: 0.8054 (mmm) REVERT: A 1791 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6454 (mm-30) REVERT: A 1794 ARG cc_start: 0.6666 (ttm170) cc_final: 0.6438 (ttm170) REVERT: A 1871 LEU cc_start: 0.7919 (mt) cc_final: 0.7545 (tp) REVERT: A 1956 MET cc_start: 0.8246 (mmm) cc_final: 0.8025 (mmm) REVERT: A 2048 ASP cc_start: 0.6890 (m-30) cc_final: 0.6669 (m-30) REVERT: A 2055 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8675 (tp) REVERT: A 2163 TYR cc_start: 0.6275 (m-80) cc_final: 0.5984 (m-80) REVERT: A 2317 MET cc_start: 0.9210 (ttp) cc_final: 0.8895 (ttm) REVERT: A 2340 VAL cc_start: 0.9025 (t) cc_final: 0.8811 (t) REVERT: A 2454 MET cc_start: 0.7276 (tpt) cc_final: 0.6806 (tpt) REVERT: B 134 SER cc_start: 0.7420 (t) cc_final: 0.7123 (m) REVERT: B 446 LEU cc_start: 0.9219 (tp) cc_final: 0.9019 (tp) REVERT: B 583 LYS cc_start: 0.9030 (tttt) cc_final: 0.8591 (tppt) REVERT: B 763 GLU cc_start: 0.7824 (tp30) cc_final: 0.7228 (tm-30) REVERT: B 767 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6425 (m170) REVERT: B 785 MET cc_start: 0.6859 (mmm) cc_final: 0.6652 (mmt) REVERT: B 804 LEU cc_start: 0.8516 (mt) cc_final: 0.8222 (tp) REVERT: B 914 GLN cc_start: 0.8623 (mt0) cc_final: 0.8264 (mt0) REVERT: B 1028 TYR cc_start: 0.6979 (t80) cc_final: 0.6489 (t80) REVERT: B 1068 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7437 (mm-40) REVERT: B 1146 LYS cc_start: 0.8127 (tttt) cc_final: 0.7811 (mttt) REVERT: B 1854 MET cc_start: 0.8176 (mtm) cc_final: 0.7810 (mmp) REVERT: B 1878 GLU cc_start: 0.8288 (tt0) cc_final: 0.8057 (mm-30) REVERT: B 1924 VAL cc_start: 0.7971 (p) cc_final: 0.7620 (m) REVERT: B 1957 MET cc_start: 0.8049 (tpp) cc_final: 0.7830 (tpp) REVERT: B 1959 TYR cc_start: 0.7528 (m-80) cc_final: 0.7001 (m-80) REVERT: B 2111 GLU cc_start: 0.5386 (mt-10) cc_final: 0.5014 (mt-10) REVERT: B 2193 GLU cc_start: 0.7237 (tt0) cc_final: 0.6768 (mt-10) REVERT: B 2285 ASN cc_start: 0.8437 (t0) cc_final: 0.8047 (t0) REVERT: B 2462 LEU cc_start: 0.6221 (tp) cc_final: 0.5812 (pp) REVERT: C 95 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7937 (mm-40) REVERT: C 218 LEU cc_start: 0.8316 (mt) cc_final: 0.7935 (tp) REVERT: C 219 GLU cc_start: 0.6448 (tp30) cc_final: 0.6230 (tp30) REVERT: C 220 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7772 (tp-100) REVERT: C 368 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7329 (tp) REVERT: C 402 ILE cc_start: 0.8134 (mm) cc_final: 0.7930 (pt) REVERT: C 622 ILE cc_start: 0.7749 (tt) cc_final: 0.7514 (mt) REVERT: C 632 ARG cc_start: 0.8423 (ttm110) cc_final: 0.7927 (ptp-110) REVERT: C 683 LYS cc_start: 0.8179 (pttt) cc_final: 0.7109 (tptt) REVERT: C 939 ASP cc_start: 0.7557 (m-30) cc_final: 0.7195 (m-30) REVERT: C 1023 LYS cc_start: 0.6788 (tttt) cc_final: 0.6428 (ptpt) REVERT: C 1040 TYR cc_start: 0.7924 (m-80) cc_final: 0.7550 (m-80) REVERT: C 1178 THR cc_start: 0.8621 (m) cc_final: 0.8246 (p) REVERT: C 1205 TYR cc_start: 0.7926 (m-80) cc_final: 0.7702 (m-80) REVERT: C 1272 ASP cc_start: 0.6925 (p0) cc_final: 0.5799 (t70) REVERT: C 1294 PHE cc_start: 0.8317 (m-10) cc_final: 0.7997 (m-80) REVERT: C 1388 TYR cc_start: 0.7033 (m-80) cc_final: 0.6764 (m-80) REVERT: C 1429 THR cc_start: 0.7439 (p) cc_final: 0.7096 (p) REVERT: C 1482 ASP cc_start: 0.6909 (m-30) cc_final: 0.6321 (m-30) REVERT: C 1645 PHE cc_start: 0.8479 (m-80) cc_final: 0.8014 (m-10) REVERT: C 1663 LEU cc_start: 0.8194 (mt) cc_final: 0.7872 (mt) REVERT: C 1681 LEU cc_start: 0.8565 (mt) cc_final: 0.8327 (mt) REVERT: C 2103 TYR cc_start: 0.7089 (t80) cc_final: 0.6383 (t80) REVERT: C 2163 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6145 (t80) REVERT: C 2185 TYR cc_start: 0.8218 (m-10) cc_final: 0.7916 (m-10) REVERT: C 2438 LYS cc_start: 0.7537 (pttt) cc_final: 0.7250 (ptmt) REVERT: C 2482 LEU cc_start: 0.9277 (tp) cc_final: 0.9001 (tt) REVERT: D 49 TYR cc_start: 0.4673 (t80) cc_final: 0.4278 (t80) REVERT: D 168 LEU cc_start: 0.8842 (tp) cc_final: 0.8609 (tt) REVERT: D 253 GLU cc_start: 0.8422 (tp30) cc_final: 0.7769 (tm-30) REVERT: D 404 GLN cc_start: 0.8744 (mm-40) cc_final: 0.7937 (pm20) REVERT: D 619 LEU cc_start: 0.8660 (mt) cc_final: 0.8362 (mt) REVERT: D 656 SER cc_start: 0.8850 (t) cc_final: 0.8591 (p) REVERT: D 785 MET cc_start: 0.8374 (mmm) cc_final: 0.7714 (ttm) REVERT: D 954 VAL cc_start: 0.8681 (t) cc_final: 0.8360 (t) REVERT: D 1028 TYR cc_start: 0.7887 (t80) cc_final: 0.7363 (t80) REVERT: D 1035 SER cc_start: 0.9337 (m) cc_final: 0.9105 (p) REVERT: D 1039 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6266 (t80) REVERT: D 1146 LYS cc_start: 0.6040 (ptpp) cc_final: 0.5588 (ptmt) REVERT: D 1336 ASP cc_start: 0.7111 (p0) cc_final: 0.6650 (m-30) REVERT: D 1422 LEU cc_start: 0.8323 (tp) cc_final: 0.8076 (tt) REVERT: D 1455 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6408 (m-30) REVERT: D 1657 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6796 (t70) REVERT: D 1677 TYR cc_start: 0.8265 (t80) cc_final: 0.7730 (t80) REVERT: D 1680 GLN cc_start: 0.5213 (mm-40) cc_final: 0.4796 (mp10) REVERT: D 1706 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: D 1709 MET cc_start: 0.7348 (tmm) cc_final: 0.7002 (tmm) REVERT: D 1869 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7495 (mtt90) REVERT: D 1956 MET cc_start: 0.8326 (mmp) cc_final: 0.7853 (mmp) REVERT: D 1973 ASN cc_start: 0.8318 (t0) cc_final: 0.7852 (t0) REVERT: D 2159 GLU cc_start: 0.7892 (tp30) cc_final: 0.7515 (mm-30) REVERT: D 2175 GLU cc_start: 0.7015 (tp30) cc_final: 0.6689 (mm-30) REVERT: D 2183 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6974 (mm-30) REVERT: D 2311 MET cc_start: 0.8062 (tpp) cc_final: 0.7457 (tpp) REVERT: D 2317 MET cc_start: 0.8789 (ttm) cc_final: 0.8498 (mtp) REVERT: E 282 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8982 (mp) REVERT: E 314 ILE cc_start: 0.8575 (mp) cc_final: 0.8220 (mm) REVERT: E 510 ASN cc_start: 0.6321 (p0) cc_final: 0.6067 (t0) REVERT: E 592 LYS cc_start: 0.9062 (tptp) cc_final: 0.8753 (tttp) REVERT: E 705 GLU cc_start: 0.8864 (pm20) cc_final: 0.7960 (mp0) REVERT: E 829 SER cc_start: 0.8924 (p) cc_final: 0.8347 (t) REVERT: E 922 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7971 (tp) REVERT: E 928 SER cc_start: 0.7398 (p) cc_final: 0.7197 (t) REVERT: E 1021 TRP cc_start: 0.6545 (t-100) cc_final: 0.6176 (t-100) REVERT: E 1141 TRP cc_start: 0.7887 (m100) cc_final: 0.7322 (m100) REVERT: E 1203 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7916 (tt) REVERT: E 1272 ASP cc_start: 0.8085 (p0) cc_final: 0.7277 (t0) REVERT: E 1405 TYR cc_start: 0.8796 (m-80) cc_final: 0.8457 (m-80) REVERT: E 1833 ASP cc_start: 0.6467 (p0) cc_final: 0.6105 (t0) REVERT: E 1952 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8520 (pt) REVERT: E 2029 MET cc_start: 0.8428 (tpp) cc_final: 0.8139 (tpp) REVERT: E 2140 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7585 (mm) REVERT: E 2477 ILE cc_start: 0.8100 (pt) cc_final: 0.7785 (pt) REVERT: F 400 ASP cc_start: 0.6994 (p0) cc_final: 0.6558 (p0) REVERT: F 454 VAL cc_start: 0.8289 (t) cc_final: 0.7969 (p) REVERT: F 465 VAL cc_start: 0.9034 (t) cc_final: 0.8787 (m) REVERT: F 706 MET cc_start: 0.8411 (mtp) cc_final: 0.8125 (mtp) REVERT: F 874 LEU cc_start: 0.9322 (tp) cc_final: 0.8988 (tt) REVERT: F 967 LEU cc_start: 0.8359 (mp) cc_final: 0.7710 (mt) REVERT: F 1555 PHE cc_start: 0.8347 (m-80) cc_final: 0.8040 (m-80) REVERT: F 1769 ASP cc_start: 0.8824 (t0) cc_final: 0.8614 (t0) REVERT: F 1883 ARG cc_start: 0.8839 (mtp-110) cc_final: 0.8369 (tpt170) outliers start: 296 outliers final: 174 residues processed: 1757 average time/residue: 0.9343 time to fit residues: 2873.5861 Evaluate side-chains 1434 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1246 time to evaluate : 8.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1846 MET Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2064 ILE Chi-restraints excluded: chain A residue 2098 SER Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 767 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1493 ILE Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain B residue 1683 ASP Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1697 VAL Chi-restraints excluded: chain B residue 1701 GLN Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1838 ASP Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2283 GLU Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1080 SER Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1766 LEU Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1981 LEU Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2131 SER Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 1039 TYR Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1063 SER Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1493 ILE Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1612 GLN Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1686 ILE Chi-restraints excluded: chain D residue 1706 LYS Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2063 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2309 THR Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 922 LEU Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1019 ILE Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1622 ASP Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1783 LEU Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1888 HIS Chi-restraints excluded: chain E residue 1901 THR Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 1952 ILE Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2246 SER Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1040 ASP Chi-restraints excluded: chain F residue 1263 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1761 LYS Chi-restraints excluded: chain F residue 1871 THR Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2143 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 1290 optimal weight: 10.0000 chunk 982 optimal weight: 2.9990 chunk 677 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 623 optimal weight: 2.9990 chunk 877 optimal weight: 4.9990 chunk 1311 optimal weight: 1.9990 chunk 1388 optimal weight: 20.0000 chunk 684 optimal weight: 4.9990 chunk 1242 optimal weight: 9.9990 chunk 374 optimal weight: 0.0770 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1361 HIS ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1785 HIS ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1929 ASN ** A1958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 GLN ** A2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 95 GLN B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 GLN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1588 HIS B1877 ASN B1961 GLN B2129 GLN C 75 GLN C 240 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1520 GLN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1979 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 ASN D 929 GLN ** D1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1810 GLN ** D1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1885 GLN D1951 GLN D1961 GLN D1973 ASN ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2452 HIS ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1105 GLN E1174 GLN E1413 ASN E1547 ASN ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1810 GLN ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1965 GLN E2129 GLN ** E2209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1898 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 116817 Z= 0.258 Angle : 0.579 11.877 158758 Z= 0.302 Chirality : 0.041 0.242 17523 Planarity : 0.004 0.058 20695 Dihedral : 4.425 37.716 15727 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 2.83 % Allowed : 11.24 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.32 (0.07), residues: 14354 helix: 1.89 (0.07), residues: 5757 sheet: 0.63 (0.10), residues: 2680 loop : 0.07 (0.08), residues: 5917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D1324 HIS 0.019 0.001 HIS B1888 PHE 0.030 0.002 PHE C 730 TYR 0.036 0.002 TYR B1024 ARG 0.009 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1695 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 1346 time to evaluate : 9.