Starting phenix.real_space_refine on Tue Feb 13 10:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/02_2024/6sue_10312.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/02_2024/6sue_10312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/02_2024/6sue_10312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/02_2024/6sue_10312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/02_2024/6sue_10312.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/02_2024/6sue_10312.pdb" } resolution = 3.4 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 332 5.16 5 C 68483 2.51 5 N 18479 2.21 5 O 20976 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 TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1050": "NH1" <-> "NH2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1173": "OE1" <-> "OE2" Residue "A TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1294": "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 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1602": "NH1" <-> "NH2" Residue "A GLU 1634": "OE1" <-> "OE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1696": "OD1" <-> "OD2" Residue "A TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1768": "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 1805": "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 TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2251": "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 2377": "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 "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 TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "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 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 555": "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 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1046": "OD1" <-> "OD2" Residue "B ARG 1050": "NH1" <-> "NH2" Residue "B PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1634": "OE1" <-> "OE2" Residue "B PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1703": "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 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2277": "OE1" <-> "OE2" Residue "B PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2377": "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 PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 842": "OD1" <-> "OD2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1050": "NH1" <-> "NH2" Residue "C PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1143": "OE1" <-> "OE2" Residue "C TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "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 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1508": "OE1" <-> "OE2" Residue "C GLU 1527": "OE1" <-> "OE2" Residue "C TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1602": "NH1" <-> "NH2" Residue "C PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1805": "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 TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2257": "NH1" <-> "NH2" 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 2393": "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 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 448": "NH1" <-> "NH2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 614": "OE1" <-> "OE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1050": "NH1" <-> "NH2" Residue "D PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1176": "OE1" <-> "OE2" Residue "D TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1602": "NH1" <-> "NH2" Residue "D PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1708": "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 1814": "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 TYR 1968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2099": "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 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2377": "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 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 390": "OE1" <-> "OE2" Residue "E PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 448": "NH1" <-> "NH2" 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 PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1311": "OE1" <-> "OE2" 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 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1711": "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 1805": "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 TYR 1959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2099": "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 2377": "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 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" 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 PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 286": "NH1" <-> "NH2" 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 ARG 306": "NH1" <-> "NH2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 572": "OE1" <-> "OE2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1010": "NH1" <-> "NH2" Residue "F ASP 1033": "OD1" <-> "OD2" Residue "F GLU 1045": "OE1" <-> "OE2" Residue "F PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1076": "OE1" <-> "OE2" Residue "F TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1178": "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 TYR 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1779": "OE1" <-> "OE2" Residue "F PHE 1822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2117": "NH1" <-> "NH2" Residue "F TYR 2118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 108270 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 18197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2292, 18197 Classifications: {'peptide': 2292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 2211} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 18197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2292, 18197 Classifications: {'peptide': 2292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 2211} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 18197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2292, 18197 Classifications: {'peptide': 2292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 2211} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 18197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2292, 18197 Classifications: {'peptide': 2292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 2211} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 18197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2292, 18197 Classifications: {'peptide': 2292} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 2211} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 17285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2168, 17285 Classifications: {'peptide': 2168} Link IDs: {'PTRANS': 117, 'TRANS': 2050} Chain breaks: 2 Time building chain proxies: 38.41, per 1000 atoms: 0.35 Number of scatterers: 108270 At special positions: 0 Unit cell: (235.32, 225.33, 364.08, 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 332 16.00 O 20976 8.00 N 18479 7.00 C 68483 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: 29.11 Conformation dependent library (CDL) restraints added in 13.9 seconds 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25742 Finding SS restraints... Secondary structure from input PDB file: 507 helices and 0 sheets defined 44.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.44 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 162 through 176 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.926A pdb=" N ASN A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 268 removed outlier: 3.559A pdb=" N LYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.905A pdb=" N ARG A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 453 through 463 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.534A pdb=" N PHE A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) 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 611 removed outlier: 3.618A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) 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 681 Processing helix chain 'A' and resid 687 through 700 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 Processing helix chain 'A' and resid 726 through 733 removed outlier: 4.032A pdb=" N PHE A 730 " --> pdb=" O THR A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 747 through 770 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 814 Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 842 through 856 Processing helix chain 'A' and resid 870 through 887 Processing helix chain 'A' and resid 891 through 897 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 removed outlier: 3.787A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN A 994 " --> pdb=" O ILE A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1040 through 1044 Processing helix chain 'A' and resid 1054 through 1065 Processing helix chain 'A' and resid 1070 through 1090 removed outlier: 4.100A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN A1090 " --> pdb=" O GLU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1137 through 1141 removed outlier: 3.607A pdb=" N TRP A1141 " --> pdb=" O ALA A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1157 removed outlier: 4.098A pdb=" N SER A1156 " --> pdb=" O PRO A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1279 through 1290 removed outlier: 3.976A pdb=" N VAL A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1378 Processing helix chain 'A' and resid 1494 through 1497 Processing helix chain 'A' and resid 1513 through 1517 Processing helix chain 'A' and resid 1540 through 1542 No H-bonds generated for 'chain 'A' and resid 1540 through 1542' Processing helix chain 'A' and resid 1609 through 1618 removed outlier: 3.570A pdb=" N THR A1618 " --> pdb=" O VAL A1614 " (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 1729 through 1731 No H-bonds generated for 'chain 'A' and resid 1729 through 1731' 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 1797 Processing helix chain 'A' and resid 1818 through 1823 Processing helix chain 'A' and resid 1836 through 1841 Processing helix chain 'A' and resid 1845 through 1869 Processing helix chain 'A' and resid 1872 through 1891 Processing helix chain 'A' and resid 1906 through 1911 Processing helix chain 'A' and resid 1953 through 1972 removed outlier: 4.062A pdb=" N TYR A1959 " --> pdb=" O VAL A1955 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP A1960 " --> pdb=" O MET A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1991 through 2003 Processing helix chain 'A' and resid 2018 through 2105 removed outlier: 3.977A pdb=" N LEU A2065 " --> pdb=" O ALA A2061 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2145 Proline residue: A2142 - end of helix Processing helix chain 'A' and resid 2154 through 2244 removed outlier: 4.303A pdb=" N ALA A2160 " --> pdb=" O ALA A2156 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN A2170 " --> pdb=" O GLU A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2284 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 4.158A pdb=" N TRP A2297 " --> pdb=" O PRO A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2304 removed outlier: 3.893A pdb=" N ALA A2302 " --> pdb=" O GLY A2299 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2325 Processing helix chain 'A' and resid 2337 through 2342 Processing helix chain 'A' and resid 2343 through 2344 No H-bonds generated for 'chain 'A' and resid 2343 through 2344' 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 2490 through 2494 Processing helix chain 'A' and resid 2499 through 2504 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.617A pdb=" N MET B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 201 through 211 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: 3.677A pdb=" N LEU B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' 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 removed outlier: 4.311A pdb=" N ARG B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 432 through 435 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 471 through 488 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 513 through 520 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 602 through 613 removed outlier: 4.015A pdb=" N ASP B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 623 through 645 removed outlier: 3.983A pdb=" N SER B 639 " --> pdb=" O ASN B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 Processing helix chain 'B' and resid 664 through 678 removed outlier: 4.970A pdb=" N LEU B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 4.456A pdb=" N ALA