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 HIS cc_start: 0.7627 (t70) cc_final: 0.7223 (m90) REVERT: A 94 ASN cc_start: 0.7733 (m110) cc_final: 0.7308 (t0) REVERT: A 148 MET cc_start: 0.8172 (ttp) cc_final: 0.7746 (ptm) REVERT: A 220 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7256 (mm-40) REVERT: A 546 TRP cc_start: 0.8041 (p-90) cc_final: 0.7783 (p-90) REVERT: A 594 LEU cc_start: 0.9136 (mt) cc_final: 0.8607 (tp) REVERT: A 658 SER cc_start: 0.8120 (m) cc_final: 0.7753 (p) REVERT: A 675 TYR cc_start: 0.9019 (t80) cc_final: 0.8799 (t80) REVERT: A 1177 ILE cc_start: 0.8888 (pt) cc_final: 0.8611 (pt) REVERT: A 1295 ASP cc_start: 0.6327 (m-30) cc_final: 0.5980 (t0) REVERT: A 1490 ASN cc_start: 0.8547 (t0) cc_final: 0.7665 (p0) REVERT: A 1625 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7879 (tt) REVERT: A 1676 ILE cc_start: 0.9055 (pt) cc_final: 0.8649 (tp) REVERT: A 1764 ASN cc_start: 0.8315 (m-40) cc_final: 0.8052 (m-40) REVERT: A 1777 MET cc_start: 0.8260 (mmm) cc_final: 0.7944 (mmm) REVERT: A 1798 TYR cc_start: 0.7121 (m-10) cc_final: 0.6769 (m-10) REVERT: A 1871 LEU cc_start: 0.8133 (mt) cc_final: 0.7854 (tp) REVERT: A 2055 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8772 (tp) REVERT: A 2077 GLU cc_start: 0.8502 (tt0) cc_final: 0.8063 (tm-30) REVERT: A 2454 MET cc_start: 0.7299 (tpt) cc_final: 0.6847 (tpt) REVERT: B 112 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6696 (ptm) REVERT: B 134 SER cc_start: 0.7505 (t) cc_final: 0.7167 (m) REVERT: B 583 LYS cc_start: 0.8985 (tttt) cc_final: 0.8456 (tppt) REVERT: B 763 GLU cc_start: 0.7764 (tp30) cc_final: 0.6313 (tm-30) REVERT: B 767 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.5994 (m170) REVERT: B 785 MET cc_start: 0.7133 (mmm) cc_final: 0.6867 (mmt) REVERT: B 804 LEU cc_start: 0.8468 (mt) cc_final: 0.8074 (tp) REVERT: B 914 GLN cc_start: 0.8710 (mt0) cc_final: 0.8358 (mt0) REVERT: B 1028 TYR cc_start: 0.6757 (t80) cc_final: 0.6285 (t80) REVERT: B 1146 LYS cc_start: 0.8273 (tttt) cc_final: 0.7874 (mttt) REVERT: B 1200 LEU cc_start: 0.7863 (mt) cc_final: 0.7560 (mt) REVERT: B 1455 ASP cc_start: 0.6882 (t0) cc_final: 0.6474 (t0) REVERT: B 1854 MET cc_start: 0.8253 (mtm) cc_final: 0.7951 (mmp) REVERT: B 1878 GLU cc_start: 0.8400 (tt0) cc_final: 0.8197 (mm-30) REVERT: B 1924 VAL cc_start: 0.7994 (p) cc_final: 0.7637 (m) REVERT: B 1959 TYR cc_start: 0.7460 (m-80) cc_final: 0.7165 (m-80) REVERT: B 2193 GLU cc_start: 0.7214 (tt0) cc_final: 0.6997 (mt-10) REVERT: B 2218 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 2285 ASN cc_start: 0.8528 (t0) cc_final: 0.8141 (t0) REVERT: C 95 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7956 (mm-40) REVERT: C 170 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8590 (mp) REVERT: C 218 LEU cc_start: 0.8405 (mt) cc_final: 0.7981 (tp) REVERT: C 619 LEU cc_start: 0.8334 (mt) cc_final: 0.8048 (mm) REVERT: C 622 ILE cc_start: 0.8087 (tt) cc_final: 0.7788 (mt) REVERT: C 632 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7928 (ptp-110) REVERT: C 683 LYS cc_start: 0.8223 (pttt) cc_final: 0.7139 (tptt) REVERT: C 886 GLN cc_start: 0.8502 (tp-100) cc_final: 0.8164 (tp40) REVERT: C 939 ASP cc_start: 0.7570 (m-30) cc_final: 0.7209 (m-30) REVERT: C 1023 LYS cc_start: 0.6814 (tttt) cc_final: 0.6485 (ptpt) REVERT: C 1040 TYR cc_start: 0.7963 (m-80) cc_final: 0.7647 (m-10) REVERT: C 1178 THR cc_start: 0.8681 (m) cc_final: 0.8293 (p) REVERT: C 1205 TYR cc_start: 0.8015 (m-80) cc_final: 0.7796 (m-80) REVERT: C 1245 LEU cc_start: 0.8002 (mt) cc_final: 0.7791 (mt) REVERT: C 1272 ASP cc_start: 0.6966 (p0) cc_final: 0.5842 (t70) REVERT: C 1278 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8342 (mmt) REVERT: C 1294 PHE cc_start: 0.8327 (m-10) cc_final: 0.8072 (m-80) REVERT: C 1324 TRP cc_start: 0.8454 (m100) cc_final: 0.8227 (m100) REVERT: C 1331 MET cc_start: 0.7744 (ptm) cc_final: 0.7482 (mtp) REVERT: C 1388 TYR cc_start: 0.7227 (m-80) cc_final: 0.6951 (m-80) REVERT: C 1429 THR cc_start: 0.7515 (p) cc_final: 0.7168 (p) REVERT: C 1473 MET cc_start: 0.7059 (mtp) cc_final: 0.6855 (mtp) REVERT: C 1482 ASP cc_start: 0.7089 (m-30) cc_final: 0.6506 (m-30) REVERT: C 1645 PHE cc_start: 0.8542 (m-80) cc_final: 0.8108 (m-10) REVERT: C 1977 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (p0) REVERT: C 2103 TYR cc_start: 0.7072 (t80) cc_final: 0.6364 (t80) REVERT: C 2163 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6241 (t80) REVERT: C 2438 LYS cc_start: 0.7542 (pttt) cc_final: 0.7295 (ptmt) REVERT: D 49 TYR cc_start: 0.4563 (t80) cc_final: 0.4146 (t80) REVERT: D 404 GLN cc_start: 0.8758 (mm-40) cc_final: 0.7899 (pm20) REVERT: D 701 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6227 (pp30) REVERT: D 785 MET cc_start: 0.8347 (mmm) cc_final: 0.7746 (ttm) REVERT: D 999 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7192 (mtp85) REVERT: D 1028 TYR cc_start: 0.8146 (t80) cc_final: 0.7596 (t80) REVERT: D 1035 SER cc_start: 0.9303 (m) cc_final: 0.9087 (p) REVERT: D 1146 LYS cc_start: 0.6182 (ptpp) cc_final: 0.5707 (ptmt) REVERT: D 1311 GLU cc_start: 0.7118 (tp30) cc_final: 0.6782 (tp30) REVERT: D 1336 ASP cc_start: 0.7100 (p0) cc_final: 0.6592 (m-30) REVERT: D 1419 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.6033 (mp10) REVERT: D 1422 LEU cc_start: 0.8397 (tp) cc_final: 0.8091 (tt) REVERT: D 1455 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6525 (m-30) REVERT: D 1657 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6836 (t70) REVERT: D 1677 TYR cc_start: 0.8308 (t80) cc_final: 0.7734 (t80) REVERT: D 1956 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7849 (mmp) REVERT: D 1973 ASN cc_start: 0.8527 (t0) cc_final: 0.8105 (t0) REVERT: D 2170 ASN cc_start: 0.7808 (m110) cc_final: 0.7555 (m110) REVERT: D 2183 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7063 (mm-30) REVERT: D 2311 MET cc_start: 0.8026 (tpp) cc_final: 0.7457 (tpp) REVERT: D 2317 MET cc_start: 0.8802 (ttm) cc_final: 0.8532 (mtp) REVERT: E 282 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8990 (mp) REVERT: E 314 ILE cc_start: 0.8513 (mp) cc_final: 0.8064 (mm) REVERT: E 510 ASN cc_start: 0.6334 (p0) cc_final: 0.6080 (t0) REVERT: E 829 SER cc_start: 0.8890 (p) cc_final: 0.8331 (t) REVERT: E 1081 TYR cc_start: 0.6640 (t80) cc_final: 0.6396 (t80) REVERT: E 1141 TRP cc_start: 0.7782 (m100) cc_final: 0.7279 (m100) REVERT: E 1229 ASN cc_start: 0.8689 (t0) cc_final: 0.8485 (t0) REVERT: E 1245 LEU cc_start: 0.8648 (tp) cc_final: 0.8339 (mt) REVERT: E 1272 ASP cc_start: 0.8189 (p0) cc_final: 0.7272 (t0) REVERT: E 1405 TYR cc_start: 0.8813 (m-80) cc_final: 0.8569 (m-80) REVERT: E 1671 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8544 (t0) REVERT: E 1833 ASP cc_start: 0.6683 (p0) cc_final: 0.6244 (t0) REVERT: E 2129 GLN cc_start: 0.7687 (tm130) cc_final: 0.7459 (tm-30) REVERT: E 2202 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7983 (tm-30) REVERT: F 400 ASP cc_start: 0.7231 (p0) cc_final: 0.6745 (p0) REVERT: F 706 MET cc_start: 0.8494 (mtp) cc_final: 0.8188 (mtp) REVERT: F 865 LEU cc_start: 0.8485 (mp) cc_final: 0.8284 (mp) REVERT: F 1260 MET cc_start: 0.7829 (mmm) cc_final: 0.7592 (mmm) REVERT: F 1363 MET cc_start: 0.6996 (tpp) cc_final: 0.6717 (tpp) REVERT: F 1555 PHE cc_start: 0.8338 (m-80) cc_final: 0.8034 (m-80) outliers start: 349 outliers final: 245 residues processed: 1594 average time/residue: 1.0653 time to fit residues: 3023.5133 Evaluate side-chains 1451 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1191 time to evaluate : 9.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1629 THR Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1846 MET Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2094 SER Chi-restraints excluded: chain A residue 2098 SER Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2408 LYS Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 767 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1298 ASN Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1493 ILE Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1697 VAL Chi-restraints excluded: chain B residue 1701 GLN Chi-restraints excluded: chain B residue 1785 HIS Chi-restraints excluded: chain B residue 1790 ASP Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2283 GLU Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1080 SER Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1254 ASP Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1607 THR Chi-restraints excluded: chain C residue 1618 THR Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1675 ILE Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1766 LEU Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2070 ILE Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2131 SER Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 689 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 966 ASP Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1361 HIS Chi-restraints excluded: chain D residue 1362 ASN Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1493 ILE Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1603 THR Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1860 LEU Chi-restraints excluded: chain D residue 1951 GLN Chi-restraints excluded: chain D residue 1956 MET Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2063 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2171 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2309 THR Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain D residue 2494 LYS Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 895 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1056 MET Chi-restraints excluded: chain E residue 1084 SER Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1435 GLU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1622 ASP Chi-restraints excluded: chain E residue 1671 ASN Chi-restraints excluded: chain E residue 1684 THR Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1783 LEU Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1856 THR Chi-restraints excluded: chain E residue 1887 LEU Chi-restraints excluded: chain E residue 1888 HIS Chi-restraints excluded: chain E residue 1901 THR Chi-restraints excluded: chain E residue 1962 THR Chi-restraints excluded: chain E residue 2045 GLU Chi-restraints excluded: chain E residue 2128 VAL Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2250 LEU Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1871 THR Chi-restraints excluded: chain F residue 2063 LEU Chi-restraints excluded: chain F residue 2143 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 1156 optimal weight: 1.9990 chunk 787 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 1033 optimal weight: 5.9990 chunk 572 optimal weight: 2.9990 chunk 1184 optimal weight: 1.9990 chunk 959 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 708 optimal weight: 1.9990 chunk 1245 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1958 ASN A1961 GLN A2021 HIS A2252 ASN ** A2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1929 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN C1090 ASN C1303 ASN C1304 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN D 709 HIS D 749 GLN D 994 GLN D1139 ASN ** D1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1951 GLN ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2452 HIS ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 337 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1631 ASN ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1368 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 116817 Z= 0.243 Angle : 0.565 11.875 158758 Z= 0.294 Chirality : 0.041 0.245 17523 Planarity : 0.004 0.058 20695 Dihedral : 4.366 37.338 15727 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 2.93 % Allowed : 11.83 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.26 (0.07), residues: 14354 helix: 1.86 (0.07), residues: 5767 sheet: 0.62 (0.10), residues: 2578 loop : 0.00 (0.08), residues: 6009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1660 HIS 0.007 0.001 HIS E1972 PHE 0.033 0.002 PHE D 937 TYR 0.037 0.002 TYR B1024 ARG 0.009 0.001 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1670 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1309 time to evaluate : 9.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.7705 (m110) cc_final: 0.7270 (t0) REVERT: A 148 MET cc_start: 0.8190 (ttp) cc_final: 0.7796 (ptm) REVERT: A 220 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7285 (mm-40) REVERT: A 341 MET cc_start: 0.6394 (ppp) cc_final: 0.6031 (ppp) REVERT: A 594 LEU cc_start: 0.9103 (mt) cc_final: 0.8639 (tp) REVERT: A 658 SER cc_start: 0.8102 (m) cc_final: 0.7741 (p) REVERT: A 785 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8255 (mpp) REVERT: A 952 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7684 (ttm-80) REVERT: A 1248 MET cc_start: 0.8030 (ttp) cc_final: 0.6710 (ttp) REVERT: A 1264 MET cc_start: 0.7633 (mtp) cc_final: 0.6801 (ttm) REVERT: A 1295 ASP cc_start: 0.6463 (m-30) cc_final: 0.6054 (t0) REVERT: A 1403 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6799 (ptm) REVERT: A 1490 ASN cc_start: 0.8536 (t0) cc_final: 0.7682 (p0) REVERT: A 1625 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 1676 ILE cc_start: 0.9078 (pt) cc_final: 0.8696 (tp) REVERT: A 1709 MET cc_start: 0.8392 (ppp) cc_final: 0.8189 (tmm) REVERT: A 1764 ASN cc_start: 0.8300 (m-40) cc_final: 0.8073 (m-40) REVERT: A 1791 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6823 (mm-30) REVERT: A 1794 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6366 (ttm170) REVERT: A 1871 LEU cc_start: 0.7955 (mt) cc_final: 0.7738 (tp) REVERT: A 2055 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8722 (tp) REVERT: A 2077 GLU cc_start: 0.8291 (tt0) cc_final: 0.8069 (tm-30) REVERT: A 2454 MET cc_start: 0.7414 (tpt) cc_final: 0.7043 (tpt) REVERT: B 112 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6955 (ptm) REVERT: B 134 SER cc_start: 0.7470 (t) cc_final: 0.7073 (m) REVERT: B 446 LEU cc_start: 0.9211 (tp) cc_final: 0.9001 (tp) REVERT: B 583 LYS cc_start: 0.8960 (tttt) cc_final: 0.8427 (tppt) REVERT: B 763 GLU cc_start: 0.7743 (tp30) cc_final: 0.6212 (tm-30) REVERT: B 767 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.5998 (m170) REVERT: B 804 LEU cc_start: 0.8343 (mt) cc_final: 0.8067 (tp) REVERT: B 914 GLN cc_start: 0.8664 (mt0) cc_final: 0.8304 (mt0) REVERT: B 1028 TYR cc_start: 0.6851 (t80) cc_final: 0.6414 (t80) REVERT: B 1146 LYS cc_start: 0.8280 (tttt) cc_final: 0.7867 (mttt) REVERT: B 1200 LEU cc_start: 0.7953 (mt) cc_final: 0.7522 (mt) REVERT: B 1455 ASP cc_start: 0.6986 (t0) cc_final: 0.6649 (t0) REVERT: B 1627 MET cc_start: 0.5962 (mmm) cc_final: 0.5577 (mmm) REVERT: B 1663 LEU cc_start: 0.8657 (mp) cc_final: 0.8433 (mt) REVERT: B 1854 MET cc_start: 0.8324 (mtm) cc_final: 0.8096 (mmp) REVERT: B 1870 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6800 (mm-40) REVERT: B 1924 VAL cc_start: 0.7997 (p) cc_final: 0.7634 (m) REVERT: B 1959 TYR cc_start: 0.7406 (m-80) cc_final: 0.7195 (m-80) REVERT: B 2111 GLU cc_start: 0.4697 (mt-10) cc_final: 0.4218 (pt0) REVERT: B 2129 GLN cc_start: 0.8357 (tp40) cc_final: 0.8046 (tp40) REVERT: B 2218 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 2248 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: B 2285 ASN cc_start: 0.8657 (t0) cc_final: 0.8318 (t0) REVERT: C 95 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7833 (mm-40) REVERT: C 170 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 218 LEU cc_start: 0.8453 (mt) cc_final: 0.7920 (tp) REVERT: C 368 LEU cc_start: 0.8190 (tp) cc_final: 0.7885 (tt) REVERT: C 462 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8140 (mtt90) REVERT: C 622 ILE cc_start: 0.8061 (tt) cc_final: 0.7754 (mt) REVERT: C 632 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7853 (ptp-110) REVERT: C 683 LYS cc_start: 0.8217 (pttt) cc_final: 0.7438 (tptt) REVERT: C 939 ASP cc_start: 0.7547 (m-30) cc_final: 0.7247 (m-30) REVERT: C 1040 TYR cc_start: 0.7956 (m-80) cc_final: 0.7488 (m-10) REVERT: C 1178 THR cc_start: 0.8687 (m) cc_final: 0.8261 (p) REVERT: C 1205 TYR cc_start: 0.8075 (m-80) cc_final: 0.7871 (m-80) REVERT: C 1272 ASP cc_start: 0.6988 (p0) cc_final: 0.5892 (t70) REVERT: C 1324 TRP cc_start: 0.8489 (m100) cc_final: 0.8286 (m100) REVERT: C 1331 MET cc_start: 0.7761 (ptm) cc_final: 0.7529 (mtp) REVERT: C 1429 THR cc_start: 0.7473 (p) cc_final: 0.7140 (p) REVERT: C 1470 TYR cc_start: 0.8058 (t80) cc_final: 0.7204 (t80) REVERT: C 1482 ASP cc_start: 0.6961 (m-30) cc_final: 0.6349 (m-30) REVERT: C 1645 PHE cc_start: 0.8460 (m-80) cc_final: 0.8185 (m-10) REVERT: C 1977 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (p0) REVERT: C 2017 TRP cc_start: 0.8735 (m100) cc_final: 0.8016 (m100) REVERT: C 2103 TYR cc_start: 0.7105 (t80) cc_final: 0.6398 (t80) REVERT: C 2163 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6279 (t80) REVERT: C 2438 LYS cc_start: 0.7420 (pttt) cc_final: 0.7191 (ptmt) REVERT: D 49 TYR cc_start: 0.4981 (t80) cc_final: 0.4323 (t80) REVERT: D 253 GLU cc_start: 0.8407 (tp30) cc_final: 0.8129 (tp30) REVERT: D 785 MET cc_start: 0.8306 (mmm) cc_final: 0.7736 (ttm) REVERT: D 869 SER cc_start: 0.8175 (OUTLIER) cc_final: 0.7815 (t) REVERT: D 999 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7188 (mtp85) REVERT: D 1028 TYR cc_start: 0.8279 (t80) cc_final: 0.7762 (t80) REVERT: D 1035 SER cc_start: 0.9220 (m) cc_final: 0.8981 (p) REVERT: D 1146 LYS cc_start: 0.6126 (ptpp) cc_final: 0.5646 (ptmt) REVERT: D 1311 GLU cc_start: 0.7107 (tp30) cc_final: 0.6830 (tp30) REVERT: D 1336 ASP cc_start: 0.7065 (p0) cc_final: 0.6708 (m-30) REVERT: D 1419 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: D 1422 LEU cc_start: 0.8370 (tp) cc_final: 0.8100 (tt) REVERT: D 1455 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: D 1657 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6840 (t70) REVERT: D 1661 PHE cc_start: 0.8174 (p90) cc_final: 0.7972 (p90) REVERT: D 1677 TYR cc_start: 0.8308 (t80) cc_final: 0.7784 (t80) REVERT: D 1956 MET cc_start: 0.8405 (mmp) cc_final: 0.7902 (mmp) REVERT: D 1973 ASN cc_start: 0.8646 (t0) cc_final: 0.8176 (t0) REVERT: D 2015 SER cc_start: 0.8669 (t) cc_final: 0.8466 (p) REVERT: D 2170 ASN cc_start: 0.7903 (m110) cc_final: 0.7676 (m110) REVERT: D 2183 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7115 (mm-30) REVERT: D 2275 MET cc_start: 0.7389 (mtp) cc_final: 0.7133 (mtp) REVERT: D 2311 MET cc_start: 0.8072 (tpp) cc_final: 0.7474 (tpp) REVERT: D 2317 MET cc_start: 0.8863 (ttm) cc_final: 0.8580 (mtp) REVERT: E 314 ILE cc_start: 0.8517 (mp) cc_final: 0.8072 (mm) REVERT: E 592 LYS cc_start: 0.8964 (tptp) cc_final: 0.8710 (tttp) REVERT: E 705 GLU cc_start: 0.8759 (pm20) cc_final: 0.8194 (mp0) REVERT: E 829 SER cc_start: 0.8842 (p) cc_final: 0.8343 (t) REVERT: E 1079 MET cc_start: 0.7889 (mmt) cc_final: 0.7413 (mmt) REVERT: E 1081 TYR cc_start: 0.6671 (t80) cc_final: 0.6470 (t80) REVERT: E 1141 TRP cc_start: 0.7682 (m100) cc_final: 0.7319 (m-10) REVERT: E 1229 ASN cc_start: 0.8755 (t0) cc_final: 0.8533 (t0) REVERT: E 1245 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (mt) REVERT: E 1810 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7010 (tp-100) REVERT: E 1833 ASP cc_start: 0.6632 (p0) cc_final: 0.6259 (t0) REVERT: E 2032 GLN cc_start: 0.8510 (tp40) cc_final: 0.7919 (tp40) REVERT: E 2064 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9114 (tt) REVERT: E 2164 VAL cc_start: 0.7538 (t) cc_final: 0.7323 (m) REVERT: E 2185 TYR cc_start: 0.8667 (m-80) cc_final: 0.8424 (m-10) REVERT: F 301 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7753 (t) REVERT: F 400 ASP cc_start: 0.7310 (p0) cc_final: 0.6983 (p0) REVERT: F 430 SER cc_start: 0.8035 (t) cc_final: 0.7654 (p) REVERT: F 706 MET cc_start: 0.8592 (mtp) cc_final: 0.8266 (mtp) REVERT: F 865 LEU cc_start: 0.8509 (mp) cc_final: 0.8298 (mp) REVERT: F 1363 MET cc_start: 0.7003 (tpp) cc_final: 0.6775 (tpp) REVERT: F 1555 PHE cc_start: 0.8378 (m-80) cc_final: 0.8062 (m-80) outliers start: 361 outliers final: 260 residues processed: 1568 average time/residue: 0.9349 time to fit residues: 2596.5835 Evaluate side-chains 1465 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1185 time to evaluate : 9.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 834 GLN Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1403 MET Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1629 THR Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2094 SER Chi-restraints excluded: chain A residue 2098 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2408 LYS Chi-restraints excluded: chain A residue 2428 ASP Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 767 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1298 ASN Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1660 TRP Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1697 VAL Chi-restraints excluded: chain B residue 1701 GLN Chi-restraints excluded: chain B residue 1785 HIS Chi-restraints excluded: chain B residue 1790 ASP Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1904 ASP Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2140 LEU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2248 GLN Chi-restraints excluded: chain B residue 2283 GLU Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1080 SER Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1254 ASP Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1387 VAL Chi-restraints excluded: chain C residue 1618 THR Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1660 TRP Chi-restraints excluded: chain C residue 1675 ILE Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1766 LEU Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2070 ILE Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2131 SER Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 689 LEU Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 966 ASP Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1156 SER Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1361 HIS Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1493 ILE Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1603 THR Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1647 ILE Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2171 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2309 THR Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain D residue 2494 LYS Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 895 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1084 SER Chi-restraints excluded: chain E residue 1146 LYS Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1245 LEU Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1435 GLU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1515 LYS Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1622 ASP Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1729 ASP Chi-restraints excluded: chain E residue 1783 LEU Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1810 GLN Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1856 THR Chi-restraints excluded: chain E residue 1881 MET Chi-restraints excluded: chain E residue 1888 HIS Chi-restraints excluded: chain E residue 1901 THR Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 2064 ILE Chi-restraints excluded: chain E residue 2128 VAL Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1263 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1416 ASP Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1871 THR Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2063 LEU Chi-restraints excluded: chain F residue 2143 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 466 optimal weight: 1.9990 chunk 1249 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 814 optimal weight: 0.6980 chunk 342 optimal weight: 0.1980 chunk 1389 optimal weight: 5.9990 chunk 1153 optimal weight: 0.6980 chunk 643 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 459 optimal weight: 0.6980 chunk 729 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2505 ASN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1667 HIS B1671 ASN B1961 GLN B2173 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 GLN C1090 ASN C1304 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1812 GLN C2235 GLN ** C2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS D 840 ASN D 994 GLN D1145 HIS D1303 ASN ** D1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1588 HIS ** D1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1961 GLN ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 ASN ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2237 GLN ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 510 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1785 HIS ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 116817 Z= 0.173 Angle : 0.527 11.685 158758 Z= 0.272 Chirality : 0.040 0.216 17523 Planarity : 0.004 0.071 20695 Dihedral : 4.202 36.501 15727 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 2.60 % Allowed : 12.59 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.38 (0.07), residues: 14354 helix: 2.03 (0.07), residues: 5732 sheet: 0.66 (0.10), residues: 2577 loop : 0.01 (0.08), residues: 6045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2154 HIS 0.011 0.001 HIS A 50 PHE 0.022 0.001 PHE C 730 TYR 0.035 0.001 TYR B1024 ARG 0.010 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1310 time to evaluate : 9.