B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'B' and resid 726 through 733 Processing helix chain 'B' and resid 747 through 770 removed outlier: 3.693A pdb=" N VAL B 753 " --> pdb=" O GLN B 749 " (cutoff:3.500A) 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 815 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 833 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 891 through 899 removed outlier: 3.613A pdb=" N ALA B 896 " --> pdb=" O GLN B 892 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B 897 " --> pdb=" O GLY B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 924 Processing helix chain 'B' and resid 927 through 954 removed outlier: 4.836A pdb=" N THR B 933 " --> pdb=" O GLN B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 984 through 1002 Processing helix chain 'B' and resid 1009 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1027 through 1040 Processing helix chain 'B' and resid 1041 through 1044 Processing helix chain 'B' and resid 1054 through 1065 Processing helix chain 'B' and resid 1070 through 1090 removed outlier: 3.988A pdb=" N VAL B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN B1090 " --> pdb=" O GLU B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1131 No H-bonds generated for 'chain 'B' and resid 1129 through 1131' Processing helix chain 'B' and resid 1153 through 1157 removed outlier: 4.179A pdb=" N SER B1156 " --> pdb=" O PRO B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1223 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1279 through 1290 removed outlier: 3.650A pdb=" N VAL B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1378 Processing helix chain 'B' and resid 1513 through 1517 removed outlier: 3.682A pdb=" N VAL B1517 " --> pdb=" O ALA B1513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1513 through 1517' Processing helix chain 'B' and resid 1609 through 1618 Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1627 through 1632 Processing helix chain 'B' and resid 1729 through 1731 No H-bonds generated for 'chain 'B' and resid 1729 through 1731' Processing helix chain 'B' and resid 1764 through 1773 removed outlier: 3.834A pdb=" N PHE B1768 " --> pdb=" O ASN B1764 " (cutoff:3.500A) 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 1823 Processing helix chain 'B' and resid 1836 through 1844 removed outlier: 4.354A pdb=" N GLN B1842 " --> pdb=" O ASP B1838 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B1843 " --> pdb=" O ALA B1839 " (cutoff:3.500A) Processing helix chain 'B' and resid 1845 through 1869 Processing helix chain 'B' and resid 1872 through 1891 Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1953 through 1972 removed outlier: 4.033A pdb=" N TYR B1959 " --> pdb=" O VAL B1955 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP B1960 " --> pdb=" O MET B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 1991 through 2004 Processing helix chain 'B' and resid 2018 through 2105 Processing helix chain 'B' and resid 2108 through 2145 Proline residue: B2142 - end of helix Processing helix chain 'B' and resid 2150 through 2154 Processing helix chain 'B' and resid 2155 through 2163 Processing helix chain 'B' and resid 2167 through 2244 removed outlier: 4.259A pdb=" N ASP B2207 " --> pdb=" O LEU B2203 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2284 Processing helix chain 'B' and resid 2293 through 2297 removed outlier: 3.859A pdb=" N ALA B2296 " --> pdb=" O LYS B2293 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TRP B2297 " --> pdb=" O PRO B2294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2293 through 2297' Processing helix chain 'B' and resid 2299 through 2304 removed outlier: 3.939A pdb=" N ALA B2302 " --> pdb=" O GLY B2299 " (cutoff:3.500A) Processing helix chain 'B' and resid 2305 through 2324 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 2394 through 2396 No H-bonds generated for 'chain 'B' and resid 2394 through 2396' Processing helix chain 'B' and resid 2398 through 2402 Processing helix chain 'B' and resid 2403 through 2407 Processing helix chain 'B' and resid 2495 through 2504 removed outlier: 4.153A pdb=" N THR B2499 " --> pdb=" O LYS B2496 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B2501 " --> pdb=" O ALA B2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.666A pdb=" N GLU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 162 through 176 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 201 through 214 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: 3.552A pdb=" N LEU C 236 " --> pdb=" O HIS C 232 " (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 287 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 432 through 435 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 453 through 465 Processing helix chain 'C' and resid 471 through 488 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 545 through 556 removed outlier: 4.127A pdb=" N THR C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 3.544A pdb=" N ILE C 568 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 598 Processing helix chain 'C' and resid 601 through 612 removed outlier: 3.721A pdb=" N LEU C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 644 Processing helix chain 'C' and resid 647 through 655 Processing helix chain 'C' and resid 664 through 679 removed outlier: 4.507A pdb=" N LEU C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 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 747 through 770 removed outlier: 3.711A pdb=" N VAL C 753 " --> pdb=" O GLN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 removed outlier: 3.561A pdb=" N ARG C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 780 " --> pdb=" O PHE C 776 " (cutoff:3.500A) 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 833 through 839 Processing helix chain 'C' and resid 842 through 856 Processing helix chain 'C' and resid 863 through 867 Processing helix chain 'C' and resid 870 through 888 removed outlier: 5.912A pdb=" N THR C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 899 removed outlier: 3.993A pdb=" N LEU C 897 " --> pdb=" O GLY C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 924 removed outlier: 3.679A pdb=" N ALA C 924 " --> pdb=" O GLY C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 954 Processing helix chain 'C' and resid 963 through 971 Processing helix chain 'C' and resid 984 through 1002 removed outlier: 3.929A pdb=" N ALA C 991 " --> pdb=" O ALA C 987 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLN C 994 " --> pdb=" O ILE C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 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 1065 Processing helix chain 'C' and resid 1070 through 1090 removed outlier: 3.915A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C1090 " --> pdb=" O GLU C1086 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1131 No H-bonds generated for 'chain 'C' and resid 1129 through 1131' Processing helix chain 'C' and resid 1217 through 1223 Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1279 through 1291 removed outlier: 4.644A pdb=" N VAL C1285 " --> pdb=" O GLU C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1378 Processing helix chain 'C' and resid 1513 through 1517 Processing helix chain 'C' and resid 1540 through 1542 No H-bonds generated for 'chain 'C' and resid 1540 through 1542' Processing helix chain 'C' and resid 1609 through 1618 Processing helix chain 'C' and resid 1620 through 1625 removed outlier: 3.608A pdb=" N ILE C1624 " --> pdb=" O GLY C1620 " (cutoff:3.500A) Processing helix chain 'C' and resid 1626 through 1630 Processing helix chain 'C' and resid 1729 through 1731 No H-bonds generated for 'chain 'C' and resid 1729 through 1731' Processing helix chain 'C' and resid 1764 through 1773 removed outlier: 3.913A pdb=" N PHE C1768 " --> pdb=" O ASN C1764 " (cutoff:3.500A) Processing helix chain 'C' and resid 1773 through 1786 Processing helix chain 'C' and resid 1788 through 1797 Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1836 through 1844 removed outlier: 4.481A pdb=" N GLN C1842 " --> pdb=" O ASP C1838 " (cutoff:3.500A) Processing helix chain 'C' and resid 1845 through 1869 Processing helix chain 'C' and resid 1872 through 1891 Processing helix chain 'C' and resid 1953 through 1972 removed outlier: 4.056A pdb=" N TYR C1959 " --> pdb=" O VAL C1955 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP C1960 " --> pdb=" O MET C1956 " (cutoff:3.500A) Processing helix chain 'C' and resid 1991 through 2003 Processing helix chain 'C' and resid 2018 through 2105 removed outlier: 3.576A pdb=" N GLN C2035 " --> pdb=" O SER C2031 " (cutoff:3.500A) Processing helix chain 'C' and resid 2108 through 2145 Proline residue: C2142 - end of helix Processing helix chain 'C' and resid 2149 through 2154 Processing helix chain 'C' and resid 2154 through 2167 Processing helix chain 'C' and resid 2167 through 2244 Processing helix chain 'C' and resid 2247 through 2284 Processing helix chain 'C' and resid 2293 through 2297 removed outlier: 3.980A pdb=" N TRP C2297 " --> pdb=" O PRO C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2299 through 2304 removed outlier: 3.939A pdb=" N ALA C2302 " --> pdb=" O GLY C2299 " (cutoff:3.500A) 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 2396 No H-bonds generated for 'chain 'C' and resid 2394 through 2396' Processing helix chain 'C' and resid 2398 through 2402 Processing helix chain 'C' and resid 2403 through 2407 Processing helix chain 'C' and resid 2490 through 2494 Processing helix chain 'C' and resid 2497 through 2502 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 162 through 176 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 241 removed outlier: 3.612A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 259 through 268 Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.502A pdb=" N LEU D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 432 through 435 Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 453 through 463 Processing helix chain 'D' and resid 471 through 488 Processing helix chain 'D' and resid 491 through 498 Processing helix chain 'D' and resid 513 through 520 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 612 removed outlier: 4.268A pdb=" N ILE D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) 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 655 Processing helix chain 'D' and resid 664 through 678 removed outlier: 5.771A pdb=" N LEU D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 671 " --> pdb=" O ILE D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 Processing helix chain 'D' and resid 692 through 700 removed outlier: 4.370A pdb=" N ALA D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 699 " --> pdb=" O TYR D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 719 Processing helix chain 'D' and resid 726 through 735 Processing helix chain 'D' and resid 747 through 770 removed outlier: 3.599A pdb=" N HIS D 751 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 782 removed outlier: 3.981A pdb=" N VAL D 780 " --> pdb=" O PHE D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 787 Processing helix chain 'D' and resid 797 through 813 Processing helix chain 'D' and resid 814 through 816 No H-bonds generated for 'chain 'D' and resid 814 through 816' Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 833 through 839 Processing helix chain 'D' and resid 842 through 854 Processing helix chain 'D' and resid 863 through 867 Processing helix chain 'D' and resid 870 through 888 Processing helix chain 'D' and resid 891 through 899 Processing helix chain 'D' and resid 911 through 923 Processing helix chain 'D' and resid 924 through 926 No H-bonds generated for 'chain 'D' and resid 924 through 926' 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 removed outlier: 3.939A pdb=" N ALA D 991 " --> pdb=" O ALA D 987 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN D 994 " --> pdb=" O ILE D 990 " (cutoff:3.500A) 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 1065 Processing helix chain 'D' and resid 1070 through 1090 removed outlier: 3.876A pdb=" N GLN D1087 " --> pdb=" O THR D1083 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN D1090 " --> pdb=" O GLU D1086 " (cutoff:3.500A) 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 1217 through 1224 removed outlier: 3.723A pdb=" N LEU D1224 " --> pdb=" O LYS D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1279 through 1291 removed outlier: 4.042A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1366 through 1379 Processing helix chain 'D' and resid 1494 through 1497 Processing helix chain 'D' and resid 1513 through 1517 Processing helix chain 'D' and resid 1540 through 1542 No H-bonds generated for 'chain 'D' and resid 1540 through 1542' Processing helix chain 'D' and resid 1609 through 