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.6380 (pttt) cc_final: 0.5927 (tttt) REVERT: A 94 ASN cc_start: 0.7627 (m110) cc_final: 0.7230 (t0) REVERT: A 148 MET cc_start: 0.8156 (ttp) cc_final: 0.7758 (ptm) REVERT: A 341 MET cc_start: 0.6687 (ppp) cc_final: 0.6479 (ppp) REVERT: A 458 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: A 466 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 546 TRP cc_start: 0.7949 (p-90) cc_final: 0.7656 (p-90) REVERT: A 594 LEU cc_start: 0.9105 (mt) cc_final: 0.8693 (tp) REVERT: A 658 SER cc_start: 0.8097 (m) cc_final: 0.7735 (p) REVERT: A 952 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7733 (ttm-80) REVERT: A 1264 MET cc_start: 0.7817 (mtp) cc_final: 0.6703 (mtp) REVERT: A 1295 ASP cc_start: 0.6618 (m-30) cc_final: 0.6175 (t0) REVERT: A 1300 ARG cc_start: 0.6228 (mtm110) cc_final: 0.5955 (mtm110) REVERT: A 1403 MET cc_start: 0.7347 (ptp) cc_final: 0.7051 (ptt) REVERT: A 1586 LEU cc_start: 0.8150 (mt) cc_final: 0.7708 (mt) REVERT: A 1625 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 1676 ILE cc_start: 0.9029 (pt) cc_final: 0.8637 (tp) REVERT: A 1783 LEU cc_start: 0.7679 (mm) cc_final: 0.7475 (mt) REVERT: A 1794 ARG cc_start: 0.6792 (ttm170) cc_final: 0.6356 (ttt180) REVERT: A 1878 GLU cc_start: 0.7346 (tp30) cc_final: 0.6983 (tp30) REVERT: A 1882 TRP cc_start: 0.8091 (m100) cc_final: 0.7827 (m100) REVERT: A 2055 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 2077 GLU cc_start: 0.8362 (tt0) cc_final: 0.8158 (tm-30) REVERT: A 2454 MET cc_start: 0.7412 (tpt) cc_final: 0.7065 (tpt) REVERT: B 112 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6742 (ptm) REVERT: B 113 PHE cc_start: 0.6899 (m-80) cc_final: 0.6558 (m-80) REVERT: B 134 SER cc_start: 0.7486 (t) cc_final: 0.7110 (m) REVERT: B 446 LEU cc_start: 0.9218 (tp) cc_final: 0.9002 (tp) REVERT: B 583 LYS cc_start: 0.8941 (tttt) cc_final: 0.8437 (tppt) REVERT: B 654 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7094 (mtt) REVERT: B 763 GLU cc_start: 0.7547 (tp30) cc_final: 0.7222 (tm-30) REVERT: B 767 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.6513 (m170) REVERT: B 804 LEU cc_start: 0.8415 (mt) cc_final: 0.8127 (tp) REVERT: B 914 GLN cc_start: 0.8612 (mt0) cc_final: 0.8277 (mt0) REVERT: B 1028 TYR cc_start: 0.6828 (t80) cc_final: 0.6402 (t80) REVERT: B 1146 LYS cc_start: 0.8274 (tttt) cc_final: 0.7780 (mttt) REVERT: B 1200 LEU cc_start: 0.7924 (mt) cc_final: 0.7697 (mt) REVERT: B 1455 ASP cc_start: 0.7038 (t0) cc_final: 0.6734 (t0) REVERT: B 1663 LEU cc_start: 0.8763 (mp) cc_final: 0.8527 (mt) REVERT: B 1854 MET cc_start: 0.8321 (mtm) cc_final: 0.8118 (mmp) REVERT: B 1870 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6790 (mm-40) REVERT: B 1924 VAL cc_start: 0.7939 (p) cc_final: 0.7567 (m) REVERT: B 1993 LYS cc_start: 0.6804 (ttpp) cc_final: 0.6439 (tptp) REVERT: B 2021 HIS cc_start: 0.7509 (t70) cc_final: 0.7263 (t70) REVERT: B 2218 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 2285 ASN cc_start: 0.8699 (t0) cc_final: 0.8386 (t0) REVERT: C 95 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7809 (mm-40) REVERT: C 170 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 218 LEU cc_start: 0.8343 (mt) cc_final: 0.7876 (tp) REVERT: C 368 LEU cc_start: 0.8220 (tp) cc_final: 0.7725 (tt) REVERT: C 462 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8094 (mtt90) REVERT: C 632 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7832 (ptp-110) REVERT: C 683 LYS cc_start: 0.8229 (pttt) cc_final: 0.7196 (tptt) REVERT: C 764 MET cc_start: 0.8552 (ttt) cc_final: 0.8245 (ttp) REVERT: C 939 ASP cc_start: 0.7501 (m-30) cc_final: 0.7199 (m-30) REVERT: C 1040 TYR cc_start: 0.7822 (m-80) cc_final: 0.7437 (m-10) REVERT: C 1178 THR cc_start: 0.8718 (m) cc_final: 0.8293 (p) REVERT: C 1205 TYR cc_start: 0.8059 (m-80) cc_final: 0.7844 (m-80) REVERT: C 1272 ASP cc_start: 0.6967 (p0) cc_final: 0.5861 (t70) REVERT: C 1278 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8514 (mmt) REVERT: C 1429 THR cc_start: 0.7449 (p) cc_final: 0.7131 (p) REVERT: C 1470 TYR cc_start: 0.8126 (t80) cc_final: 0.7181 (t80) REVERT: C 1482 ASP cc_start: 0.6779 (m-30) cc_final: 0.6330 (m-30) REVERT: C 1645 PHE cc_start: 0.8423 (m-80) cc_final: 0.8178 (m-10) REVERT: C 1681 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8289 (mt) REVERT: C 1977 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (p0) REVERT: C 2102 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7873 (mt) REVERT: C 2103 TYR cc_start: 0.7040 (t80) cc_final: 0.6423 (t80) REVERT: C 2115 MET cc_start: 0.6986 (mtp) cc_final: 0.6582 (mtm) REVERT: C 2163 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.6250 (t80) REVERT: C 2235 GLN cc_start: 0.8863 (tp-100) cc_final: 0.8286 (tm-30) REVERT: C 2438 LYS cc_start: 0.7293 (pttt) cc_final: 0.7081 (ptmt) REVERT: C 2496 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8139 (mtmm) REVERT: D 49 TYR cc_start: 0.4998 (t80) cc_final: 0.4155 (t80) REVERT: D 253 GLU cc_start: 0.8384 (tp30) cc_final: 0.8005 (tp30) REVERT: D 701 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6212 (pp30) REVERT: D 785 MET cc_start: 0.8226 (mmm) cc_final: 0.7718 (ttm) REVERT: D 869 SER cc_start: 0.8157 (OUTLIER) cc_final: 0.7866 (t) REVERT: D 999 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7054 (mtp85) REVERT: D 1028 TYR cc_start: 0.8201 (t80) cc_final: 0.7697 (t80) REVERT: D 1049 MET cc_start: 0.8577 (ppp) cc_final: 0.8024 (ptm) REVERT: D 1146 LYS cc_start: 0.6191 (ptpp) cc_final: 0.5682 (ptmt) REVERT: D 1311 GLU cc_start: 0.7097 (tp30) cc_final: 0.6772 (tp30) REVERT: D 1419 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.6298 (mp10) REVERT: D 1422 LEU cc_start: 0.8329 (tp) cc_final: 0.8047 (tt) REVERT: D 1455 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: D 1657 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6888 (t70) REVERT: D 1677 TYR cc_start: 0.8331 (t80) cc_final: 0.7763 (t80) REVERT: D 1796 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8014 (tt) REVERT: D 1869 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7358 (mtt90) REVERT: D 1956 MET cc_start: 0.8245 (mmp) cc_final: 0.7858 (mmp) REVERT: D 1973 ASN cc_start: 0.8630 (t0) cc_final: 0.8151 (t0) REVERT: D 2120 SER cc_start: 0.8035 (m) cc_final: 0.7805 (t) REVERT: D 2170 ASN cc_start: 0.7893 (m110) cc_final: 0.7659 (m110) REVERT: D 2183 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7047 (mm-30) REVERT: D 2193 GLU cc_start: 0.6628 (tt0) cc_final: 0.6343 (tt0) REVERT: D 2311 MET cc_start: 0.8036 (tpp) cc_final: 0.7532 (tpp) REVERT: D 2317 MET cc_start: 0.8877 (ttm) cc_final: 0.8590 (mtp) REVERT: D 2452 HIS cc_start: 0.7372 (t70) cc_final: 0.6631 (t-90) REVERT: E 247 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8922 (tp) REVERT: E 314 ILE cc_start: 0.8486 (mp) cc_final: 0.8017 (mm) REVERT: E 705 GLU cc_start: 0.8719 (pm20) cc_final: 0.8185 (mp0) REVERT: E 829 SER cc_start: 0.8784 (p) cc_final: 0.8277 (t) REVERT: E 1079 MET cc_start: 0.7886 (mmt) cc_final: 0.7512 (mmt) REVERT: E 1081 TYR cc_start: 0.6583 (t80) cc_final: 0.6325 (t80) REVERT: E 1141 TRP cc_start: 0.7618 (m100) cc_final: 0.7168 (m100) REVERT: E 1203 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7891 (tt) REVERT: E 1229 ASN cc_start: 0.8848 (t0) cc_final: 0.8620 (t0) REVERT: E 1245 LEU cc_start: 0.8536 (tp) cc_final: 0.8299 (mt) REVERT: E 1361 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7972 (m-70) REVERT: E 1833 ASP cc_start: 0.6834 (p0) cc_final: 0.6388 (t0) REVERT: E 2107 ILE cc_start: 0.7761 (mm) cc_final: 0.7535 (tt) REVERT: E 2188 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: E 2202 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8143 (tm-30) REVERT: F 301 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7666 (t) REVERT: F 400 ASP cc_start: 0.7389 (p0) cc_final: 0.7049 (p0) REVERT: F 430 SER cc_start: 0.8069 (t) cc_final: 0.7697 (p) REVERT: F 706 MET cc_start: 0.8636 (mtp) cc_final: 0.8254 (mtp) REVERT: F 964 PRO cc_start: 0.8556 (Cg_endo) cc_final: 0.8155 (Cg_exo) REVERT: F 1363 MET cc_start: 0.7162 (tpp) cc_final: 0.6959 (tpp) REVERT: F 1555 PHE cc_start: 0.8371 (m-80) cc_final: 0.8064 (m-80) outliers start: 321 outliers final: 222 residues processed: 1537 average time/residue: 0.9289 time to fit residues: 2536.7384 Evaluate side-chains 1433 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1184 time to evaluate : 9.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1024 TYR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2098 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 767 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1432 SER Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1701 GLN Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2283 GLU Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 701 GLN Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1080 SER Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1618 THR Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1660 TRP Chi-restraints excluded: chain C residue 1675 ILE Chi-restraints excluded: chain C residue 1681 LEU Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1766 LEU Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2102 LEU Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2131 SER Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain C residue 2496 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 533 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 689 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1156 SER Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1361 HIS Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1465 ASP Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1686 ILE Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1860 LEU Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2063 LEU Chi-restraints excluded: chain D residue 2078 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2309 THR Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 768 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1049 MET Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1146 LYS Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1349 LEU Chi-restraints excluded: chain E residue 1361 HIS Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1622 ASP Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1856 THR Chi-restraints excluded: chain E residue 1881 MET Chi-restraints excluded: chain E residue 1888 HIS Chi-restraints excluded: chain E residue 1901 THR Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 2126 THR Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2188 ARG Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1263 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1416 ASP Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2063 LEU Chi-restraints excluded: chain F residue 2143 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 1339 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 791 optimal weight: 0.6980 chunk 1014 optimal weight: 7.9990 chunk 786 optimal weight: 0.9980 chunk 1169 optimal weight: 0.0980 chunk 775 optimal weight: 0.7980 chunk 1384 optimal weight: 6.9990 chunk 866 optimal weight: 9.9990 chunk 843 optimal weight: 0.9990 chunk 639 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1958 ASN A1961 GLN ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1612 GLN B1929 ASN ** B1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2129 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C1090 ASN C1304 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2459 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS ** D1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 ASN ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2237 GLN ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 510 ASN E 709 HIS ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 116817 Z= 0.157 Angle : 0.523 12.052 158758 Z= 0.267 Chirality : 0.040 0.212 17523 Planarity : 0.003 0.050 20695 Dihedral : 4.085 35.493 15727 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 2.42 % Allowed : 13.15 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.42 (0.07), residues: 14354 helix: 2.08 (0.07), residues: 5762 sheet: 0.65 (0.10), residues: 2622 loop : 0.01 (0.08), residues: 5970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1660 HIS 0.012 0.001 HIS A 50 PHE 0.033 0.001 PHE C1294 TYR 0.037 0.001 TYR B1024 ARG 0.012 0.000 ARG F 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1617 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1319 time to evaluate : 9.