1618 Processing helix chain 'D' and resid 1620 through 1625 Processing helix chain 'D' and resid 1627 through 1631 Processing helix chain 'D' and resid 1729 through 1731 No H-bonds generated for 'chain 'D' and resid 1729 through 1731' 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 1797 Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1836 through 1844 removed outlier: 3.961A pdb=" N GLN D1842 " --> pdb=" O ASP D1838 " (cutoff:3.500A) Processing helix chain 'D' and resid 1845 through 1869 Processing helix chain 'D' and resid 1872 through 1891 Processing helix chain 'D' and resid 1906 through 1911 Processing helix chain 'D' and resid 1953 through 1972 removed outlier: 4.063A pdb=" N TYR D1959 " --> pdb=" O VAL D1955 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP D1960 " --> pdb=" O MET D1956 " (cutoff:3.500A) Processing helix chain 'D' and resid 1991 through 2003 Processing helix chain 'D' and resid 2018 through 2105 Processing helix chain 'D' and resid 2108 through 2139 Processing helix chain 'D' and resid 2140 through 2145 Processing helix chain 'D' and resid 2150 through 2154 Processing helix chain 'D' and resid 2155 through 2167 Processing helix chain 'D' and resid 2167 through 2242 Processing helix chain 'D' and resid 2247 through 2284 Processing helix chain 'D' and resid 2293 through 2297 removed outlier: 3.993A pdb=" N ALA D2296 " --> pdb=" O LYS D2293 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP D2297 " --> pdb=" O PRO D2294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2293 through 2297' Processing helix chain 'D' and resid 2299 through 2304 removed outlier: 4.392A pdb=" N GLY D2303 " --> pdb=" O THR D2300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2305 through 2325 Processing helix chain 'D' and resid 2337 through 2342 Processing helix chain 'D' and resid 2343 through 2344 No H-bonds generated for 'chain 'D' and resid 2343 through 2344' Processing helix chain 'D' and resid 2345 through 2349 Processing helix chain 'D' and resid 2352 through 2363 Processing helix chain 'D' and resid 2394 through 2396 No H-bonds generated for 'chain 'D' and resid 2394 through 2396' Processing helix chain 'D' and resid 2398 through 2402 Processing helix chain 'D' and resid 2403 through 2407 Processing helix chain 'D' and resid 2499 through 2504 Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.722A pdb=" N GLU E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 162 through 176 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.779A pdb=" N GLN E 212 " --> pdb=" O ARG E 208 " (cutoff:3.500A) 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: 3.584A pdb=" N LEU E 236 " --> pdb=" O HIS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing helix chain 'E' and resid 259 through 268 Processing helix chain 'E' and resid 272 through 277 removed outlier: 3.507A pdb=" N LEU E 276 " --> pdb=" O GLU E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 287 Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 432 through 435 Processing helix chain 'E' and resid 437 through 450 Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'E' and resid 471 through 488 Processing helix chain 'E' and resid 491 through 498 Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 545 through 556 removed outlier: 3.588A pdb=" N THR E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 597 Processing helix chain 'E' and resid 602 through 613 removed outlier: 4.179A pdb=" N ASP E 606 " --> pdb=" O ILE E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 645 removed outlier: 3.965A pdb=" N SER E 639 " --> pdb=" O ASN E 635 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TRP E 640 " --> pdb=" O THR E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 655 Processing helix chain 'E' and resid 664 through 678 removed outlier: 5.163A pdb=" N LEU E 670 " --> pdb=" O GLU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 700 Proline residue: E 694 - end of helix removed outlier: 4.256A pdb=" N ALA E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 719 Processing helix chain 'E' and resid 726 through 738 Processing helix chain 'E' and resid 747 through 770 Processing helix chain 'E' and resid 772 through 782 removed outlier: 4.017A pdb=" N VAL E 780 " --> pdb=" O PHE E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 787 Processing helix chain 'E' and resid 797 through 815 Processing helix chain 'E' and resid 817 through 827 Processing helix chain 'E' and resid 834 through 839 Processing helix chain 'E' and resid 842 through 855 Processing helix chain 'E' and resid 863 through 867 Processing helix chain 'E' and resid 870 through 888 Processing helix chain 'E' and resid 891 through 899 removed outlier: 4.145A pdb=" N LEU E 897 " --> pdb=" O GLY E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 923 Processing helix chain 'E' and resid 924 through 926 No H-bonds generated for 'chain 'E' and resid 924 through 926' 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 removed outlier: 3.779A pdb=" N ALA E 991 " --> pdb=" O ALA E 987 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN E 994 " --> pdb=" O ILE E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1014 Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1027 through 1040 Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1066 removed outlier: 3.659A pdb=" N GLN E1066 " --> pdb=" O GLN E1062 " (cutoff:3.500A) Processing helix chain 'E' and resid 1070 through 1086 Processing helix chain 'E' and resid 1129 through 1131 No H-bonds generated for 'chain 'E' and resid 1129 through 1131' Processing helix chain 'E' and resid 1137 through 1141 removed outlier: 3.534A pdb=" N TRP E1141 " --> pdb=" O ALA E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1223 Processing helix chain 'E' and resid 1255 through 1260 Processing helix chain 'E' and resid 1279 through 1289 removed outlier: 4.257A pdb=" N VAL E1285 " --> pdb=" O GLU E1281 " (cutoff:3.500A) Processing helix chain 'E' and resid 1366 through 1378 Processing helix chain 'E' and resid 1513 through 1517 Processing helix chain 'E' and resid 1609 through 1618 Processing helix chain 'E' and resid 1620 through 1625 Processing helix chain 'E' and resid 1626 through 1631 Processing helix chain 'E' and resid 1729 through 1731 No H-bonds generated for 'chain 'E' and resid 1729 through 1731' Processing helix chain 'E' and resid 1764 through 1773 removed outlier: 3.810A pdb=" N PHE E1768 " --> pdb=" O ASN E1764 " (cutoff:3.500A) Processing helix chain 'E' and resid 1773 through 1786 Processing helix chain 'E' and resid 1788 through 1797 Processing helix chain 'E' and resid 1818 through 1823 Processing helix chain 'E' and resid 1836 through 1844 removed outlier: 4.016A pdb=" N GLN E1842 " --> pdb=" O ASP E1838 " (cutoff:3.500A) Processing helix chain 'E' and resid 1845 through 1869 Processing helix chain 'E' and resid 1872 through 1891 Processing helix chain 'E' and resid 1906 through 1911 Processing helix chain 'E' and resid 1953 through 1972 removed outlier: 4.001A pdb=" N TYR E1959 " --> pdb=" O VAL E1955 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TRP E1960 " --> pdb=" O MET E1956 " (cutoff:3.500A) Processing helix chain 'E' and resid 1991 through 2004 Processing helix chain 'E' and resid 2005 through 2007 No H-bonds generated for 'chain 'E' and resid 2005 through 2007' Processing helix chain 'E' and resid 2018 through 2105 removed outlier: 3.631A pdb=" N ARG E2046 " --> pdb=" O ASN E2042 " (cutoff:3.500A) Processing helix chain 'E' and resid 2108 through 2138 Processing helix chain 'E' and resid 2140 through 2147 Processing helix chain 'E' and resid 2150 through 2154 Processing helix chain 'E' and resid 2155 through 2167 Processing helix chain 'E' and resid 2167 through 2244 Processing helix chain 'E' and resid 2247 through 2284 Processing helix chain 'E' and resid 2293 through 2297 removed outlier: 4.147A pdb=" N TRP E2297 " --> pdb=" O PRO E2294 " (cutoff:3.500A) Processing helix chain 'E' and resid 2299 through 2304 removed outlier: 3.949A pdb=" N ALA E2302 " --> pdb=" O GLY E2299 " (cutoff:3.500A) Processing helix chain 'E' and resid 2305 through 2325 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 2363 Processing helix chain 'E' and resid 2394 through 2396 No H-bonds generated for 'chain 'E' and resid 2394 through 2396' Processing helix chain 'E' and resid 2398 through 2402 Processing helix chain 'E' and resid 2403 through 2407 Processing helix chain 'E' and resid 2499 through 2504 Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 213 through 219 Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.501A pdb=" N SER F 249 " --> pdb=" O LEU F 246 " (cutoff:3.500A) 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 495 through 498 Processing helix chain 'F' and resid 601 through 605 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 730 Processing helix chain 'F' and resid 817 through 824 removed outlier: 3.997A pdb=" N SER F 822 " --> pdb=" O ASN F 819 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 864 Processing helix chain 'F' and resid 972 through 976 removed outlier: 3.571A pdb=" N TYR F 976 " --> pdb=" O ALA F 973 " (cutoff:3.500A) Processing helix chain 'F' and resid 977 through 982 removed outlier: 3.894A pdb=" N GLN F 982 " --> pdb=" O GLN F 979 " (cutoff:3.500A) Processing helix chain 'F' and resid 1017 through 1021 Processing helix chain 'F' and resid 1027 through 1032 Processing helix chain 'F' and resid 1082 through 1089 Processing helix chain 'F' and resid 1093 through 1104 Processing helix chain 'F' and resid 1202 through 1204 No H-bonds generated for 'chain 'F' and resid 1202 through 1204' Processing helix chain 'F' and resid 1256 through 1260 removed outlier: 4.313A pdb=" N TRP F1259 " --> pdb=" O PRO F1256 " (cutoff:3.500A) Processing helix chain 'F' and resid 1264 through 1272 Processing helix chain 'F' and resid 1274 through 1282 removed outlier: 4.006A pdb=" N LYS F1278 " --> pdb=" O GLN F1274 " (cutoff:3.500A) Processing helix chain 'F' and resid 1292 through 1302 Processing helix chain 'F' and resid 1306 through 1314 removed outlier: 3.697A pdb=" N SER F1311 " --> pdb=" O GLN F1308 " (cutoff:3.500A) Processing helix chain 'F' and resid 1414 through 1422 removed outlier: 3.719A pdb=" N GLN F1420 " --> pdb=" O ASP F1416 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F1421 " --> pdb=" O SER F1417 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS F1422 " --> pdb=" O ALA F1418 " (cutoff:3.500A) Processing helix chain 'F' and resid 1465 through 1470 removed outlier: 4.133A pdb=" N LYS F1470 " --> pdb=" O ALA F1467 " (cutoff:3.500A) Processing helix chain 'F' and resid 1484 through 1489 Processing helix chain 'F' and resid 1538 through 1548 Processing helix chain 'F' and resid 1635 through 1640 Processing helix chain 'F' and resid 1688 through 1693 Processing helix chain 'F' and resid 1694 through 1696 No H-bonds generated for 'chain 'F' and resid 1694 through 1696' Processing helix chain 'F' and resid 1865 through 1869 Processing helix chain 'F' and resid 1922 through 1930 removed outlier: 4.650A pdb=" N ASP F1927 " --> pdb=" O ALA F1924 " (cutoff:3.500A) Processing helix chain 'F' and resid 2090 through 2095 Processing helix chain 'F' and resid 2143 through 2147 Processing helix chain 'F' and resid 2153 through 2157 removed outlier: 3.536A pdb=" N LEU F2157 " --> pdb=" O PRO F2154 " (cutoff:3.500A) 3974 hydrogen bonds defined for protein. 11370 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: 33.70 Time building geometry restraints manager: 32.