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.8398 (mm) cc_final: 0.8102 (mm) REVERT: A 68 LYS cc_start: 0.6426 (pttt) cc_final: 0.6092 (tttt) REVERT: A 94 ASN cc_start: 0.7676 (m110) cc_final: 0.7459 (t0) REVERT: A 148 MET cc_start: 0.8159 (ttp) cc_final: 0.7795 (ptm) REVERT: A 594 LEU cc_start: 0.9062 (mt) cc_final: 0.8691 (tp) REVERT: A 658 SER cc_start: 0.8102 (m) cc_final: 0.7763 (p) REVERT: A 1248 MET cc_start: 0.8179 (ttp) cc_final: 0.7904 (ptm) REVERT: A 1295 ASP cc_start: 0.6564 (m-30) cc_final: 0.6266 (t0) REVERT: A 1300 ARG cc_start: 0.6386 (mtm110) cc_final: 0.6104 (mtm110) REVERT: A 1403 MET cc_start: 0.7318 (ptp) cc_final: 0.7046 (ptt) REVERT: A 1490 ASN cc_start: 0.8492 (t0) cc_final: 0.7387 (p0) REVERT: A 1586 LEU cc_start: 0.8181 (mt) cc_final: 0.7793 (mt) REVERT: A 1590 GLU cc_start: 0.8035 (pm20) cc_final: 0.7818 (pm20) REVERT: A 1625 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8041 (tt) REVERT: A 1676 ILE cc_start: 0.9015 (pt) cc_final: 0.8649 (tp) REVERT: A 1783 LEU cc_start: 0.7710 (mm) cc_final: 0.7469 (mt) REVERT: A 1882 TRP cc_start: 0.7996 (m100) cc_final: 0.7761 (m100) REVERT: A 2077 GLU cc_start: 0.8382 (tt0) cc_final: 0.7891 (tm-30) REVERT: A 2203 LEU cc_start: 0.9447 (mt) cc_final: 0.8951 (tt) REVERT: A 2454 MET cc_start: 0.7348 (tpt) cc_final: 0.7006 (tpt) REVERT: B 112 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6753 (ptm) REVERT: B 134 SER cc_start: 0.7451 (t) cc_final: 0.7076 (m) REVERT: B 200 TYR cc_start: 0.8360 (t80) cc_final: 0.7746 (t80) REVERT: B 583 LYS cc_start: 0.8941 (tttt) cc_final: 0.8445 (tppt) REVERT: B 763 GLU cc_start: 0.7610 (tp30) cc_final: 0.7351 (tm-30) REVERT: B 764 MET cc_start: 0.8845 (tmm) cc_final: 0.8224 (tmm) REVERT: B 804 LEU cc_start: 0.8449 (mt) cc_final: 0.8112 (tp) REVERT: B 1028 TYR cc_start: 0.6902 (t80) cc_final: 0.6441 (t80) REVERT: B 1146 LYS cc_start: 0.8233 (tttt) cc_final: 0.7738 (mttt) REVERT: B 1200 LEU cc_start: 0.7900 (mt) cc_final: 0.7591 (mt) REVERT: B 1278 MET cc_start: 0.7402 (tpp) cc_final: 0.7032 (mmt) REVERT: B 1449 ASN cc_start: 0.7560 (p0) cc_final: 0.7358 (p0) REVERT: B 1455 ASP cc_start: 0.7119 (t0) cc_final: 0.6809 (t0) REVERT: B 1870 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6803 (mm-40) REVERT: B 1993 LYS cc_start: 0.6822 (ttpp) cc_final: 0.6440 (tptp) REVERT: B 2218 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 2248 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: B 2285 ASN cc_start: 0.8683 (t0) cc_final: 0.8376 (t0) REVERT: C 95 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7713 (mm-40) REVERT: C 218 LEU cc_start: 0.8340 (mt) cc_final: 0.7843 (tp) REVERT: C 368 LEU cc_start: 0.8175 (tp) cc_final: 0.7872 (tt) REVERT: C 462 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8189 (mtt90) REVERT: C 632 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7934 (ptp-110) REVERT: C 683 LYS cc_start: 0.8248 (pttt) cc_final: 0.7183 (tptt) REVERT: C 939 ASP cc_start: 0.7495 (m-30) cc_final: 0.7178 (m-30) REVERT: C 1040 TYR cc_start: 0.7734 (m-80) cc_final: 0.7421 (m-80) REVERT: C 1178 THR cc_start: 0.8692 (m) cc_final: 0.8247 (p) REVERT: C 1205 TYR cc_start: 0.8039 (m-80) cc_final: 0.7815 (m-80) REVERT: C 1272 ASP cc_start: 0.6887 (p0) cc_final: 0.5769 (t70) REVERT: C 1294 PHE cc_start: 0.8112 (m-80) cc_final: 0.7899 (m-80) REVERT: C 1429 THR cc_start: 0.7433 (p) cc_final: 0.7124 (p) REVERT: C 1470 TYR cc_start: 0.8096 (t80) cc_final: 0.7180 (t80) REVERT: C 1482 ASP cc_start: 0.6732 (m-30) cc_final: 0.6308 (m-30) REVERT: C 1645 PHE cc_start: 0.8442 (m-80) cc_final: 0.8186 (m-10) REVERT: C 1681 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8339 (mt) REVERT: C 1977 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8125 (p0) REVERT: C 2103 TYR cc_start: 0.7093 (t80) cc_final: 0.6419 (t80) REVERT: C 2115 MET cc_start: 0.6981 (mtp) cc_final: 0.6581 (mtm) REVERT: C 2185 TYR cc_start: 0.8210 (m-10) cc_final: 0.7959 (m-10) REVERT: C 2235 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8355 (tm-30) REVERT: C 2438 LYS cc_start: 0.7294 (pttt) cc_final: 0.6996 (ptmm) REVERT: C 2496 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8152 (mtmm) REVERT: D 49 TYR cc_start: 0.4894 (t80) cc_final: 0.4570 (t80) REVERT: D 93 ASN cc_start: 0.8121 (m-40) cc_final: 0.7781 (t0) REVERT: D 253 GLU cc_start: 0.8439 (tp30) cc_final: 0.8009 (tp30) REVERT: D 701 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.6211 (pp30) REVERT: D 785 MET cc_start: 0.8111 (mmm) cc_final: 0.7451 (ttm) REVERT: D 869 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7852 (t) REVERT: D 908 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8023 (mp0) REVERT: D 1028 TYR cc_start: 0.8228 (t80) cc_final: 0.8010 (t80) REVERT: D 1049 MET cc_start: 0.8553 (ppp) cc_final: 0.8038 (ptm) REVERT: D 1311 GLU cc_start: 0.7066 (tp30) cc_final: 0.6699 (tp30) REVERT: D 1401 LYS cc_start: 0.7532 (tmtt) cc_final: 0.7318 (tptt) REVERT: D 1419 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.6174 (mp10) REVERT: D 1422 LEU cc_start: 0.8377 (tp) cc_final: 0.8102 (tt) REVERT: D 1455 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: D 1657 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6704 (t70) REVERT: D 1677 TYR cc_start: 0.8339 (t80) cc_final: 0.7790 (t80) REVERT: D 1796 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7999 (tt) REVERT: D 1869 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7436 (mtt90) REVERT: D 1973 ASN cc_start: 0.8628 (t0) cc_final: 0.8129 (t0) REVERT: D 2170 ASN cc_start: 0.7875 (m110) cc_final: 0.7576 (m110) REVERT: D 2183 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6945 (mm-30) REVERT: D 2193 GLU cc_start: 0.6514 (tt0) cc_final: 0.6273 (tt0) REVERT: D 2311 MET cc_start: 0.8033 (tpp) cc_final: 0.7576 (tpp) REVERT: D 2317 MET cc_start: 0.8885 (ttm) cc_final: 0.8601 (mtp) REVERT: E 73 GLN cc_start: 0.7238 (mp10) cc_final: 0.7006 (mp10) REVERT: E 247 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8932 (tp) REVERT: E 314 ILE cc_start: 0.8450 (mp) cc_final: 0.7984 (mm) REVERT: E 705 GLU cc_start: 0.8665 (pm20) cc_final: 0.8198 (mp0) REVERT: E 829 SER cc_start: 0.8741 (p) cc_final: 0.8238 (t) REVERT: E 1079 MET cc_start: 0.7800 (mmt) cc_final: 0.7427 (mmp) REVERT: E 1081 TYR cc_start: 0.6503 (t80) cc_final: 0.6217 (t80) REVERT: E 1141 TRP cc_start: 0.7588 (m100) cc_final: 0.7175 (m100) REVERT: E 1203 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7900 (tt) REVERT: E 1229 ASN cc_start: 0.8853 (t0) cc_final: 0.8621 (t0) REVERT: E 1245 LEU cc_start: 0.8509 (tp) cc_final: 0.8293 (mt) REVERT: E 1273 MET cc_start: 0.8013 (mmp) cc_final: 0.7723 (mmp) REVERT: E 1361 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7860 (m-70) REVERT: E 1833 ASP cc_start: 0.6676 (p0) cc_final: 0.6289 (t0) REVERT: E 1884 MET cc_start: 0.8338 (mmm) cc_final: 0.7886 (mmt) REVERT: E 2188 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: E 2202 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 2250 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8923 (tt) REVERT: F 301 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7791 (t) REVERT: F 400 ASP cc_start: 0.7261 (p0) cc_final: 0.7005 (p0) REVERT: F 430 SER cc_start: 0.8201 (t) cc_final: 0.7828 (p) REVERT: F 706 MET cc_start: 0.8646 (mtp) cc_final: 0.8259 (mtp) REVERT: F 964 PRO cc_start: 0.8535 (Cg_endo) cc_final: 0.8141 (Cg_exo) REVERT: F 1555 PHE cc_start: 0.8324 (m-80) cc_final: 0.8010 (m-80) REVERT: F 2122 TRP cc_start: 0.5418 (OUTLIER) cc_final: 0.4889 (p90) outliers start: 298 outliers final: 220 residues processed: 1527 average time/residue: 0.9357 time to fit residues: 2532.3747 Evaluate side-chains 1433 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1193 time to evaluate : 10.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1625 LEU Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1846 MET Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2124 LEU Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1275 SER Chi-restraints excluded: chain B residue 1298 ASN Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1432 SER Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1904 ASP Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2140 LEU Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2248 GLN Chi-restraints excluded: chain B residue 2283 GLU Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain B residue 2381 THR Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1080 SER Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1618 THR Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1660 TRP Chi-restraints excluded: chain C residue 1681 LEU Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2131 SER Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain C residue 2496 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 689 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 1013 ILE Chi-restraints excluded: chain D residue 1046 ASP Chi-restraints excluded: chain D residue 1048 THR Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1156 SER Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1214 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1361 HIS Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1465 ASP Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1686 ILE Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1784 LEU Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2078 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1049 MET Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1146 LYS Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1349 LEU Chi-restraints excluded: chain E residue 1361 HIS Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1445 LEU Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1622 ASP Chi-restraints excluded: chain E residue 1662 LYS Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1881 MET Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 2126 THR Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2188 ARG Chi-restraints excluded: chain E residue 2250 LEU Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain E residue 2503 THR Chi-restraints excluded: chain E residue 2504 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 513 ASP Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1263 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1416 ASP Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2063 LEU Chi-restraints excluded: chain F residue 2122 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 856 optimal weight: 4.9990 chunk 552 optimal weight: 0.9980 chunk 826 optimal weight: 6.9990 chunk 416 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 879 optimal weight: 8.9990 chunk 942 optimal weight: 5.9990 chunk 684 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 1087 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1919 HIS ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 ASN A2143 ASN ** A2355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN C1090 ASN C1304 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS D 994 GLN D1105 GLN ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 ASN ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2237 GLN ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 ASN E1361 HIS ** E1594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1785 HIS ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1394 ASN ** F1693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 116817 Z= 0.231 Angle : 0.561 13.053 158758 Z= 0.287 Chirality : 0.041 0.259 17523 Planarity : 0.004 0.049 20695 Dihedral : 4.156 36.139 15727 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 2.70 % Allowed : 13.21 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.32 (0.07), residues: 14354 helix: 2.01 (0.07), residues: 5732 sheet: 0.61 (0.10), residues: 2622 loop : -0.04 (0.08), residues: 6000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP C1324 HIS 0.013 0.001 HIS A 50 PHE 0.023 0.002 PHE C1294 TYR 0.037 0.001 TYR B1024 ARG 0.024 0.001 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1209 time to evaluate : 9.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7285 (t0) cc_final: 0.6985 (t0) REVERT: A 94 ASN cc_start: 0.7796 (m110) cc_final: 0.7428 (t0) REVERT: A 148 MET cc_start: 0.8172 (ttp) cc_final: 0.7786 (ptm) REVERT: A 546 TRP cc_start: 0.8049 (p-90) cc_final: 0.7817 (p-90) REVERT: A 594 LEU cc_start: 0.9062 (mt) cc_final: 0.8677 (tp) REVERT: A 658 SER cc_start: 0.8131 (m) cc_final: 0.7779 (p) REVERT: A 1244 THR cc_start: 0.9253 (t) cc_final: 0.8992 (p) REVERT: A 1403 MET cc_start: 0.7344 (ptp) cc_final: 0.7053 (ptt) REVERT: A 1490 ASN cc_start: 0.8588 (t0) cc_final: 0.7552 (p0) REVERT: A 1590 GLU cc_start: 0.8027 (pm20) cc_final: 0.7804 (pm20) REVERT: A 1676 ILE cc_start: 0.9043 (pt) cc_final: 0.8695 (tp) REVERT: A 1791 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 2055 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8748 (tp) REVERT: A 2077 GLU cc_start: 0.8434 (tt0) cc_final: 0.7911 (tm-30) REVERT: A 2159 GLU cc_start: 0.7928 (tp30) cc_final: 0.7715 (tp30) REVERT: A 2163 TYR cc_start: 0.6302 (m-80) cc_final: 0.6062 (m-80) REVERT: A 2203 LEU cc_start: 0.9565 (mt) cc_final: 0.9088 (tt) REVERT: A 2454 MET cc_start: 0.7385 (tpt) cc_final: 0.7072 (tpt) REVERT: B 112 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6818 (ptm) REVERT: B 134 SER cc_start: 0.7462 (t) cc_final: 0.7083 (m) REVERT: B 583 LYS cc_start: 0.8983 (tttt) cc_final: 0.8483 (tppt) REVERT: B 764 MET cc_start: 0.8949 (tmm) cc_final: 0.8571 (ttt) REVERT: B 804 LEU cc_start: 0.8384 (mt) cc_final: 0.8044 (tp) REVERT: B 1028 TYR cc_start: 0.6848 (t80) cc_final: 0.6416 (t80) REVERT: B 1146 LYS cc_start: 0.8342 (tttt) cc_final: 0.7856 (mttt) REVERT: B 1200 LEU cc_start: 0.7977 (mt) cc_final: 0.7655 (mt) REVERT: B 1455 ASP cc_start: 0.7302 (t0) cc_final: 0.6958 (t0) REVERT: B 1870 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6729 (mm-40) REVERT: B 1924 VAL cc_start: 0.7986 (p) cc_final: 0.7612 (m) REVERT: B 1993 LYS cc_start: 0.6756 (ttpp) cc_final: 0.6414 (tptp) REVERT: B 2218 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 2248 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: B 2285 ASN cc_start: 0.8559 (t0) cc_final: 0.8282 (t0) REVERT: B 2311 MET cc_start: 0.8001 (tpt) cc_final: 0.7616 (tpt) REVERT: B 2388 GLN cc_start: 0.8448 (pt0) cc_final: 0.8247 (pp30) REVERT: C 95 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7770 (mm-40) REVERT: C 368 LEU cc_start: 0.8332 (tp) cc_final: 0.8056 (tt) REVERT: C 462 ARG cc_start: 0.8528 (mtt90) cc_final: 0.8093 (mtt90) REVERT: C 632 ARG cc_start: 0.8387 (ttm110) cc_final: 0.7965 (ptp-110) REVERT: C 683 LYS cc_start: 0.8227 (pttt) cc_final: 0.7349 (tptt) REVERT: C 939 ASP cc_start: 0.7595 (m-30) cc_final: 0.7314 (m-30) REVERT: C 1031 TRP cc_start: 0.6571 (t60) cc_final: 0.6307 (t60) REVERT: C 1040 TYR cc_start: 0.7747 (m-80) cc_final: 0.7404 (m-10) REVERT: C 1178 THR cc_start: 0.8745 (m) cc_final: 0.8313 (p) REVERT: C 1205 TYR cc_start: 0.8081 (m-80) cc_final: 0.7853 (m-80) REVERT: C 1272 ASP cc_start: 0.6768 (p0) cc_final: 0.5743 (t70) REVERT: C 1276 LYS cc_start: 0.8018 (mttt) cc_final: 0.7635 (tttt) REVERT: C 1278 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8548 (mmt) REVERT: C 1362 ASN cc_start: 0.6500 (m-40) cc_final: 0.6039 (p0) REVERT: C 1429 THR cc_start: 0.7471 (p) cc_final: 0.7187 (p) REVERT: C 1470 TYR cc_start: 0.8154 (t80) cc_final: 0.7430 (t80) REVERT: C 1482 ASP cc_start: 0.7090 (m-30) cc_final: 0.6535 (m-30) REVERT: C 1947 LEU cc_start: 0.7463 (mp) cc_final: 0.6881 (tp) REVERT: C 1977 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8211 (p0) REVERT: C 2102 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 2103 TYR cc_start: 0.7058 (t80) cc_final: 0.6389 (t80) REVERT: C 2115 MET cc_start: 0.6964 (mtp) cc_final: 0.6574 (mtm) REVERT: C 2235 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8416 (tm-30) REVERT: C 2438 LYS cc_start: 0.7281 (pttt) cc_final: 0.6975 (ptmm) REVERT: C 2496 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (mtmm) REVERT: D 49 TYR cc_start: 0.4922 (t80) cc_final: 0.4573 (t80) REVERT: D 209 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6673 (mm-30) REVERT: D 701 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6248 (pp30) REVERT: D 725 MET cc_start: 0.7936 (mtp) cc_final: 0.7705 (mtp) REVERT: D 767 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7520 (m170) REVERT: D 785 MET cc_start: 0.8021 (mmm) cc_final: 0.7612 (ttm) REVERT: D 869 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.8052 (t) REVERT: D 908 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8054 (mp0) REVERT: D 1028 TYR cc_start: 0.8300 (t80) cc_final: 0.7919 (t80) REVERT: D 1049 MET cc_start: 0.8574 (ppp) cc_final: 0.8064 (ptm) REVERT: D 1311 GLU cc_start: 0.7088 (tp30) cc_final: 0.6782 (tp30) REVERT: D 1419 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: D 1422 LEU cc_start: 0.8454 (tp) cc_final: 0.8154 (tt) REVERT: D 1455 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: D 1657 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6743 (t70) REVERT: D 1677 TYR cc_start: 0.8365 (t80) cc_final: 0.7736 (t80) REVERT: D 1796 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8038 (tt) REVERT: D 1869 ARG cc_start: 0.7657 (mtt90) cc_final: 0.7207 (mtt90) REVERT: D 1973 ASN cc_start: 0.8693 (t0) cc_final: 0.8235 (t0) REVERT: D 2170 ASN cc_start: 0.7889 (m110) cc_final: 0.7598 (m110) REVERT: D 2183 GLU cc_start: 0.7978 (mm-30) cc_final: 0.6998 (mm-30) REVERT: D 2311 MET cc_start: 0.8086 (tpp) cc_final: 0.7562 (tpp) REVERT: D 2317 MET cc_start: 0.8895 (ttm) cc_final: 0.8608 (mtp) REVERT: E 73 GLN cc_start: 0.7372 (mp10) cc_final: 0.7148 (mp10) REVERT: E 90 ILE cc_start: 0.8430 (mt) cc_final: 0.8133 (tt) REVERT: E 247 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8923 (tp) REVERT: E 314 ILE cc_start: 0.8516 (mp) cc_final: 0.8049 (mm) REVERT: E 705 GLU cc_start: 0.8658 (pm20) cc_final: 0.8224 (mp0) REVERT: E 829 SER cc_start: 0.8696 (p) cc_final: 0.8169 (t) REVERT: E 1079 MET cc_start: 0.7917 (mmt) cc_final: 0.7432 (mmt) REVERT: E 1081 TYR cc_start: 0.6611 (t80) cc_final: 0.6333 (t80) REVERT: E 1141 TRP cc_start: 0.7522 (m100) cc_final: 0.6983 (m100) REVERT: E 1245 LEU cc_start: 0.8468 (tp) cc_final: 0.8199 (mt) REVERT: E 1273 MET cc_start: 0.8031 (mmp) cc_final: 0.7704 (mmp) REVERT: E 1758 MET cc_start: 0.6050 (ptp) cc_final: 0.5670 (mtp) REVERT: E 1810 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6934 (tp-100) REVERT: E 1833 ASP cc_start: 0.6618 (p0) cc_final: 0.6267 (t0) REVERT: E 1884 MET cc_start: 0.8330 (mmm) cc_final: 0.7900 (mmt) REVERT: E 1965 GLN cc_start: 0.8397 (tp-100) cc_final: 0.7933 (tp-100) REVERT: E 2188 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7663 (ttm170) REVERT: E 2202 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8200 (tm-30) REVERT: F 400 ASP cc_start: 0.7361 (p0) cc_final: 0.7037 (p0) REVERT: F 706 MET cc_start: 0.8625 (mtp) cc_final: 0.8274 (mtp) REVERT: F 964 PRO cc_start: 0.8497 (Cg_endo) cc_final: 0.8101 (Cg_exo) REVERT: F 1363 MET cc_start: 0.7092 (tpp) cc_final: 0.6815 (tpp) REVERT: F 1555 PHE cc_start: 0.8352 (m-80) cc_final: 0.8017 (m-80) REVERT: F 2122 TRP cc_start: 0.5538 (OUTLIER) cc_final: 0.4953 (p90) outliers start: 333 outliers final: 258 residues processed: 1449 average time/residue: 0.9260 time to fit residues: 2384.9778 Evaluate side-chains 1422 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1145 time to evaluate : 9.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1629 THR Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1846 MET Chi-restraints excluded: chain A residue 1896 LEU Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1963 LEU Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2063 LEU Chi-restraints excluded: chain A residue 2098 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2500 MET Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1298 ASN Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1701 GLN Chi-restraints excluded: chain B residue 1752 ASN Chi-restraints excluded: chain B residue 1790 ASP Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1901 THR Chi-restraints excluded: chain B residue 1904 ASP Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2140 LEU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2248 GLN Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain B residue 2381 THR Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 869 SER Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1080 SER Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1254 ASP Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1618 THR Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1660 TRP Chi-restraints excluded: chain C residue 1675 ILE Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2070 ILE Chi-restraints excluded: chain C residue 2102 LEU Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2182 SER Chi-restraints excluded: chain C residue 2496 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 689 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 1013 ILE Chi-restraints excluded: chain D residue 1048 THR Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1156 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1214 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1361 HIS Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1465 ASP Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1784 LEU Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1860 LEU Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2078 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2171 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 HIS Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 895 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1084 SER Chi-restraints excluded: chain E residue 1146 LYS Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1349 LEU Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1452 ILE Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1662 LYS Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1729 ASP Chi-restraints excluded: chain E residue 1783 LEU Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1810 GLN Chi-restraints excluded: chain E residue 1856 THR Chi-restraints excluded: chain E residue 1881 MET Chi-restraints excluded: chain E residue 1901 THR Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 1962 THR Chi-restraints excluded: chain E residue 1995 LEU Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2161 THR Chi-restraints excluded: chain E residue 2188 ARG Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain E residue 2503 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 513 ASP Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1237 ASN Chi-restraints excluded: chain F residue 1263 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1394 ASN Chi-restraints excluded: chain F residue 1416 ASP Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2063 LEU Chi-restraints excluded: chain F residue 2122 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 1259 optimal weight: 6.9990 chunk 1325 optimal weight: 9.9990 chunk 1209 optimal weight: 0.7980 chunk 1289 optimal weight: 6.9990 chunk 776 optimal weight: 0.4980 chunk 561 optimal weight: 3.9990 chunk 1012 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 1165 optimal weight: 0.0770 chunk 1219 optimal weight: 0.7980 chunk 1285 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2355 GLN A2430 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS D 994 GLN ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 ASN ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2237 GLN ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1361 HIS ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1394 ASN F1766 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 116817 Z= 0.168 Angle : 0.545 12.340 158758 Z= 0.276 Chirality : 0.040 0.217 17523 Planarity : 0.003 0.048 20695 Dihedral : 4.072 34.827 15727 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.37 % Rotamer: Outliers : 2.20 % Allowed : 13.80 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.35 (0.07), residues: 14354 helix: 2.02 (0.07), residues: 5792 sheet: 0.60 (0.10), residues: 2648 loop : -0.03 (0.08), residues: 5914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C1324 HIS 0.013 0.001 HIS A 50 PHE 0.036 0.001 PHE D1472 TYR 0.037 0.001 TYR B1024 ARG 0.010 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1528 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1257 time to evaluate : 9.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7219 (t0) cc_final: 0.6975 (t0) REVERT: A 94 ASN cc_start: 0.7846 (m110) cc_final: 0.7477 (t0) REVERT: A 148 MET cc_start: 0.8154 (ttp) cc_final: 0.7798 (ptm) REVERT: A 546 TRP cc_start: 0.7975 (p-90) cc_final: 0.7770 (p-90) REVERT: A 594 LEU cc_start: 0.9020 (mt) cc_final: 0.8670 (tp) REVERT: A 658 SER cc_start: 0.8077 (m) cc_final: 0.7789 (p) REVERT: A 1244 THR cc_start: 0.9202 (t) cc_final: 0.8942 (p) REVERT: A 1295 ASP cc_start: 0.6106 (t0) cc_final: 0.5814 (t0) REVERT: A 1403 MET cc_start: 0.7236 (ptp) cc_final: 0.7002 (ptt) REVERT: A 1490 ASN cc_start: 0.8504 (t0) cc_final: 0.7424 (p0) REVERT: A 1676 ILE cc_start: 0.9005 (pt) cc_final: 0.8642 (tp) REVERT: A 1882 TRP cc_start: 0.7973 (m100) cc_final: 0.7719 (m100) REVERT: A 2055 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (tp) REVERT: A 2077 GLU cc_start: 0.8446 (tt0) cc_final: 0.7935 (tm-30) REVERT: A 2165 MET cc_start: 0.7636 (ttm) cc_final: 0.7433 (ttm) REVERT: A 2203 LEU cc_start: 0.9516 (mt) cc_final: 0.9091 (tt) REVERT: A 2454 MET cc_start: 0.7626 (tpt) cc_final: 0.7313 (tpt) REVERT: B 75 GLN cc_start: 0.6180 (mt0) cc_final: 0.5306 (tp40) REVERT: B 112 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6019 (ptt) REVERT: B 134 SER cc_start: 0.7474 (t) cc_final: 0.7100 (m) REVERT: B 341 MET cc_start: 0.7495 (pmm) cc_final: 0.7146 (pmm) REVERT: B 583 LYS cc_start: 0.8948 (tttt) cc_final: 0.8461 (tppt) REVERT: B 804 LEU cc_start: 0.8436 (mt) cc_final: 0.8052 (tp) REVERT: B 1146 LYS cc_start: 0.8280 (tttt) cc_final: 0.7798 (mttt) REVERT: B 1200 LEU cc_start: 0.7991 (mt) cc_final: 0.7633 (mt) REVERT: B 1455 ASP cc_start: 0.7314 (t0) cc_final: 0.7026 (t0) REVERT: B 1663 LEU cc_start: 0.8772 (mp) cc_final: 0.8518 (mt) REVERT: B 1758 MET cc_start: 0.5435 (mtp) cc_final: 0.5097 (mtm) REVERT: B 1778 LEU cc_start: 0.6266 (tp) cc_final: 0.6009 (tt) REVERT: B 1870 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6705 (mm-40) REVERT: B 1924 VAL cc_start: 0.8051 (p) cc_final: 0.7657 (m) REVERT: B 1993 LYS cc_start: 0.6831 (ttpp) cc_final: 0.6454 (tptp) REVERT: B 2191 GLU cc_start: 0.7939 (tp30) cc_final: 0.7574 (tp30) REVERT: B 2218 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8031 (tm-30) REVERT: B 2248 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 2285 ASN cc_start: 0.8571 (t0) cc_final: 0.8314 (t0) REVERT: B 2311 MET cc_start: 0.7970 (tpt) cc_final: 0.7610 (tpt) REVERT: C 95 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7747 (mm-40) REVERT: C 368 LEU cc_start: 0.8298 (tp) cc_final: 0.7902 (tt) REVERT: C 462 ARG cc_start: 0.8508 (mtt90) cc_final: 0.8156 (mtt90) REVERT: C 632 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8110 (ptp-110) REVERT: C 683 LYS cc_start: 0.8241 (pttt) cc_final: 0.7278 (tptt) REVERT: C 939 ASP cc_start: 0.7530 (m-30) cc_final: 0.7235 (m-30) REVERT: C 