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 18773 1.30 - 1.44: 32955 1.44 - 1.58: 58184 1.58 - 1.72: 138 1.72 - 1.86: 593 Bond restraints: 110643 Sorted by residual: bond pdb=" CD ARG B1124 " pdb=" NE ARG B1124 " ideal model delta sigma weight residual 1.458 1.318 0.140 1.40e-02 5.10e+03 9.94e+01 bond pdb=" CB HIS B1843 " pdb=" CG HIS B1843 " ideal model delta sigma weight residual 1.497 1.358 0.139 1.40e-02 5.10e+03 9.83e+01 bond pdb=" CB HIS A1843 " pdb=" CG HIS A1843 " ideal model delta sigma weight residual 1.497 1.364 0.133 1.40e-02 5.10e+03 8.97e+01 bond pdb=" CB HIS F 744 " pdb=" CG HIS F 744 " ideal model delta sigma weight residual 1.497 1.365 0.132 1.40e-02 5.10e+03 8.89e+01 bond pdb=" CB HIS C1843 " pdb=" CG HIS C1843 " ideal model delta sigma weight residual 1.497 1.373 0.124 1.40e-02 5.10e+03 7.89e+01 ... (remaining 110638 not shown) Histogram of bond angle deviations from ideal: 94.64 - 102.60: 838 102.60 - 110.56: 33780 110.56 - 118.52: 53321 118.52 - 126.48: 60993 126.48 - 134.45: 1400 Bond angle restraints: 150332 Sorted by residual: angle pdb=" N VAL F 816 " pdb=" CA VAL F 816 " pdb=" C VAL F 816 " ideal model delta sigma weight residual 113.71 101.27 12.44 9.50e-01 1.11e+00 1.71e+02 angle pdb=" N GLU F 754 " pdb=" CA GLU F 754 " pdb=" C GLU F 754 " ideal model delta sigma weight residual 110.50 95.77 14.73 1.41e+00 5.03e-01 1.09e+02 angle pdb=" C THR D 664 " pdb=" N PRO D 665 " pdb=" CA PRO D 665 " ideal model delta sigma weight residual 119.56 129.89 -10.33 1.02e+00 9.61e-01 1.03e+02 angle pdb=" N THR E 161 " pdb=" CA THR E 161 " pdb=" C THR E 161 " ideal model delta sigma weight residual 110.41 98.33 12.08 1.23e+00 6.61e-01 9.64e+01 angle pdb=" C SER C1354 " pdb=" N PRO C1355 " pdb=" CA PRO C1355 " ideal model delta sigma weight residual 120.03 129.63 -9.60 9.90e-01 1.02e+00 9.39e+01 ... (remaining 150327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 63759 17.89 - 35.79: 1673 35.79 - 53.68: 380 53.68 - 71.57: 355 71.57 - 89.47: 49 Dihedral angle restraints: 66216 sinusoidal: 26183 harmonic: 40033 Sorted by residual: dihedral pdb=" C ARG C1124 " pdb=" N ARG C1124 " pdb=" CA ARG C1124 " pdb=" CB ARG C1124 " ideal model delta harmonic sigma weight residual -122.60 -111.42 -11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C ARG E1124 " pdb=" N ARG E1124 " pdb=" CA ARG E1124 " pdb=" CB ARG E1124 " ideal model delta harmonic sigma weight residual -122.60 -111.47 -11.13 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" C TYR E1868 " pdb=" N TYR E1868 " pdb=" CA TYR E1868 " pdb=" CB TYR E1868 " ideal model delta harmonic sigma weight residual -122.60 -111.86 -10.74 0 2.50e+00 1.60e-01 1.85e+01 ... (remaining 66213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 11524 0.096 - 0.192: 4250 0.192 - 0.288: 749 0.288 - 0.384: 58 0.384 - 0.480: 8 Chirality restraints: 16589 Sorted by residual: chirality pdb=" CA ASN C 584 " pdb=" N ASN C 584 " pdb=" C ASN C 584 " pdb=" CB ASN C 584 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA ASN A 584 " pdb=" N ASN A 584 " pdb=" C ASN A 584 " pdb=" CB ASN A 584 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA ASN E 584 " pdb=" N ASN E 584 " pdb=" C ASN E 584 " pdb=" CB ASN E 584 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 16586 not shown) Planarity restraints: 19578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 766 " -0.147 2.00e-02 2.50e+03 7.66e-02 1.17e+02 pdb=" CG TYR D 766 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR D 766 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR D 766 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 TYR D 766 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 766 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 766 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 766 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 308 " 0.070 2.00e-02 2.50e+03 4.32e-02 3.73e+01 pdb=" CG TYR B 308 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 308 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 308 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR B 308 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 308 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR B 308 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 308 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 766 " -0.079 2.00e-02 2.50e+03 4.18e-02 3.49e+01 pdb=" CG TYR C 766 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 766 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR C 766 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 766 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR C 766 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 766 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 766 " -0.058 2.00e-02 2.50e+03 ... (remaining 19575 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 21705 2.75 - 3.29: 108565 3.29 - 3.83: 191099 3.83 - 4.36: 242735 4.36 - 4.90: 384274 Nonbonded interactions: 948378 Sorted by model distance: nonbonded pdb=" OH TYR E1774 " pdb=" OH TYR E1848 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR B1774 " pdb=" OH TYR B1848 " model vdw 2.243 2.440 nonbonded pdb=" OH TYR A1774 " pdb=" OH TYR A1848 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR D1774 " pdb=" OH TYR D1848 " model vdw 2.276 2.440 nonbonded pdb=" N ALA E1841 " pdb=" O ALA E1841 " model vdw 2.277 2.496 ... (remaining 948373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 14.680 Check model and map are aligned: 1.150 Set scattering table: 0.740 Process input model: 196.280 Find NCS groups from input model: 5.260 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 222.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.021 0.170 110643 Z= 1.354 Angle : 1.715 16.829 150332 Z= 1.167 Chirality : 0.096 0.480 16589 Planarity : 0.011 0.136 19578 Dihedral : 10.890 89.466 40474 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.07 % Favored : 97.65 % Rotamer: Outliers : 0.01 % Allowed : 0.42 % Favored : 99.57 % Cbeta Deviations : 0.04 % 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: 0.31 (0.07), residues: 13592 helix: -0.09 (0.06), residues: 5156 sheet: 1.06 (0.11), residues: 2246 loop : 0.33 (0.08), residues: 6190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.009 TRP D 640 HIS 0.018 0.003 HIS E1667 PHE 0.049 0.006 PHE C1555 TYR 0.147 0.010 TYR D 766 ARG 0.012 0.001 ARG E2018 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2368 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2367 time to evaluate : 8.710 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: A 319 ASN cc_start: 0.7260 (t0) cc_final: 0.6389 (m-40) REVERT: A 450 THR cc_start: 0.8922 (p) cc_final: 0.8719 (t) REVERT: A 452 LEU cc_start: 0.7823 (mt) cc_final: 0.7458 (mt) REVERT: A 482 LYS cc_start: 0.8343 (tptt) cc_final: 0.7891 (tppt) REVERT: A 646 TRP cc_start: 0.5975 (m-10) cc_final: 0.5659 (m-10) REVERT: A 764 MET cc_start: 0.8705 (mtm) cc_final: 0.8345 (mtm) REVERT: A 785 MET cc_start: 0.8480 (mmp) cc_final: 0.8161 (mpp) REVERT: A 804 LEU cc_start: 0.8145 (mt) cc_final: 0.7325 (mt) REVERT: A 841 LEU cc_start: 0.7462 (tp) cc_final: 0.7172 (tp) REVERT: A 871 TRP cc_start: 0.7483 (t-100) cc_final: 0.7092 (t-100) REVERT: A 934 LEU cc_start: 0.9332 (tp) cc_final: 0.8746 (tp) REVERT: A 983 THR cc_start: 0.8817 (t) cc_final: 0.8546 (p) REVERT: A 1229 ASN cc_start: 0.7435 (p0) cc_final: 0.6851 (p0) REVERT: A 1322 TYR cc_start: 0.8244 (p90) cc_final: 0.7925 (p90) REVERT: A 1774 TYR cc_start: 0.8631 (m-80) cc_final: 0.8074 (m-80) REVERT: A 1838 ASP cc_start: 0.7697 (m-30) cc_final: 0.7443 (m-30) REVERT: A 1846 MET cc_start: 0.8642 (mmm) cc_final: 0.8428 (tpt) REVERT: A 2046 ARG cc_start: 0.7276 (tpt90) cc_final: 0.7004 (mmm160) REVERT: A 2382 ASP cc_start: 0.8362 (p0) cc_final: 0.7871 (p0) REVERT: A 2459 GLN cc_start: 0.8481 (mp10) cc_final: 0.8193 (mm-40) REVERT: B 284 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7797 (ptp90) REVERT: B 912 TYR cc_start: 0.6813 (p90) cc_final: 0.6518 (p90) REVERT: B 983 THR cc_start: 0.9288 (t) cc_final: 0.8918 (t) REVERT: B 1243 ASP cc_start: 0.6710 (m-30) cc_final: 0.6497 (m-30) REVERT: B 1244 THR cc_start: 0.8809 (m) cc_final: 0.8495 (t) REVERT: B 1353 ILE cc_start: 0.8760 (mt) cc_final: 0.8505 (pt) REVERT: B 1530 TYR cc_start: 0.8023 (m-80) cc_final: 0.7422 (m-80) REVERT: B 1551 ILE cc_start: 0.9028 (mt) cc_final: 0.8401 (tt) REVERT: B 1567 TYR cc_start: 0.7410 (p90) cc_final: 0.6935 (p90) REVERT: B 2278 GLN cc_start: 0.8406 (tp40) cc_final: 0.8082 (tp40) REVERT: B 2281 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7644 (mtt90) REVERT: B 2286 ASP cc_start: 0.8345 (t0) cc_final: 0.7560 (p0) REVERT: B 2347 ASP cc_start: 0.7291 (p0) cc_final: 0.6788 (t70) REVERT: B 2365 SER cc_start: 0.7553 (t) cc_final: 0.7224 (m) REVERT: B 2414 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8652 (tm-30) REVERT: C 209 GLU cc_start: 0.8559 (tp30) cc_final: 0.8292 (tp30) REVERT: C 276 LEU cc_start: 0.8623 (mt) cc_final: 0.8089 (mp) REVERT: C 397 LEU cc_start: 0.7065 (mt) cc_final: 0.6853 (mm) REVERT: C 455 THR cc_start: 0.8988 (p) cc_final: 0.8491 (t) REVERT: C 470 ILE cc_start: 0.7877 (mm) cc_final: 0.7378 (tp) REVERT: C 646 TRP cc_start: 0.6220 (m-10) cc_final: 0.5940 (m-10) REVERT: C 679 GLN cc_start: 0.8431 (tp40) cc_final: 0.7249 (mt0) REVERT: C 811 VAL cc_start: 0.9161 (t) cc_final: 0.8943 (t) REVERT: C 1139 ASN cc_start: 0.7903 (p0) cc_final: 0.7635 (p0) REVERT: C 1205 TYR cc_start: 0.7094 (m-80) cc_final: 0.6342 (m-80) REVERT: C 1290 SER cc_start: 0.8614 (m) cc_final: 0.8356 (t) REVERT: C 1336 ASP cc_start: 0.7614 (p0) cc_final: 0.6976 (m-30) REVERT: C 1337 ILE cc_start: 0.8934 (mt) cc_final: 0.8597 (mm) REVERT: C 1517 VAL cc_start: 0.7582 (t) cc_final: 0.7378 (p) REVERT: C 1528 MET cc_start: 0.7102 (mtp) cc_final: 0.6307 (tmm) REVERT: C 1669 VAL cc_start: 0.7634 (m) cc_final: 0.7262 (t) REVERT: C 1944 LEU cc_start: 0.6544 (mt) cc_final: 0.6305 (mp) REVERT: C 1985 ILE cc_start: 0.9313 (mt) cc_final: 0.8758 (mm) REVERT: C 2281 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.8007 (mtt90) REVERT: C 2400 GLU cc_start: 0.7924 (mp0) cc_final: 0.7444 (mm-30) REVERT: C 2456 ASP cc_start: 0.7803 (t0) cc_final: 0.7502 (t0) REVERT: C 2464 PHE cc_start: 0.8016 (m-80) cc_final: 0.7772 (m-80) REVERT: D 209 GLU cc_start: 0.8484 (tp30) cc_final: 0.8208 (tp30) REVERT: D 488 TYR cc_start: 0.4083 (m-80) cc_final: 0.3880 (m-80) REVERT: D 883 VAL cc_start: 0.8055 (t) cc_final: 0.7816 (m) REVERT: D 966 ASP cc_start: 0.7471 (m-30) cc_final: 0.6948 (m-30) REVERT: D 1058 ASP cc_start: 0.7338 (m-30) cc_final: 0.7127 (m-30) REVERT: D 1072 ASP cc_start: 0.7757 (m-30) cc_final: 0.7297 (m-30) REVERT: D 1079 MET cc_start: 0.7777 (mtp) cc_final: 0.7451 (mtm) REVERT: D 1328 TYR cc_start: 0.8467 (m-80) cc_final: 0.8187 (m-80) REVERT: D 1337 ILE cc_start: 0.8696 (mp) cc_final: 0.8295 (mm) REVERT: D 1675 ILE cc_start: 0.9351 (mt) cc_final: 0.9122 (tt) REVERT: D 1773 TYR cc_start: 0.9055 (t80) cc_final: 0.8728 (t80) REVERT: D 1854 MET cc_start: 0.8378 (mtt) cc_final: 0.8009 (mtt) REVERT: D 1858 ASP cc_start: 0.7695 (m-30) cc_final: 0.7434 (m-30) REVERT: D 2323 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8074 (mtmt) REVERT: D 2409 ILE cc_start: 0.9263 (mt) cc_final: 0.8935 (tt) REVERT: D 2430 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7809 (mp10) REVERT: E 398 ASN cc_start: 0.7420 (p0) cc_final: 0.6717 (m-40) REVERT: E 640 TRP cc_start: 0.7763 (t60) cc_final: 0.7553 (t60) REVERT: E 1015 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7958 (mtt-85) REVERT: E 1046 ASP cc_start: 0.7833 (t0) cc_final: 0.7620 (t70) REVERT: E 1336 ASP cc_start: 0.7764 (p0) cc_final: 0.7561 (p0) REVERT: E 1500 ILE cc_start: 0.8510 (mt) cc_final: 0.8309 (mm) REVERT: E 1551 ILE cc_start: 0.8612 (mt) cc_final: 0.8323 (mt) REVERT: E 1552 ASP cc_start: 0.7573 (t0) cc_final: 0.7222 (m-30) REVERT: E 1568 GLU cc_start: 0.7619 (tt0) cc_final: 0.6850 (mt-10) REVERT: E 1574 VAL cc_start: 0.8844 (t) cc_final: 0.8426 (m) REVERT: E 2381 THR cc_start: 0.8648 (p) cc_final: 0.8429 (p) REVERT: E 2456 ASP cc_start: 0.8091 (t0) cc_final: 0.7843 (t0) REVERT: F 76 VAL cc_start: 0.8244 (t) cc_final: 0.7849 (p) REVERT: F 393 ILE cc_start: 0.9206 (pt) cc_final: 0.8735 (pt) REVERT: F 469 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8106 (Cg_exo) REVERT: F 561 ASP cc_start: 0.7629 (t0) cc_final: 0.6969 (t0) REVERT: F 666 ASP cc_start: 0.6807 (t0) cc_final: 0.6405 (t0) REVERT: F 734 THR cc_start: 0.8487 (m) cc_final: 0.8256 (t) outliers start: 1 outliers final: 1 residues processed: 2368 average time/residue: 1.0072 time to fit residues: 4048.8376 Evaluate side-chains 1208 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1207 time to evaluate : 8.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1149 optimal weight: 3.9990 chunk 1031 optimal weight: 5.9990 chunk 572 optimal weight: 5.9990 chunk 352 optimal weight: 7.9990 chunk 695 optimal weight: 0.9980 chunk 551 optimal weight: 0.9980 chunk 1066 optimal weight: 1.9990 chunk 412 optimal weight: 0.8980 chunk 648 optimal weight: 30.0000 chunk 793 optimal weight: 6.9990 chunk 1235 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 587 ASN A 709 HIS A 796 HIS A 892 GLN A 932 ASN A 953 GLN A1007 ASN A1036 GLN A1189 GLN A1265 GLN ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1341 ASN A1680 GLN A2113 GLN A2205 GLN A2363 GLN A2461 GLN ** A2488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 130 HIS B 679 GLN B 749 GLN B 767 HIS B1036 GLN B1087 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1674 HIS B2021 HIS B2223 GLN B2363 GLN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 587 ASN C 927 ASN C1202 HIS C1252 GLN C1671 ASN C2021 HIS C2035 GLN D 130 HIS D 580 ASN D 587 ASN D 848 GLN D1068 GLN D1189 GLN D1499 GLN D1520 GLN D1793 ASN D1842 GLN D2021 HIS D2129 GLN D2170 ASN D2205 GLN D2237 GLN E 130 HIS E 580 ASN E 676 HIS E 709 HIS E 854 GLN E 976 GLN E1202 HIS E1599 GLN E1680 GLN E1781 GLN E1965 GLN E2059 GLN F 230 HIS ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN F 591 GLN F 668 GLN F 700 ASN F 989 GLN F1089 ASN F1252 GLN F1274 GLN F1342 GLN F1530 HIS F1546 GLN F1558 GLN F1671 GLN F1946 ASN F1954 GLN F2003 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 110643 Z= 0.271 Angle : 0.673 11.024 150332 Z= 0.360 Chirality : 0.043 0.218 16589 Planarity : 0.005 0.070 19578 Dihedral : 5.219 51.479 14893 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 1.64 % Allowed : 6.13 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.02 % 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: 0.76 (0.07), residues: 13592 helix: 1.17 (0.07), residues: 5255 sheet: 0.68 (0.10), residues: 2382 loop : -0.06 (0.08), residues: 5955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 871 HIS 0.017 0.001 HIS F1766 PHE 0.033 0.002 PHE C 730 TYR 0.032 0.002 TYR C 912 ARG 0.010 0.001 ARG A2243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1427 time to evaluate : 8.787 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: A 136 TYR cc_start: 0.8233 (m-80) cc_final: 0.7472 (m-80) REVERT: A 287 ASN cc_start: 0.8363 (t0) cc_final: 0.8126 (t0) REVERT: A 319 ASN cc_start: 0.6899 (t0) cc_final: 0.6312 (m-40) REVERT: A 603 ASP cc_start: 0.8620 (m-30) cc_final: 0.8198 (t70) REVERT: A 733 TRP cc_start: 0.7837 (m100) cc_final: 0.7402 (m100) REVERT: A 764 MET cc_start: 0.8682 (mtm) cc_final: 0.8300 (mmm) REVERT: A 804 LEU cc_start: 0.8587 (mt) cc_final: 0.8230 (mt) REVERT: A 841 LEU cc_start: 0.7858 (tp) cc_final: 0.7446 (mp) REVERT: A 1099 ASP cc_start: 0.7735 (t0) cc_final: 0.7478 (t0) REVERT: A 1229 ASN cc_start: 0.7427 (p0) cc_final: 0.6703 (p0) REVERT: A 1321 ASP cc_start: 0.8493 (m-30) cc_final: 0.8175 (m-30) REVERT: A 1356 LYS cc_start: 0.7941 (tttt) cc_final: 0.7689 (mmmt) REVERT: A 1774 TYR cc_start: 0.8382 (m-80) cc_final: 0.7765 (m-80) REVERT: A 2283 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6764 (mt-10) REVERT: A 2311 MET cc_start: 0.8229 (tpt) cc_final: 0.7876 (tpt) REVERT: A 2382 ASP cc_start: 0.8087 (p0) cc_final: 0.7644 (p0) REVERT: A 2468 LYS cc_start: 0.8943 (mttt) cc_final: 0.8211 (mttm) REVERT: B 460 ILE cc_start: 0.9402 (mt) cc_final: 0.9051 (tt) REVERT: B 804 LEU cc_start: 0.9056 (mt) cc_final: 0.8789 (mt) REVERT: B 1243 ASP cc_start: 0.6568 (m-30) cc_final: 0.6293 (m-30) REVERT: B 1244 THR cc_start: 0.8521 (m) cc_final: 0.8304 (p) REVERT: B 1273 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7158 (mmp) REVERT: B 1321 ASP cc_start: 0.6700 (t70) cc_final: 0.6492 (t70) REVERT: B 1353 ILE cc_start: 0.8742 (mt) cc_final: 0.8426 (pt) REVERT: B 1375 MET cc_start: 0.5698 (ptm) cc_final: 0.5314 (tpt) REVERT: B 1499 GLN cc_start: 0.8113 (pt0) cc_final: 0.7895 (pm20) REVERT: B 1555 PHE cc_start: 0.7708 (m-80) cc_final: 0.7297 (t80) REVERT: B 1793 ASN cc_start: 0.8952 (t0) cc_final: 0.8728 (t0) REVERT: B 2172 MET cc_start: 0.8483 (mtp) cc_final: 0.8043 (mtp) REVERT: B 2278 GLN cc_start: 0.8304 (tp40) cc_final: 0.7901 (tp40) REVERT: B 2286 ASP cc_start: 0.8288 (t0) cc_final: 0.7644 (p0) REVERT: B 2500 MET cc_start: 0.7980 (tmm) cc_final: 0.7451 (tmm) REVERT: C 186 MET cc_start: 0.7956 (mtp) cc_final: 0.7745 (mtp) REVERT: C 209 GLU cc_start: 0.8409 (tp30) cc_final: 0.8081 (tp30) REVERT: C 276 LEU cc_start: 0.8436 (mt) cc_final: 0.8161 (mt) REVERT: C 355 LEU cc_start: 0.8359 (tt) cc_final: 0.7820 (mt) REVERT: C 357 TYR cc_start: 0.6475 (t80) cc_final: 0.6093 (t80) REVERT: C 470 ILE cc_start: 0.7983 (mm) cc_final: 0.7530 (tp) REVERT: C 679 GLN cc_start: 0.8545 (tp40) cc_final: 0.7594 (mt0) REVERT: C 1205 TYR cc_start: 0.7124 (m-80) cc_final: 0.6603 (m-80) REVERT: C 1290 SER cc_start: 0.8576 (m) cc_final: 0.8059 (t) REVERT: C 1305 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7588 (mtm180) REVERT: C 1709 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7539 (tpp) REVERT: C 1756 GLU cc_start: 0.7663 (pt0) cc_final: 0.7351 (pt0) REVERT: C 2045 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6706 (mt-10) REVERT: C 2281 ARG cc_start: 0.8304 (mtm-85) cc_final: 0.8070 (mtt90) REVERT: C 2283 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 2318 GLU cc_start: 0.7864 (tt0) cc_final: 0.7629 (tt0) REVERT: C 2330 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6571 (mt-10) REVERT: C 2468 LYS cc_start: 0.8835 (mttt) cc_final: 0.8422 (mttp) REVERT: D 209 GLU cc_start: 0.8350 (tp30) cc_final: 0.8042 (tp30) REVERT: D 236 LEU cc_start: 0.7038 (pp) cc_final: 0.6735 (mt) REVERT: D 883 VAL cc_start: 0.7999 (t) cc_final: 0.7755 (m) REVERT: D 1229 ASN cc_start: 0.7148 (p0) cc_final: 0.6783 (p0) REVERT: D 1328 TYR cc_start: 0.8395 (m-80) cc_final: 0.8129 (m-80) REVERT: D 1354 SER cc_start: 0.8147 (m) cc_final: 0.7884 (t) REVERT: D 1788 ASN cc_start: 0.8529 (t0) cc_final: 0.8213 (t0) REVERT: D 1791 GLU cc_start: 0.7892 (mp0) cc_final: 0.7666 (mp0) REVERT: D 2409 ILE cc_start: 0.9130 (mt) cc_final: 0.8822 (tt) REVERT: E 398 ASN cc_start: 0.7356 (p0) cc_final: 0.6572 (m-40) REVERT: E 594 LEU cc_start: 0.8595 (mt) cc_final: 0.8370 (mm) REVERT: E 614 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: E 654 MET cc_start: 0.6875 (mtt) cc_final: 0.6252 (mpp) REVERT: E 678 LEU cc_start: 0.7810 (mt) cc_final: 0.7381 (mp) REVERT: E 725 MET cc_start: 0.0798 (ptp) cc_final: 0.0023 (tpp) REVERT: E 1015 ARG cc_start: 0.8305 (mtp85) cc_final: 0.8100 (mtp85) REVERT: E 1048 THR cc_start: 0.8737 (m) cc_final: 0.8512 (p) REVERT: E 1568 GLU cc_start: 0.7887 (tt0) cc_final: 0.6612 (mt-10) REVERT: E 1596 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7099 (ptm) REVERT: E 1781 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: E 1846 MET cc_start: 0.8620 (mmm) cc_final: 0.7871 (mmm) REVERT: E 1858 ASP cc_start: 0.7845 (m-30) cc_final: 0.7612 (m-30) REVERT: E 1985 ILE cc_start: 0.9195 (mt) cc_final: 0.8663 (pt) REVERT: E 2473 GLU cc_start: 0.8203 (tt0) cc_final: 0.7965 (tt0) REVERT: F 76 VAL cc_start: 0.7854 (t) cc_final: 0.7540 (p) REVERT: F 469 PRO cc_start: 0.8521 (Cg_endo) cc_final: 0.8266 (Cg_exo) REVERT: F 561 ASP cc_start: 0.7440 (t0) cc_final: 0.6942 (t0) REVERT: F 666 ASP cc_start: 0.6512 (t0) cc_final: 0.6037 (t0) REVERT: F 733 GLN cc_start: 0.7732 (mp10) cc_final: 0.7473 (mp10) REVERT: F 1363 MET cc_start: 0.7643 (mmm) cc_final: 0.7276 (mmm) outliers start: 192 outliers final: 103 residues processed: 1538 average time/residue: 0.9416 time to fit residues: 2538.0889 Evaluate side-chains 1183 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1075 time to evaluate : 8.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1272 ASP Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1874 ASP Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1273 MET Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1900 THR Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2355 GLN Chi-restraints excluded: chain B residue 2370 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 1069 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1347 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1728 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1957 MET Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2064 ILE Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2448 LEU Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 1048 THR Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1499 GLN Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 2133 LEU Chi-restraints excluded: chain D residue 2246 SER Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain D residue 2395 ASP Chi-restraints excluded: chain D residue 2481 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 614 GLU Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 912 TYR Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1304 ASN Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1353 ILE Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1596 MET Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1781 GLN Chi-restraints excluded: chain E residue 1785 HIS Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 397 GLN Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 844 ASP Chi-restraints excluded: chain F residue 877 LEU Chi-restraints excluded: chain F residue 912 SER Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1561 LEU Chi-restraints excluded: chain F residue 2026 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 686 optimal weight: 0.9990 chunk 383 optimal weight: 0.0980 chunk 1028 optimal weight: 5.9990 chunk 841 optimal weight: 0.6980 chunk 340 optimal weight: 5.9990 chunk 1238 optimal weight: 5.9990 chunk 1337 optimal weight: 5.9990 chunk 1102 optimal weight: 9.9990 chunk 1227 optimal weight: 7.9990 chunk 422 optimal weight: 50.0000 chunk 993 optimal weight: 0.0050 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 679 GLN ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 GLN ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1341 ASN A1529 ASN A1793 ASN A1916 GLN A2461 GLN B 93 ASN B1087 GLN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN B2497 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 642 HIS C 969 GLN C1132 ASN C1303 ASN C1764 ASN C1951 GLN C1961 GLN D 580 ASN ** D1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1303 ASN D1499 GLN E 222 ASN E 259 ASN E 352 ASN ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 676 HIS ** E 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1781 GLN E1965 GLN E2059 GLN E2505 ASN F 145 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 110643 Z= 0.225 Angle : 0.580 11.260 150332 Z= 0.306 Chirality : 0.041 0.315 16589 Planarity : 0.004 0.065 19578 Dihedral : 4.885 33.161 14893 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 1.79 % Allowed : 7.63 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.02 % 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: 0.82 (0.07), residues: 13592 helix: 1.44 (0.07), residues: 5316 sheet: 0.59 (0.11), residues: 2344 loop : -0.23 (0.08), residues: 5932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 871 HIS 0.010 0.001 HIS E 709 PHE 0.028 0.002 PHE C 730 TYR 0.026 0.002 TYR F 906 ARG 0.012 0.001 ARG C1319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1194 time to evaluate : 10.228 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: A 136 TYR cc_start: 0.8160 (m-80) cc_final: 0.7949 (m-10) REVERT: A 231 MET cc_start: 0.6111 (tpt) cc_final: 0.5798 (mmm) REVERT: A 287 ASN cc_start: 0.8360 (t0) cc_final: 0.7950 (t0) REVERT: A 319 ASN cc_start: 0.6963 (t0) cc_final: 0.6284 (m-40) REVERT: A 485 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: A 603 ASP cc_start: 0.8647 (m-30) cc_final: 0.8287 (t70) REVERT: A 764 MET cc_start: 0.8677 (mtm) cc_final: 0.8368 (mmm) REVERT: A 804 LEU cc_start: 0.8718 (mt) cc_final: 0.8467 (mt) REVERT: A 846 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7626 (mm) REVERT: A 1099 ASP cc_start: 0.7838 (t0) cc_final: 0.7553 (t0) REVERT: A 1229 ASN cc_start: 0.7425 (p0) cc_final: 0.6871 (p0) REVERT: A 1793 ASN cc_start: 0.8664 (t0) cc_final: 0.8251 (t0) REVERT: A 2382 ASP cc_start: 0.8112 (p0) cc_final: 0.7686 (p0) REVERT: A 2468 LYS cc_start: 0.8884 (mttt) cc_final: 0.8612 (mtpp) REVERT: B 93 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6864 (t0) REVERT: B 218 LEU cc_start: 0.8127 (mm) cc_final: 0.7878 (mt) REVERT: B 603 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6420 (t0) REVERT: B 654 MET cc_start: 0.5221 (mmt) cc_final: 0.4830 (mmt) REVERT: B 1244 THR cc_start: 0.8673 (m) cc_final: 0.8410 (p) REVERT: B 1353 ILE cc_start: 0.8634 (mt) cc_final: 0.8354 (pt) REVERT: B 1375 MET cc_start: 0.5833 (ptm) cc_final: 0.5429 (tpt) REVERT: B 1497 LYS cc_start: 0.8283 (tppt) cc_final: 0.8065 (tppt) REVERT: B 1793 ASN cc_start: 0.8875 (t0) cc_final: 0.8656 (t0) REVERT: B 2172 MET cc_start: 0.8599 (mtp) cc_final: 0.8350 (mtp) REVERT: B 2286 ASP cc_start: 0.8354 (t0) cc_final: 0.7609 (p0) REVERT: B 2318 GLU cc_start: 0.7407 (tt0) cc_final: 0.7093 (tt0) REVERT: B 2395 ASP cc_start: 0.7475 (p0) cc_final: 0.7218 (p0) REVERT: B 2406 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8924 (mm) REVERT: B 2497 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: B 2500 MET cc_start: 0.8051 (tmm) cc_final: 0.7545 (tmm) REVERT: C 209 GLU cc_start: 0.8436 (tp30) cc_final: 0.8115 (tp30) REVERT: C 278 MET cc_start: 0.8233 (mpp) cc_final: 0.7925 (mpp) REVERT: C 470 ILE cc_start: 0.7988 (mm) cc_final: 0.7514 (tp) REVERT: C 679 GLN cc_start: 0.8451 (tp40) cc_final: 0.7544 (mt0) REVERT: C 889 VAL cc_start: 0.8088 (m) cc_final: 0.7886 (m) REVERT: C 1321 ASP cc_start: 0.7368 (t0) cc_final: 0.7131 (t0) REVERT: C 1322 TYR cc_start: 0.8166 (p90) cc_final: 0.7933 (p90) REVERT: C 1501 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 1709 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7480 (tpp) REVERT: C 2045 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6835 (mt-10) REVERT: C 2281 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.8015 (mtt90) REVERT: C 2283 