1040 TYR cc_start: 0.7677 (m-80) cc_final: 0.7393 (m-80) REVERT: C 1178 THR cc_start: 0.8714 (m) cc_final: 0.8284 (p) REVERT: C 1205 TYR cc_start: 0.8072 (m-80) cc_final: 0.7852 (m-80) REVERT: C 1272 ASP cc_start: 0.6737 (p0) cc_final: 0.5748 (t70) REVERT: C 1276 LYS cc_start: 0.8088 (mttt) cc_final: 0.7712 (ttpt) REVERT: C 1278 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8489 (mmt) REVERT: C 1331 MET cc_start: 0.7678 (mtp) cc_final: 0.7477 (mtp) REVERT: C 1362 ASN cc_start: 0.6445 (m-40) cc_final: 0.6062 (p0) REVERT: C 1429 THR cc_start: 0.7494 (p) cc_final: 0.7189 (p) REVERT: C 1470 TYR cc_start: 0.8098 (t80) cc_final: 0.7445 (t80) REVERT: C 1482 ASP cc_start: 0.7100 (m-30) cc_final: 0.6711 (m-30) REVERT: C 1681 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8357 (mt) REVERT: C 1947 LEU cc_start: 0.7489 (mp) cc_final: 0.6981 (tp) REVERT: C 1977 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8120 (p0) REVERT: C 2102 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7870 (mt) REVERT: C 2103 TYR cc_start: 0.7041 (t80) cc_final: 0.6394 (t80) REVERT: C 2115 MET cc_start: 0.6971 (mtp) cc_final: 0.6586 (mtm) REVERT: C 2235 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8416 (tm-30) REVERT: C 2438 LYS cc_start: 0.7190 (pttt) cc_final: 0.6898 (ptmm) REVERT: C 2496 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8196 (mtmm) REVERT: D 49 TYR cc_start: 0.4915 (t80) cc_final: 0.4539 (t80) REVERT: D 209 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6713 (mm-30) REVERT: D 334 TYR cc_start: 0.6596 (m-80) cc_final: 0.6328 (m-10) REVERT: D 701 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6213 (pp30) REVERT: D 725 MET cc_start: 0.7675 (mtp) cc_final: 0.7471 (mtp) REVERT: D 767 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7412 (m170) REVERT: D 785 MET cc_start: 0.7879 (mmm) cc_final: 0.7644 (ttm) REVERT: D 869 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.8041 (t) REVERT: D 908 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7971 (mp0) REVERT: D 1049 MET cc_start: 0.8552 (ppp) cc_final: 0.8053 (ptm) REVERT: D 1264 MET cc_start: 0.8209 (tpp) cc_final: 0.7942 (tpp) REVERT: D 1311 GLU cc_start: 0.7151 (tp30) cc_final: 0.6799 (tp30) REVERT: D 1401 LYS cc_start: 0.7415 (tmtt) cc_final: 0.7206 (tptt) REVERT: D 1419 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6209 (mp10) REVERT: D 1455 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: D 1657 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6973 (t70) REVERT: D 1677 TYR cc_start: 0.8358 (t80) cc_final: 0.7731 (t80) REVERT: D 1791 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 1796 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8175 (tt) REVERT: D 1869 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7179 (mtt90) REVERT: D 1896 LEU cc_start: 0.8048 (mm) cc_final: 0.7738 (mt) REVERT: D 1973 ASN cc_start: 0.8672 (t0) cc_final: 0.8222 (t0) REVERT: D 2068 LEU cc_start: 0.9617 (tp) cc_final: 0.9326 (tt) REVERT: D 2170 ASN cc_start: 0.7863 (m110) cc_final: 0.7592 (m110) REVERT: D 2183 GLU cc_start: 0.7921 (mm-30) cc_final: 0.6963 (mm-30) REVERT: D 2213 LEU cc_start: 0.9355 (tp) cc_final: 0.9112 (tp) REVERT: D 2235 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8430 (tp40) REVERT: D 2311 MET cc_start: 0.8191 (tpp) cc_final: 0.7645 (tpp) REVERT: D 2317 MET cc_start: 0.8867 (ttm) cc_final: 0.8582 (mtp) REVERT: E 73 GLN cc_start: 0.7384 (mp10) cc_final: 0.7108 (mp10) REVERT: E 79 HIS cc_start: 0.5237 (OUTLIER) cc_final: 0.4325 (t-90) REVERT: E 247 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8940 (tp) REVERT: E 314 ILE cc_start: 0.8489 (mp) cc_final: 0.8025 (mm) REVERT: E 705 GLU cc_start: 0.8616 (pm20) cc_final: 0.8203 (mp0) REVERT: E 829 SER cc_start: 0.8726 (p) cc_final: 0.8184 (t) REVERT: E 1079 MET cc_start: 0.7884 (mmt) cc_final: 0.7446 (mmt) REVERT: E 1081 TYR cc_start: 0.6569 (t80) cc_final: 0.6223 (t80) REVERT: E 1141 TRP cc_start: 0.7627 (m100) cc_final: 0.7169 (m100) REVERT: E 1146 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6255 (ttpp) REVERT: E 1245 LEU cc_start: 0.8415 (tp) cc_final: 0.8180 (mt) REVERT: E 1273 MET cc_start: 0.8014 (mmp) cc_final: 0.7664 (mmp) REVERT: E 1729 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.7914 (t0) REVERT: E 1758 MET cc_start: 0.5768 (ptp) cc_final: 0.5489 (mtp) REVERT: E 1833 ASP cc_start: 0.6640 (p0) cc_final: 0.6260 (t0) REVERT: E 1965 GLN cc_start: 0.8376 (tp-100) cc_final: 0.7909 (tp-100) REVERT: E 2188 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7563 (ttm170) REVERT: E 2202 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8201 (tm-30) REVERT: F 400 ASP cc_start: 0.7391 (p0) cc_final: 0.7115 (p0) REVERT: F 706 MET cc_start: 0.8560 (mtp) cc_final: 0.8203 (mtp) REVERT: F 761 VAL cc_start: 0.8786 (t) cc_final: 0.8526 (p) REVERT: F 964 PRO cc_start: 0.8476 (Cg_endo) cc_final: 0.8057 (Cg_exo) REVERT: F 1363 MET cc_start: 0.7257 (tpp) cc_final: 0.6983 (tpp) REVERT: F 1555 PHE cc_start: 0.8369 (m-80) cc_final: 0.8065 (m-80) REVERT: F 1569 GLU cc_start: 0.9105 (tt0) cc_final: 0.8772 (mp0) REVERT: F 2122 TRP cc_start: 0.5550 (OUTLIER) cc_final: 0.4950 (p90) outliers start: 271 outliers final: 218 residues processed: 1446 average time/residue: 0.9303 time to fit residues: 2389.0630 Evaluate side-chains 1419 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1179 time to evaluate : 9.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1024 TYR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1861 ILE Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1148 ASP Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1298 ASN Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1418 ASN Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1790 ASP Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1901 THR Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2140 LEU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2248 GLN Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain B residue 2381 THR Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 961 ILE Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1423 LEU Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1660 TRP Chi-restraints excluded: chain C residue 1681 LEU Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2070 ILE Chi-restraints excluded: chain C residue 2102 LEU Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2496 LYS Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 1013 ILE Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1156 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1214 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1361 HIS Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1465 ASP Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1784 LEU Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2078 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2171 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 HIS Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 895 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1146 LYS Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1349 LEU Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1729 ASP Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1881 MET Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2188 ARG Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain E residue 2503 THR Chi-restraints excluded: chain E residue 2504 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 513 ASP Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 749 THR Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1416 ASP Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2122 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 846 optimal weight: 1.9990 chunk 1363 optimal weight: 8.9990 chunk 832 optimal weight: 0.9990 chunk 647 optimal weight: 5.9990 chunk 948 optimal weight: 0.7980 chunk 1430 optimal weight: 20.0000 chunk 1316 optimal weight: 5.9990 chunk 1139 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 879 optimal weight: 0.0980 chunk 698 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1961 GLN ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1520 GLN ** B2021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 ASN C1090 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 ASN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1361 HIS E1362 ASN ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1724 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 116817 Z= 0.197 Angle : 0.556 12.528 158758 Z= 0.283 Chirality : 0.040 0.251 17523 Planarity : 0.004 0.051 20695 Dihedral : 4.079 34.536 15727 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 2.08 % Allowed : 14.17 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.33 (0.07), residues: 14354 helix: 2.03 (0.07), residues: 5747 sheet: 0.60 (0.10), residues: 2613 loop : -0.05 (0.08), residues: 5994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C1031 HIS 0.012 0.001 HIS A 50 PHE 0.029 0.001 PHE D 937 TYR 0.035 0.001 TYR B1024 ARG 0.012 0.000 ARG E1204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 28708 Ramachandran restraints generated. 14354 Oldfield, 0 Emsley, 14354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1214 time to evaluate : 9.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.7188 (t0) cc_final: 0.6958 (t0) REVERT: A 94 ASN cc_start: 0.7789 (m110) cc_final: 0.7440 (t0) REVERT: A 148 MET cc_start: 0.8168 (ttp) cc_final: 0.7769 (ptm) REVERT: A 594 LEU cc_start: 0.9002 (mt) cc_final: 0.8659 (tp) REVERT: A 658 SER cc_start: 0.8076 (m) cc_final: 0.7796 (p) REVERT: A 1244 THR cc_start: 0.9192 (t) cc_final: 0.8973 (p) REVERT: A 1295 ASP cc_start: 0.6227 (t0) cc_final: 0.5926 (t0) REVERT: A 1403 MET cc_start: 0.7243 (ptp) cc_final: 0.7015 (ptt) REVERT: A 1676 ILE cc_start: 0.9031 (pt) cc_final: 0.8675 (tp) REVERT: A 2055 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8746 (tp) REVERT: A 2077 GLU cc_start: 0.8449 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 2163 TYR cc_start: 0.6172 (m-80) cc_final: 0.5968 (m-80) REVERT: A 2203 LEU cc_start: 0.9567 (mt) cc_final: 0.9142 (tt) REVERT: A 2454 MET cc_start: 0.7646 (tpt) cc_final: 0.7363 (tpt) REVERT: B 75 GLN cc_start: 0.6257 (mt0) cc_final: 0.5316 (tp40) REVERT: B 134 SER cc_start: 0.7431 (t) cc_final: 0.7086 (m) REVERT: B 341 MET cc_start: 0.7563 (pmm) cc_final: 0.7169 (pmm) REVERT: B 496 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 583 LYS cc_start: 0.8964 (tttt) cc_final: 0.8492 (tppt) REVERT: B 654 MET cc_start: 0.8475 (mmt) cc_final: 0.8249 (mmt) REVERT: B 803 MET cc_start: 0.8371 (tmm) cc_final: 0.8165 (tmm) REVERT: B 804 LEU cc_start: 0.8328 (mt) cc_final: 0.8055 (tp) REVERT: B 1146 LYS cc_start: 0.8331 (tttt) cc_final: 0.7818 (mttt) REVERT: B 1200 LEU cc_start: 0.7969 (mt) cc_final: 0.7619 (mt) REVERT: B 1455 ASP cc_start: 0.7424 (t0) cc_final: 0.7080 (t0) REVERT: B 1468 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8053 (mptt) REVERT: B 1663 LEU cc_start: 0.8699 (mp) cc_final: 0.8437 (mt) REVERT: B 1778 LEU cc_start: 0.6436 (tp) cc_final: 0.6155 (tt) REVERT: B 1870 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6719 (mm-40) REVERT: B 1924 VAL cc_start: 0.8034 (p) cc_final: 0.7659 (m) REVERT: B 1993 LYS cc_start: 0.6792 (ttpp) cc_final: 0.6435 (tptp) REVERT: B 2218 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 2248 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 2285 ASN cc_start: 0.8588 (t0) cc_final: 0.8365 (t0) REVERT: B 2311 MET cc_start: 0.7998 (tpt) cc_final: 0.7608 (tpt) REVERT: C 92 TYR cc_start: 0.7969 (t80) cc_final: 0.7675 (t80) REVERT: C 95 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7799 (mm-40) REVERT: C 368 LEU cc_start: 0.8362 (tp) cc_final: 0.8118 (tt) REVERT: C 462 ARG cc_start: 0.8541 (mtt90) cc_final: 0.8161 (mtt90) REVERT: C 632 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7889 (ptp-110) REVERT: C 683 LYS cc_start: 0.8226 (pttt) cc_final: 0.7360 (tptt) REVERT: C 939 ASP cc_start: 0.7560 (m-30) cc_final: 0.7267 (m-30) REVERT: C 1031 TRP cc_start: 0.6600 (t60) cc_final: 0.6364 (t60) REVERT: C 1040 TYR cc_start: 0.7735 (m-80) cc_final: 0.7444 (m-80) REVERT: C 1178 THR cc_start: 0.8745 (m) cc_final: 0.8315 (p) REVERT: C 1205 TYR cc_start: 0.8084 (m-80) cc_final: 0.7857 (m-80) REVERT: C 1272 ASP cc_start: 0.6722 (p0) cc_final: 0.5698 (t70) REVERT: C 1276 LYS cc_start: 0.8127 (mttt) cc_final: 0.7747 (ttpt) REVERT: C 1278 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8426 (mmt) REVERT: C 1362 ASN cc_start: 0.6402 (m-40) cc_final: 0.6008 (p0) REVERT: C 1429 THR cc_start: 0.7495 (p) cc_final: 0.7186 (p) REVERT: C 1470 TYR cc_start: 0.8100 (t80) cc_final: 0.7420 (t80) REVERT: C 1482 ASP cc_start: 0.7017 (m-30) cc_final: 0.6687 (m-30) REVERT: C 1681 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (mt) REVERT: C 1947 LEU cc_start: 0.7523 (mp) cc_final: 0.7045 (tp) REVERT: C 1977 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8112 (p0) REVERT: C 2102 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7848 (mt) REVERT: C 2103 TYR cc_start: 0.7036 (t80) cc_final: 0.6424 (t80) REVERT: C 2115 MET cc_start: 0.7017 (mtp) cc_final: 0.6627 (mtm) REVERT: C 2235 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8427 (tm-30) REVERT: C 2438 LYS cc_start: 0.7115 (pttt) cc_final: 0.6865 (ptmm) REVERT: C 2496 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8245 (mtmm) REVERT: D 49 TYR cc_start: 0.4965 (t80) cc_final: 0.4577 (t80) REVERT: D 209 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6624 (mm-30) REVERT: D 334 TYR cc_start: 0.6639 (m-80) cc_final: 0.6248 (m-10) REVERT: D 341 MET cc_start: 0.7114 (ppp) cc_final: 0.6836 (tmm) REVERT: D 701 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6262 (pp30) REVERT: D 767 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7413 (m170) REVERT: D 869 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.8060 (t) REVERT: D 908 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7964 (mp0) REVERT: D 1002 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6631 (mm-30) REVERT: D 1049 MET cc_start: 0.8559 (ppp) cc_final: 0.8058 (ptm) REVERT: D 1264 MET cc_start: 0.8266 (tpp) cc_final: 0.8048 (tpp) REVERT: D 1311 GLU cc_start: 0.7089 (tp30) cc_final: 0.6748 (tp30) REVERT: D 1419 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6078 (mp10) REVERT: D 1455 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: D 1657 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6755 (t70) REVERT: D 1677 TYR cc_start: 0.8365 (t80) cc_final: 0.7750 (t80) REVERT: D 1796 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8138 (tt) REVERT: D 1869 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7211 (mtt90) REVERT: D 1896 LEU cc_start: 0.7997 (mm) cc_final: 0.7684 (mt) REVERT: D 1973 ASN cc_start: 0.8555 (t0) cc_final: 0.8107 (t0) REVERT: D 2170 ASN cc_start: 0.7867 (m110) cc_final: 0.7375 (m110) REVERT: D 2213 LEU cc_start: 0.9367 (tp) cc_final: 0.9124 (tp) REVERT: D 2235 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8403 (tp40) REVERT: D 2237 GLN cc_start: 0.8080 (pt0) cc_final: 0.7791 (pt0) REVERT: D 2317 MET cc_start: 0.8863 (ttm) cc_final: 0.8564 (mtp) REVERT: E 73 GLN cc_start: 0.7311 (mp10) cc_final: 0.6993 (mp10) REVERT: E 247 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8946 (tp) REVERT: E 314 ILE cc_start: 0.8557 (mp) cc_final: 0.8060 (mm) REVERT: E 690 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6163 (t70) REVERT: E 705 GLU cc_start: 0.8625 (pm20) cc_final: 0.8247 (mp0) REVERT: E 829 SER cc_start: 0.8622 (p) cc_final: 0.8077 (t) REVERT: E 1079 MET cc_start: 0.7919 (mmt) cc_final: 0.7440 (mmt) REVERT: E 1081 TYR cc_start: 0.6551 (t80) cc_final: 0.6205 (t80) REVERT: E 1141 TRP cc_start: 0.7579 (m100) cc_final: 0.7075 (m100) REVERT: E 1245 LEU cc_start: 0.8414 (tp) cc_final: 0.8133 (mt) REVERT: E 1729 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.7969 (t0) REVERT: E 1758 MET cc_start: 0.5950 (ptp) cc_final: 0.5516 (mtp) REVERT: E 1833 ASP cc_start: 0.6662 (p0) cc_final: 0.6413 (t0) REVERT: E 1965 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7905 (tp-100) REVERT: E 2029 MET cc_start: 0.8406 (tpp) cc_final: 0.8123 (tpp) REVERT: E 2188 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7532 (ttm170) REVERT: E 2202 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8196 (tm-30) REVERT: F 400 ASP cc_start: 0.7482 (p0) cc_final: 0.7203 (p0) REVERT: F 706 MET cc_start: 0.8576 (mtp) cc_final: 0.8228 (mtp) REVERT: F 761 VAL cc_start: 0.8785 (t) cc_final: 0.8520 (p) REVERT: F 964 PRO cc_start: 0.8498 (Cg_endo) cc_final: 0.8069 (Cg_exo) REVERT: F 1363 MET cc_start: 0.7408 (tpp) cc_final: 0.7140 (tpp) REVERT: F 1555 PHE cc_start: 0.8359 (m-80) cc_final: 0.8065 (m-80) REVERT: F 1569 GLU cc_start: 0.9106 (tt0) cc_final: 0.8781 (mp0) REVERT: F 2122 TRP cc_start: 0.5608 (OUTLIER) cc_final: 0.5070 (p90) outliers start: 257 outliers final: 220 residues processed: 1392 average time/residue: 0.9195 time to fit residues: 2278.1774 Evaluate side-chains 1406 residues out of total 12331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1165 time to evaluate : 9.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 ASP Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1362 ASN Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1619 THR Chi-restraints excluded: chain A residue 1629 THR Chi-restraints excluded: chain A residue 1657 ASP Chi-restraints excluded: chain A residue 1702 ASP Chi-restraints excluded: chain A residue 1766 LEU Chi-restraints excluded: chain A residue 1807 VAL Chi-restraints excluded: chain A residue 1861 ILE Chi-restraints excluded: chain A residue 1912 ASP Chi-restraints excluded: chain A residue 1977 ASP Chi-restraints excluded: chain A residue 1995 LEU Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2184 THR Chi-restraints excluded: chain A residue 2308 GLU Chi-restraints excluded: chain A residue 2441 LEU Chi-restraints excluded: chain A residue 2452 HIS Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 690 HIS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 844 ASN Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 912 TYR Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1024 TYR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1229 ASN Chi-restraints excluded: chain B residue 1246 LEU Chi-restraints excluded: chain B residue 1298 ASN Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1357 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1473 MET Chi-restraints excluded: chain B residue 1545 ILE Chi-restraints excluded: chain B residue 1685 ASN Chi-restraints excluded: chain B residue 1687 ASN Chi-restraints excluded: chain B residue 1689 THR Chi-restraints excluded: chain B residue 1790 ASP Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1825 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1901 THR Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 1996 LEU Chi-restraints excluded: chain B residue 2140 LEU Chi-restraints excluded: chain B residue 2141 VAL Chi-restraints excluded: chain B residue 2226 SER Chi-restraints excluded: chain B residue 2248 GLN Chi-restraints excluded: chain B residue 2310 LEU Chi-restraints excluded: chain B residue 2381 THR Chi-restraints excluded: chain B residue 2501 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 790 THR Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1114 SER Chi-restraints excluded: chain C residue 1254 ASP Chi-restraints excluded: chain C residue 1278 MET Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1423 LEU Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1622 ASP Chi-restraints excluded: chain C residue 1660 TRP Chi-restraints excluded: chain C residue 1681 LEU Chi-restraints excluded: chain C residue 1696 ASP Chi-restraints excluded: chain C residue 1734 THR Chi-restraints excluded: chain C residue 1881 MET Chi-restraints excluded: chain C residue 1889 LEU Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2038 SER Chi-restraints excluded: chain C residue 2063 LEU Chi-restraints excluded: chain C residue 2070 ILE Chi-restraints excluded: chain C residue 2102 LEU Chi-restraints excluded: chain C residue 2126 THR Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2140 LEU Chi-restraints excluded: chain C residue 2178 LYS Chi-restraints excluded: chain C residue 2496 LYS Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 869 SER Chi-restraints excluded: chain D residue 1013 ILE Chi-restraints excluded: chain D residue 1048 THR Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1083 THR Chi-restraints excluded: chain D residue 1156 SER Chi-restraints excluded: chain D residue 1170 LEU Chi-restraints excluded: chain D residue 1208 THR Chi-restraints excluded: chain D residue 1214 THR Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1428 THR Chi-restraints excluded: chain D residue 1455 ASP Chi-restraints excluded: chain D residue 1465 ASP Chi-restraints excluded: chain D residue 1522 SER Chi-restraints excluded: chain D residue 1526 ASP Chi-restraints excluded: chain D residue 1607 THR Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1748 ASN Chi-restraints excluded: chain D residue 1784 LEU Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1962 THR Chi-restraints excluded: chain D residue 1976 ILE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2078 LEU Chi-restraints excluded: chain D residue 2094 SER Chi-restraints excluded: chain D residue 2108 ASN Chi-restraints excluded: chain D residue 2126 THR Chi-restraints excluded: chain D residue 2171 VAL Chi-restraints excluded: chain D residue 2230 GLN Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2429 VAL Chi-restraints excluded: chain E residue 79 HIS Chi-restraints excluded: chain E residue 102 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 407 GLU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 606 ASP Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 690 HIS Chi-restraints excluded: chain E residue 699 THR Chi-restraints excluded: chain E residue 702 LEU Chi-restraints excluded: chain E residue 704 SER Chi-restraints excluded: chain E residue 895 SER Chi-restraints excluded: chain E residue 934 LEU Chi-restraints excluded: chain E residue 1004 VAL Chi-restraints excluded: chain E residue 1051 ILE Chi-restraints excluded: chain E residue 1084 SER Chi-restraints excluded: chain E residue 1146 LYS Chi-restraints excluded: chain E residue 1203 ILE Chi-restraints excluded: chain E residue 1269 ILE Chi-restraints excluded: chain E residue 1349 LEU Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1444 SER Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1498 VAL Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1729 ASP Chi-restraints excluded: chain E residue 1808 HIS Chi-restraints excluded: chain E residue 1838 ASP Chi-restraints excluded: chain E residue 1881 MET Chi-restraints excluded: chain E residue 1924 VAL Chi-restraints excluded: chain E residue 1995 LEU Chi-restraints excluded: chain E residue 2140 LEU Chi-restraints excluded: chain E residue 2141 VAL Chi-restraints excluded: chain E residue 2188 ARG Chi-restraints excluded: chain E residue 2452 HIS Chi-restraints excluded: chain E residue 2503 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 513 ASP Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 749 THR Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 1002 VAL Chi-restraints excluded: chain F residue 1148 LEU Chi-restraints excluded: chain F residue 1344 VAL Chi-restraints excluded: chain F residue 1416 ASP Chi-restraints excluded: chain F residue 1515 ASN Chi-restraints excluded: chain F residue 1579 LEU Chi-restraints excluded: chain F residue 1956 VAL Chi-restraints excluded: chain F residue 2122 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1436 random chunks: chunk 904 optimal weight: 7.9990 chunk 1213 optimal weight: 0.4980 chunk 348 optimal weight: 1.9990 chunk 1050 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 316 optimal weight: 0.8980 chunk 1141 optimal weight: 0.6980 chunk 477 optimal weight: 8.9990 chunk 1171 optimal weight: 0.0670 chunk 144 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1253 GLN ** A1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 HIS ** A1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 GLN B1003 ASN ** B1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 ASN C1090 ASN C1449 ASN ** C1591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1334 ASN ** D1813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2173 ASN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2479 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 ASN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1361 HIS E1362 ASN ** E1885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS ** F 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.086747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073340 restraints weight = 407067.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075132 restraints weight = 212469.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.076273 restraints weight = 132902.488| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 116817 Z= 0.157 Angle : 0.544 12.796 158758 Z= 0.275 Chirality : 0.040 0.220 17523 Planarity : 0.003 0.052 20695 Dihedral : 3.984 33.185 15727 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 1.95 % Allowed : 14.47 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: 1.38 (0.07), residues: 14354 helix: 2.08 (0.07), residues: 5759 sheet: 0.61 (0.11), residues: 2613 loop : -0.03 (0.08), residues: 5982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 546 HIS 0.013 0.001 HIS B 642 PHE 0.030 0.001 PHE D1472 TYR 0.036 0.001 TYR A2163 ARG 0.010 0.000 ARG E1204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39528.99 seconds wall clock time: 686 minutes 22.58 seconds (41182.58 seconds total)