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 2318 GLU cc_start: 0.7884 (tt0) cc_final: 0.7651 (tt0) REVERT: C 2324 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8204 (mtm180) REVERT: C 2330 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6512 (mt-10) REVERT: C 2506 ASP cc_start: 0.8010 (t0) cc_final: 0.7784 (t0) REVERT: D 209 GLU cc_start: 0.8420 (tp30) cc_final: 0.8142 (tp30) REVERT: D 439 LYS cc_start: 0.7224 (tmtt) cc_final: 0.6734 (tmmt) REVERT: D 491 HIS cc_start: 0.7393 (t-90) cc_final: 0.7139 (t70) REVERT: D 641 LEU cc_start: 0.7945 (mt) cc_final: 0.7563 (tp) REVERT: D 764 MET cc_start: 0.4103 (mtp) cc_final: 0.3388 (mmp) REVERT: D 1229 ASN cc_start: 0.7160 (p0) cc_final: 0.6795 (p0) REVERT: D 1328 TYR cc_start: 0.8413 (m-80) cc_final: 0.8171 (m-80) REVERT: D 1777 MET cc_start: 0.8516 (mmm) cc_final: 0.8305 (mmm) REVERT: D 1958 ASN cc_start: 0.8178 (m-40) cc_final: 0.7971 (m-40) REVERT: D 1976 ILE cc_start: 0.8966 (tp) cc_final: 0.8738 (tt) REVERT: D 2409 ILE cc_start: 0.9162 (mt) cc_final: 0.8817 (tt) REVERT: D 2463 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7059 (p0) REVERT: E 614 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: E 678 LEU cc_start: 0.7863 (mt) cc_final: 0.7616 (mp) REVERT: E 725 MET cc_start: 0.0761 (ptp) cc_final: 0.0461 (tpp) REVERT: E 1003 ASN cc_start: 0.8196 (t0) cc_final: 0.7980 (t0) REVERT: E 1568 GLU cc_start: 0.7945 (tt0) cc_final: 0.6978 (mt-10) REVERT: E 1596 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7146 (ptm) REVERT: E 1777 MET cc_start: 0.8717 (mmm) cc_final: 0.8510 (mmp) REVERT: E 1846 MET cc_start: 0.8652 (mmm) cc_final: 0.8077 (mmm) REVERT: F 76 VAL cc_start: 0.8020 (t) cc_final: 0.7753 (p) REVERT: F 469 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8242 (Cg_exo) REVERT: F 561 ASP cc_start: 0.7492 (t0) cc_final: 0.6756 (t0) REVERT: F 666 ASP cc_start: 0.6719 (t0) cc_final: 0.6177 (t0) REVERT: F 1353 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8747 (tp) REVERT: F 1695 MET cc_start: 0.7937 (mpp) cc_final: 0.7719 (mpp) outliers start: 209 outliers final: 129 residues processed: 1333 average time/residue: 0.8865 time to fit residues: 2097.9494 Evaluate side-chains 1159 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1017 time to evaluate : 8.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1272 ASP Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1874 ASP Chi-restraints excluded: chain A residue 1913 ILE Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2015 SER Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2078 LEU Chi-restraints excluded: chain A residue 2332 GLU Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1900 THR Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2038 SER Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2105 GLU Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2385 THR Chi-restraints excluded: chain B residue 2406 LEU Chi-restraints excluded: chain B residue 2408 LYS Chi-restraints excluded: chain B residue 2497 GLN Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 649 PHE Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1069 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 1957 MET Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2015 SER Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2287 ASP Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2490 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 1048 THR Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 2016 LEU Chi-restraints excluded: chain D residue 2022 MET Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2133 LEU Chi-restraints excluded: chain D residue 2246 SER Chi-restraints excluded: chain D residue 2463 ASP Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 614 GLU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 695 TYR Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 912 TYR Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1199 LYS Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1304 ASN Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1596 MET Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1785 HIS Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 1965 GLN Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2177 ASP Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2505 ASN Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 823 THR Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 855 ASP Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1353 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1223 optimal weight: 2.9990 chunk 930 optimal weight: 9.9990 chunk 642 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 590 optimal weight: 40.0000 chunk 831 optimal weight: 10.0000 chunk 1242 optimal weight: 10.0000 chunk 1315 optimal weight: 20.0000 chunk 649 optimal weight: 30.0000 chunk 1177 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 HIS ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1341 ASN A1764 ASN A1877 ASN A2021 HIS B 93 ASN B1951 GLN B2032 GLN B2510 HIS ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 287 ASN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS C 709 HIS C 892 GLN C1016 GLN C1812 GLN C1951 GLN C1961 GLN C2195 GLN C2455 ASN D 295 GLN D 340 GLN D 361 ASN D 642 HIS D 812 ASN D 886 GLN D1202 HIS ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1499 GLN D1842 GLN D1951 GLN D2231 GLN D2459 GLN ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1303 ASN E1781 GLN E1965 GLN E2059 GLN E2195 GLN E2505 ASN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 790 HIS F 856 ASN ** F1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1337 GLN F1650 HIS F1859 GLN F1870 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 110643 Z= 0.482 Angle : 0.694 18.993 150332 Z= 0.360 Chirality : 0.045 0.296 16589 Planarity : 0.005 0.067 19578 Dihedral : 5.086 33.875 14891 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 2.48 % Allowed : 8.13 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: 0.50 (0.07), residues: 13592 helix: 1.28 (0.07), residues: 5328 sheet: 0.39 (0.11), residues: 2369 loop : -0.52 (0.08), residues: 5895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 810 HIS 0.033 0.002 HIS F 377 PHE 0.029 0.002 PHE D 296 TYR 0.030 0.002 TYR C1868 ARG 0.008 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1060 time to evaluate : 8.981 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: A 231 MET cc_start: 0.6089 (tpt) cc_final: 0.5773 (mmm) REVERT: A 319 ASN cc_start: 0.7021 (t0) cc_final: 0.6519 (m-40) REVERT: A 603 ASP cc_start: 0.8466 (m-30) cc_final: 0.8221 (t70) REVERT: A 764 MET cc_start: 0.8781 (mtm) cc_final: 0.8314 (mmm) REVERT: A 1229 ASN cc_start: 0.7465 (p0) cc_final: 0.6897 (p0) REVERT: A 1356 LYS cc_start: 0.8160 (tttm) cc_final: 0.7802 (tptm) REVERT: A 1531 GLN cc_start: 0.8536 (tp40) cc_final: 0.7667 (tp40) REVERT: A 1793 ASN cc_start: 0.8766 (t0) cc_final: 0.8343 (t0) REVERT: A 2311 MET cc_start: 0.8282 (tpt) cc_final: 0.7837 (tpt) REVERT: A 2326 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8362 (tttm) REVERT: A 2468 LYS cc_start: 0.8909 (mttt) cc_final: 0.8618 (mttm) REVERT: B 603 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6462 (t0) REVERT: B 654 MET cc_start: 0.5557 (mmt) cc_final: 0.5215 (mmt) REVERT: B 1244 THR cc_start: 0.8717 (m) cc_final: 0.8439 (p) REVERT: B 1353 ILE cc_start: 0.8636 (mt) cc_final: 0.8352 (pt) REVERT: B 1375 MET cc_start: 0.5836 (ptm) cc_final: 0.5460 (tpt) REVERT: B 1497 LYS cc_start: 0.8182 (tppt) cc_final: 0.7586 (tptm) REVERT: B 1501 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8624 (mm) REVERT: B 1530 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7492 (m-10) REVERT: B 1836 ASP cc_start: 0.8003 (t0) cc_final: 0.7779 (t0) REVERT: B 2172 MET cc_start: 0.8636 (mtp) cc_final: 0.8380 (mtp) REVERT: B 2286 ASP cc_start: 0.8394 (t0) cc_final: 0.7658 (p0) REVERT: B 2341 TYR cc_start: 0.8882 (m-80) cc_final: 0.8669 (m-80) REVERT: B 2497 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8708 (mt0) REVERT: C 209 GLU cc_start: 0.8496 (tp30) cc_final: 0.8056 (tp30) REVERT: C 341 MET cc_start: 0.5040 (mmm) cc_final: 0.4447 (mmt) REVERT: C 679 GLN cc_start: 0.8472 (tp40) cc_final: 0.7473 (mt0) REVERT: C 1321 ASP cc_start: 0.7258 (t0) cc_final: 0.7010 (t0) REVERT: C 1501 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8816 (tt) REVERT: C 1622 ASP cc_start: 0.7935 (t0) cc_final: 0.7735 (t0) REVERT: C 1709 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7775 (tpp) REVERT: C 2014 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5158 (pmm) REVERT: C 2318 GLU cc_start: 0.7920 (tt0) cc_final: 0.7586 (tt0) REVERT: C 2324 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8215 (mtm180) REVERT: C 2330 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6761 (mt-10) REVERT: D 209 GLU cc_start: 0.8375 (tp30) cc_final: 0.8147 (tp30) REVERT: D 439 LYS cc_start: 0.7274 (tmtt) cc_final: 0.6719 (tmmt) REVERT: D 488 TYR cc_start: 0.4132 (m-80) cc_final: 0.3012 (m-80) REVERT: D 641 LEU cc_start: 0.7962 (mt) cc_final: 0.7740 (tp) REVERT: D 692 MET cc_start: 0.3489 (mmt) cc_final: 0.2863 (mmm) REVERT: D 846 LEU cc_start: 0.7830 (tt) cc_final: 0.7460 (mp) REVERT: D 1229 ASN cc_start: 0.7260 (p0) cc_final: 0.6879 (p0) REVERT: D 1328 TYR cc_start: 0.8483 (m-80) cc_final: 0.8037 (m-80) REVERT: D 2463 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7403 (p0) REVERT: E 614 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: E 678 LEU cc_start: 0.7866 (mt) cc_final: 0.7580 (mp) REVERT: E 766 TYR cc_start: 0.5897 (m-80) cc_final: 0.5239 (m-80) REVERT: E 1553 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8595 (m) REVERT: E 1773 TYR cc_start: 0.9090 (t80) cc_final: 0.8720 (t80) REVERT: F 561 ASP cc_start: 0.7420 (t0) cc_final: 0.6930 (t0) REVERT: F 666 ASP cc_start: 0.6947 (t0) cc_final: 0.6653 (t0) REVERT: F 1353 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8874 (tp) REVERT: F 2158 MET cc_start: 0.5126 (mtp) cc_final: 0.4513 (mtp) outliers start: 289 outliers final: 179 residues processed: 1252 average time/residue: 0.9043 time to fit residues: 1988.1428 Evaluate side-chains 1133 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 942 time to evaluate : 8.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1272 ASP Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2015 SER Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2078 LEU Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1261 ASN Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1530 TYR Chi-restraints excluded: chain B residue 1542 LEU Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1570 PHE Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2038 SER Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2319 ASP Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2385 THR Chi-restraints excluded: chain B residue 2409 ILE Chi-restraints excluded: chain B residue 2497 GLN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 990 ILE Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1170 LEU Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1347 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1500 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1710 THR Chi-restraints excluded: chain C residue 1728 ASP Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1797 LYS Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 2003 SER Chi-restraints excluded: chain C residue 2014 MET Chi-restraints excluded: chain C residue 2015 SER Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2448 LEU Chi-restraints excluded: chain C residue 2455 ASN Chi-restraints excluded: chain C residue 2479 GLN Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 TYR Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 926 LEU Chi-restraints excluded: chain D residue 966 ASP Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1278 MET Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1758 MET Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1900 THR Chi-restraints excluded: chain D residue 1979 GLN Chi-restraints excluded: chain D residue 2016 LEU Chi-restraints excluded: chain D residue 2022 MET Chi-restraints excluded: chain D residue 2246 SER Chi-restraints excluded: chain D residue 2319 ASP Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain D residue 2395 ASP Chi-restraints excluded: chain D residue 2463 ASP Chi-restraints excluded: chain D residue 2481 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 614 GLU Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1022 ASP Chi-restraints excluded: chain E residue 1199 LYS Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1553 VAL Chi-restraints excluded: chain E residue 1627 MET Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1761 SER Chi-restraints excluded: chain E residue 1873 ARG Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2177 ASP Chi-restraints excluded: chain E residue 2207 ASP Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 823 THR Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1353 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1095 optimal weight: 1.9990 chunk 746 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 979 optimal weight: 30.0000 chunk 542 optimal weight: 2.9990 chunk 1122 optimal weight: 3.9990 chunk 909 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 671 optimal weight: 0.9980 chunk 1180 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 ASN ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1961 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1961 GLN D 866 ASN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1499 GLN D1842 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 969 GLN E1303 ASN E1748 ASN ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1965 GLN F 5 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F1126 HIS ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 110643 Z= 0.168 Angle : 0.548 20.793 150332 Z= 0.283 Chirality : 0.040 0.272 16589 Planarity : 0.004 0.056 19578 Dihedral : 4.735 33.965 14891 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 1.82 % Allowed : 9.33 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % 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: 0.74 (0.07), residues: 13592 helix: 1.59 (0.07), residues: 5334 sheet: 0.46 (0.11), residues: 2357 loop : -0.47 (0.08), residues: 5901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 810 HIS 0.009 0.001 HIS A 767 PHE 0.023 0.001 PHE D2167 TYR 0.032 0.001 TYR E 431 ARG 0.009 0.000 ARG C2186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1101 time to evaluate : 8.890 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: A 319 ASN cc_start: 0.7436 (t0) cc_final: 0.6524 (m110) REVERT: A 603 ASP cc_start: 0.8476 (m-30) cc_final: 0.8214 (t70) REVERT: A 764 MET cc_start: 0.8770 (mtm) cc_final: 0.8309 (mmm) REVERT: A 846 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7771 (mm) REVERT: A 1099 ASP cc_start: 0.7800 (t0) cc_final: 0.7545 (t0) REVERT: A 1229 ASN cc_start: 0.7504 (p0) cc_final: 0.6944 (p0) REVERT: A 1793 ASN cc_start: 0.8655 (t0) cc_final: 0.8295 (t0) REVERT: A 2311 MET cc_start: 0.8246 (tpt) cc_final: 0.7664 (tpt) REVERT: A 2401 ASP cc_start: 0.7518 (m-30) cc_final: 0.7281 (m-30) REVERT: A 2468 LYS cc_start: 0.8946 (mttt) cc_final: 0.8667 (mttm) REVERT: B 328 TYR cc_start: 0.8426 (m-80) cc_final: 0.8137 (m-80) REVERT: B 496 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7983 (tp) REVERT: B 654 MET cc_start: 0.5627 (mmt) cc_final: 0.5222 (mmt) REVERT: B 1244 THR cc_start: 0.8637 (m) cc_final: 0.8345 (p) REVERT: B 1353 ILE cc_start: 0.8508 (mt) cc_final: 0.8188 (pt) REVERT: B 1375 MET cc_start: 0.5829 (ptm) cc_final: 0.5528 (tpt) REVERT: B 1497 LYS cc_start: 0.8238 (tppt) cc_final: 0.7610 (tptm) REVERT: B 1501 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 1530 TYR cc_start: 0.7808 (m-10) cc_final: 0.7474 (m-10) REVERT: B 1836 ASP cc_start: 0.7886 (t0) cc_final: 0.7583 (t0) REVERT: B 2286 ASP cc_start: 0.8369 (t0) cc_final: 0.7703 (p0) REVERT: B 2341 TYR cc_start: 0.8842 (m-80) cc_final: 0.8621 (m-80) REVERT: B 2463 ASP cc_start: 0.7574 (t0) cc_final: 0.7354 (t0) REVERT: C 209 GLU cc_start: 0.8438 (tp30) cc_final: 0.8174 (tp30) REVERT: C 240 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8334 (p0) REVERT: C 341 MET cc_start: 0.5252 (mmm) cc_final: 0.4976 (mmm) REVERT: C 430 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5290 (tt0) REVERT: C 553 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7334 (mmp80) REVERT: C 634 LEU cc_start: 0.8965 (tt) cc_final: 0.8470 (mt) REVERT: C 679 GLN cc_start: 0.8438 (tp40) cc_final: 0.7522 (mt0) REVERT: C 1321 ASP cc_start: 0.7345 (t0) cc_final: 0.7013 (t0) REVERT: C 1501 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8813 (tt) REVERT: C 1709 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7548 (tpp) REVERT: C 2318 GLU cc_start: 0.7845 (tt0) cc_final: 0.7565 (tt0) REVERT: C 2324 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: C 2454 MET cc_start: 0.7806 (mtp) cc_final: 0.7587 (mtm) REVERT: D 209 GLU cc_start: 0.8351 (tp30) cc_final: 0.8096 (tp30) REVERT: D 341 MET cc_start: 0.1545 (OUTLIER) cc_final: 0.1303 (tpt) REVERT: D 439 LYS cc_start: 0.7218 (tmtt) cc_final: 0.6713 (tmmt) REVERT: D 641 LEU cc_start: 0.8054 (mt) cc_final: 0.7665 (tp) REVERT: D 692 MET cc_start: 0.3087 (mmt) cc_final: 0.2426 (mmm) REVERT: D 1229 ASN cc_start: 0.7264 (p0) cc_final: 0.6907 (p0) REVERT: D 1311 GLU cc_start: 0.7750 (mp0) cc_final: 0.7318 (mp0) REVERT: D 1328 TYR cc_start: 0.8401 (m-80) cc_final: 0.7986 (m-80) REVERT: D 1777 MET cc_start: 0.8587 (mmm) cc_final: 0.8323 (mmm) REVERT: D 2165 MET cc_start: 0.8814 (ppp) cc_final: 0.8572 (tmm) REVERT: E 678 LEU cc_start: 0.7844 (mt) cc_final: 0.7568 (mp) REVERT: E 709 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8125 (p90) REVERT: E 766 TYR cc_start: 0.6036 (m-80) cc_final: 0.5421 (m-80) REVERT: E 839 MET cc_start: 0.6558 (mmm) cc_final: 0.6303 (mmm) REVERT: E 1003 ASN cc_start: 0.8191 (t0) cc_final: 0.7950 (t0) REVERT: E 2172 MET cc_start: 0.8592 (mtt) cc_final: 0.8241 (mtm) REVERT: F 1 MET cc_start: 0.3076 (tpt) cc_final: 0.0563 (ttm) REVERT: F 28 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7608 (tp) REVERT: F 91 ASP cc_start: 0.7440 (p0) cc_final: 0.6946 (p0) REVERT: F 561 ASP cc_start: 0.7453 (t0) cc_final: 0.6680 (t0) REVERT: F 666 ASP cc_start: 0.6736 (t0) cc_final: 0.6385 (t0) REVERT: F 777 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: F 1353 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (tt) REVERT: F 2158 MET cc_start: 0.5056 (mtp) cc_final: 0.4444 (mtp) outliers start: 213 outliers final: 141 residues processed: 1241 average time/residue: 0.8717 time to fit residues: 1914.6608 Evaluate side-chains 1151 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 997 time to evaluate : 7.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1272 ASP Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1913 ILE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2078 LEU Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1051 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2038 SER Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 649 PHE Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 1069 LEU Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1170 LEU Chi-restraints excluded: chain C residue 1291 TYR Chi-restraints excluded: chain C residue 1299 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1500 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2413 LYS Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 926 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1242 GLU Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1683 ASP Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 1979 GLN Chi-restraints excluded: chain D residue 2015 SER Chi-restraints excluded: chain D residue 2016 LEU Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 897 LEU Chi-restraints excluded: chain E residue 912 TYR Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1072 ASP Chi-restraints excluded: chain E residue 1264 MET Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1726 VAL Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2177 ASP Chi-restraints excluded: chain E residue 2267 ASP Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain E residue 2446 GLU Chi-restraints excluded: chain E residue 2505 ASN Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 777 GLU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 855 ASP Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1260 MET Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1353 LEU Chi-restraints excluded: chain F residue 1568 THR Chi-restraints excluded: chain F residue 2026 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 442 optimal weight: 6.9990 chunk 1184 optimal weight: 4.9990 chunk 260 optimal weight: 9.9990 chunk 772 optimal weight: 3.9990 chunk 324 optimal weight: 0.0050 chunk 1316 optimal weight: 9.9990 chunk 1093 optimal weight: 4.9990 chunk 609 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 435 optimal weight: 0.9980 chunk 691 optimal weight: 5.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1189 GLN B1210 ASN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 GLN B2032 GLN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 295 GLN ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1289 ASN C1951 GLN D 854 GLN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1499 GLN D1842 GLN E 587 ASN ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1007 ASN E1667 HIS E1781 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 110643 Z= 0.249 Angle : 0.559 16.924 150332 Z= 0.287 Chirality : 0.041 0.273 16589 Planarity : 0.004 0.057 19578 Dihedral : 4.644 32.512 14891 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 2.24 % Allowed : 9.56 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.07), residues: 13592 helix: 1.66 (0.07), residues: 5343 sheet: 0.46 (0.11), residues: 2375 loop : -0.49 (0.08), residues: 5874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP B 810 HIS 0.009 0.001 HIS C 642 PHE 0.024 0.001 PHE D2167 TYR 0.026 0.001 TYR C 912 ARG 0.007 0.000 ARG C2186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1022 time to evaluate : 8.853 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: A 319 ASN cc_start: 0.7431 (t0) cc_final: 0.6567 (m110) REVERT: A 457 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 603 ASP cc_start: 0.8499 (m-30) cc_final: 0.8208 (t70) REVERT: A 764 MET cc_start: 0.8753 (mtm) cc_final: 0.8211 (mmm) REVERT: A 1099 ASP cc_start: 0.7927 (t0) cc_final: 0.7554 (t0) REVERT: A 1229 ASN cc_start: 0.7483 (p0) cc_final: 0.6916 (p0) REVERT: A 1793 ASN cc_start: 0.8681 (t0) cc_final: 0.8329 (t0) REVERT: A 1881 MET cc_start: 0.8753 (tmm) cc_final: 0.8156 (ttp) REVERT: A 2238 LEU cc_start: 0.8670 (tp) cc_final: 0.8402 (mt) REVERT: A 2311 MET cc_start: 0.8235 (tpt) cc_final: 0.7693 (tpt) REVERT: A 2401 ASP cc_start: 0.7310 (m-30) cc_final: 0.7035 (m-30) REVERT: A 2468 LYS cc_start: 0.8965 (mttt) cc_final: 0.8656 (mttm) REVERT: B 328 TYR cc_start: 0.8384 (m-80) cc_final: 0.8114 (m-80) REVERT: B 603 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6309 (t0) REVERT: B 654 MET cc_start: 0.5577 (mmt) cc_final: 0.5149 (mmt) REVERT: B 1341 ASN cc_start: 0.7784 (m110) cc_final: 0.7458 (m110) REVERT: B 1353 ILE cc_start: 0.8412 (mt) cc_final: 0.8192 (pt) REVERT: B 1375 MET cc_start: 0.5837 (ptm) cc_final: 0.5459 (tpt) REVERT: B 1497 LYS cc_start: 0.8232 (tppt) cc_final: 0.7600 (tptm) REVERT: B 1501 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8597 (mm) REVERT: B 1530 TYR cc_start: 0.7776 (m-10) cc_final: 0.7475 (m-10) REVERT: B 1836 ASP cc_start: 0.7898 (t0) cc_final: 0.7582 (t0) REVERT: B 2341 TYR cc_start: 0.8864 (m-80) cc_final: 0.8658 (m-80) REVERT: B 2463 ASP cc_start: 0.7585 (t0) cc_final: 0.7373 (t0) REVERT: C 209 GLU cc_start: 0.8429 (tp30) cc_final: 0.8176 (tp30) REVERT: C 231 MET cc_start: 0.7325 (mmm) cc_final: 0.7063 (mmm) REVERT: C 430 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5293 (tt0) REVERT: C 553 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7310 (mmp80) REVERT: C 679 GLN cc_start: 0.8433 (tp40) cc_final: 0.7535 (mt0) REVERT: C 1321 ASP cc_start: 0.7453 (t0) cc_final: 0.7161 (t0) REVERT: C 1501 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8832 (tt) REVERT: C 1532 PHE cc_start: 0.7838 (m-80) cc_final: 0.7404 (m-80) REVERT: C 1709 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7504 (tpp) REVERT: C 2014 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5249 (pmm) REVERT: C 2172 MET cc_start: 0.8291 (mtt) cc_final: 0.8009 (mtm) REVERT: C 2318 GLU cc_start: 0.7879 (tt0) cc_final: 0.7649 (tt0) REVERT: C 2324 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8165 (mtm180) REVERT: D 209 GLU cc_start: 0.8345 (tp30) cc_final: 0.8096 (tp30) REVERT: D 248 PHE cc_start: 0.8280 (t80) cc_final: 0.8024 (t80) REVERT: D 341 MET cc_start: 0.1708 (OUTLIER) cc_final: 0.1284 (tpt) REVERT: D 439 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6716 (tmmt) REVERT: D 641 LEU cc_start: 0.8093 (mt) cc_final: 0.7693 (tp) REVERT: D 654 MET cc_start: 0.5022 (mmp) cc_final: 0.4021 (ptm) REVERT: D 692 MET cc_start: 0.3190 (mmt) cc_final: 0.2490 (mmm) REVERT: D 1229 ASN cc_start: 0.7228 (p0) cc_final: 0.7018 (p0) REVERT: D 1311 GLU cc_start: 0.7731 (mp0) cc_final: 0.7294 (mp0) REVERT: D 1328 TYR cc_start: 0.8406 (m-80) cc_final: 0.7984 (m-80) REVERT: D 1375 MET cc_start: 0.8241 (pmm) cc_final: 0.7804 (mtp) REVERT: D 1535 LEU cc_start: 0.8556 (mt) cc_final: 0.8327 (mt) REVERT: D 1773 TYR cc_start: 0.8873 (t80) cc_final: 0.8489 (t80) REVERT: D 1777 MET cc_start: 0.8616 (mmm) cc_final: 0.8295 (mmm) REVERT: D 2165 MET cc_start: 0.8826 (ppp) cc_final: 0.8563 (tmm) REVERT: D 2267 ASP cc_start: 0.8112 (p0) cc_final: 0.7853 (p0) REVERT: E 678 LEU cc_start: 0.7866 (mt) cc_final: 0.7544 (mp) REVERT: E 709 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.7963 (p90) REVERT: E 763 GLU cc_start: 0.6454 (tp30) cc_final: 0.6113 (mm-30) REVERT: E 766 TYR cc_start: 0.6332 (m-10) cc_final: 0.5650 (m-80) REVERT: E 839 MET cc_start: 0.6575 (mmm) cc_final: 0.6331 (mmm) REVERT: E 1003 ASN cc_start: 0.8232 (t0) cc_final: 0.7973 (t0) REVERT: E 1790 ASP cc_start: 0.7974 (p0) cc_final: 0.7695 (p0) REVERT: E 1791 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7347 (mm-30) REVERT: E 2172 MET cc_start: 0.8620 (mtt) cc_final: 0.8290 (mtm) REVERT: F 1 MET cc_start: 0.3233 (tpt) cc_final: 0.0870 (ttm) REVERT: F 91 ASP cc_start: 0.7476 (p0) cc_final: 0.6957 (p0) REVERT: F 561 ASP cc_start: 0.7480 (t0) cc_final: 0.6728 (t0) REVERT: F 666 ASP cc_start: 0.6722 (t0) cc_final: 0.6353 (t0) REVERT: F 777 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: F 2158 MET cc_start: 0.5114 (mtp) cc_final: 0.4492 (mtp) outliers start: 261 outliers final: 186 residues processed: 1210 average time/residue: 0.8852 time to fit residues: 1897.3624 Evaluate side-chains 1167 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 970 time to evaluate : 8.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1272 ASP Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1874 ASP Chi-restraints excluded: chain A residue 1913 ILE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2078 LEU Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1570 PHE Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2038 SER Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2385 THR Chi-restraints excluded: chain B residue 2454 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 649 PHE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1069 LEU Chi-restraints excluded: chain C residue 1087 GLN Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1170 LEU Chi-restraints excluded: chain C residue 1291 TYR Chi-restraints excluded: chain C residue 1299 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1500 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1710 THR Chi-restraints excluded: chain C residue 1728 ASP Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1797 LYS Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 1900 THR Chi-restraints excluded: chain C residue 2014 MET Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2287 ASP Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2413 LYS Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 871 TRP Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 926 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1683 ASP Chi-restraints excluded: chain D residue 1758 MET Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1901 THR Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 2016 LEU Chi-restraints excluded: chain D residue 2022 MET Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2246 SER Chi-restraints excluded: chain D residue 2319 ASP Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain D residue 2395 ASP Chi-restraints excluded: chain D residue 2409 ILE Chi-restraints excluded: chain D residue 2491 MET Chi-restraints excluded: chain D residue 2511 ILE Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 640 TRP Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1072 ASP Chi-restraints excluded: chain E residue 1199 LYS Chi-restraints excluded: chain E residue 1264 MET Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1304 ASN Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1627 MET Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1726 VAL Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1873 ARG Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2177 ASP Chi-restraints excluded: chain E residue 2267 ASP Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2357 ILE Chi-restraints excluded: chain E residue 2395 ASP Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 663 GLN Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 777 GLU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 855 ASP Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1260 MET Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1269 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 750 optimal weight: 5.9990 chunk 961 optimal weight: 30.0000 chunk 745 optimal weight: 20.0000 chunk 1108 optimal weight: 50.0000 chunk 735 optimal weight: 40.0000 chunk 1311 optimal weight: 8.9990 chunk 820 optimal weight: 10.0000 chunk 799 optimal weight: 6.9990 chunk 605 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B1007 ASN B1303 ASN B1951 GLN B2032 GLN B2497 GLN C 287 ASN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1289 ASN C1951 GLN D 571 HIS ** D 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1499 GLN ** D2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2505 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1303 GLN F1337 GLN F2062 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 110643 Z= 0.463 Angle : 0.669 15.696 150332 Z= 0.344 Chirality : 0.044 0.292 16589 Planarity : 0.005 0.062 19578 Dihedral : 4.947 31.766 14891 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 2.41 % Allowed : 9.69 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % 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: 0.44 (0.07), residues: 13592 helix: 1.41 (0.07), residues: 5355 sheet: 0.20 (0.11), residues: 2390 loop : -0.68 (0.08), residues: 5847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 810 HIS 0.009 0.002 HIS A 767 PHE 0.035 0.002 PHE C 786 TYR 0.030 0.002 TYR C1868 ARG 0.011 0.001 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 986 time to evaluate : 8.879 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: A 188 MET cc_start: 0.7020 (mpp) cc_final: 0.6802 (mpp) REVERT: A 319 ASN cc_start: 0.7496 (t0) cc_final: 0.6718 (m110) REVERT: A 603 ASP cc_start: 0.8632 (m-30) cc_final: 0.8198 (t70) REVERT: A 764 MET cc_start: 0.8771 (mtm) cc_final: 0.8339 (tpt) REVERT: A 1229 ASN cc_start: 0.7445 (p0) cc_final: 0.6903 (p0) REVERT: A 1570 PHE cc_start: 0.8300 (m-80) cc_final: 0.7941 (m-10) REVERT: A 1793 ASN cc_start: 0.8768 (t0) cc_final: 0.8394 (t0) REVERT: A 1881 MET cc_start: 0.8806 (tmm) cc_final: 0.8331 (tmm) REVERT: A 2324 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: A 2401 ASP cc_start: 0.7533 (m-30) cc_final: 0.7316 (m-30) REVERT: A 2468 LYS cc_start: 0.8906 (mttt) cc_final: 0.8606 (mttm) REVERT: B 496 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8319 (tp) REVERT: B 603 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6386 (t0) REVERT: B 1243 ASP cc_start: 0.7037 (t0) cc_final: 0.6673 (t0) REVERT: B 1353 ILE cc_start: 0.8530 (mt) cc_final: 0.8231 (pt) REVERT: B 1375 MET cc_start: 0.5821 (ptm) cc_final: 0.5587 (tpt) REVERT: B 1497 LYS cc_start: 0.8350 (tppt) cc_final: 0.7792 (tptm) REVERT: B 1530 TYR cc_start: 0.7776 (m-80) cc_final: 0.7562 (m-10) REVERT: B 1535 LEU cc_start: 0.8894 (mt) cc_final: 0.8609 (mp) REVERT: B 1784 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9113 (tp) REVERT: B 1836 ASP cc_start: 0.7963 (t0) cc_final: 0.7690 (t0) REVERT: B 2105 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5652 (tm-30) REVERT: B 2497 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8928 (mt0) REVERT: C 209 GLU cc_start: 0.8427 (tp30) cc_final: 0.8020 (tp30) REVERT: C 231 MET cc_start: 0.7387 (mmm) cc_final: 0.7052 (mmm) REVERT: C 634 LEU cc_start: 0.8971 (tt) cc_final: 0.8598 (mt) REVERT: C 679 GLN cc_start: 0.8504 (tp40) cc_final: 0.7558 (mt0) REVERT: C 965 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: C 1321 ASP cc_start: 0.7524 (t0) cc_final: 0.7273 (t0) REVERT: C 1511 PHE cc_start: 0.7775 (m-80) cc_final: 0.7231 (m-80) REVERT: C 1622 ASP cc_start: 0.7921 (t0) cc_final: 0.7720 (t0) REVERT: C 1782 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8059 (mtp85) REVERT: C 2014 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.5616 (pmm) REVERT: C 2172 MET cc_start: 0.8299 (mtt) cc_final: 0.8012 (mtm) REVERT: C 2324 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8199 (mtm180) REVERT: D 287 ASN cc_start: 0.8414 (m-40) cc_final: 0.7962 (p0) REVERT: D 439 LYS cc_start: 0.7229 (tmtt) cc_final: 0.6686 (pttm) REVERT: D 452 LEU cc_start: 0.6951 (pp) cc_final: 0.6669 (pp) REVERT: D 485 MET cc_start: 0.8406 (tpt) cc_final: 0.8205 (mmm) REVERT: D 640 TRP cc_start: 0.7441 (t60) cc_final: 0.7201 (t60) REVERT: D 803 MET cc_start: 0.6981 (ttp) cc_final: 0.6764 (ptm) REVERT: D 1229 ASN cc_start: 0.7237 (p0) cc_final: 0.7028 (p0) REVERT: D 1311 GLU cc_start: 0.7734 (mp0) cc_final: 0.7290 (mp0) REVERT: D 1328 TYR cc_start: 0.8427 (m-80) cc_final: 0.7984 (m-80) REVERT: D 1375 MET cc_start: 0.8380 (pmm) cc_final: 0.7869 (ttt) REVERT: D 1570 PHE cc_start: 0.7297 (m-80) cc_final: 0.6809 (m-80) REVERT: D 2165 MET cc_start: 0.8817 (ppp) cc_final: 0.8544 (tmm) REVERT: D 2267 ASP cc_start: 0.8105 (p0) cc_final: 0.7849 (p0) REVERT: E 646 TRP cc_start: 0.7351 (m-10) cc_final: 0.7132 (m-10) REVERT: E 709 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8143 (p90) REVERT: E 763 GLU cc_start: 0.6521 (tp30) cc_final: 0.6147 (mm-30) REVERT: E 766 TYR cc_start: 0.6171 (m-10) cc_final: 0.5372 (m-80) REVERT: E 796 HIS cc_start: 0.4438 (m170) cc_final: 0.4190 (m170) REVERT: E 839 MET cc_start: 0.6433 (mmm) cc_final: 0.6166 (mmm) REVERT: E 1003 ASN cc_start: 0.8313 (t0) cc_final: 0.8095 (t0) REVERT: E 1164 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8276 (mtpp) REVERT: E 1242 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4253 (mp0) REVERT: E 1773 TYR cc_start: 0.9097 (t80) cc_final: 0.8714 (t80) REVERT: E 1790 ASP cc_start: 0.8030 (p0) cc_final: 0.7744 (p0) REVERT: E 1791 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7365 (mm-30) REVERT: E 2172 MET cc_start: 0.8666 (mtt) cc_final: 0.8304 (mtm) REVERT: F 561 ASP cc_start: 0.7404 (t0) cc_final: 0.6866 (t0) REVERT: F 753 ASP cc_start: 0.8072 (t0) cc_final: 0.7839 (t70) REVERT: F 777 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: F 2158 MET cc_start: 0.5271 (mtp) cc_final: 0.4640 (mtp) outliers start: 281 outliers final: 209 residues processed: 1175 average time/residue: 0.8832 time to fit residues: 1845.9872 Evaluate side-chains 1158 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 936 time to evaluate : 8.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1272 ASP Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2078 LEU Chi-restraints excluded: chain A residue 2324 ARG Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 868 PHE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1261 ASN Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1555 PHE Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2038 SER Chi-restraints excluded: chain B residue 2043 ILE Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2105 GLU Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2385 THR Chi-restraints excluded: chain B residue 2409 ILE Chi-restraints excluded: chain B residue 2454 MET Chi-restraints excluded: chain B residue 2497 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 649 PHE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain C residue 1087 GLN Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1223 GLU Chi-restraints excluded: chain C residue 1299 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1347 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1554 THR Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1710 THR Chi-restraints excluded: chain C residue 1728 ASP Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1797 LYS Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 2003 SER Chi-restraints excluded: chain C residue 2014 MET Chi-restraints excluded: chain C residue 2015 SER Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2413 LYS Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 308 TYR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 339 TYR Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 871 TRP Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 926 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1613 LEU Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1655 HIS Chi-restraints excluded: chain D residue 1683 ASP Chi-restraints excluded: chain D residue 1758 MET Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1900 THR Chi-restraints excluded: chain D residue 1901 THR Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 1985 ILE Chi-restraints excluded: chain D residue 2015 SER Chi-restraints excluded: chain D residue 2016 LEU Chi-restraints excluded: chain D residue 2022 MET Chi-restraints excluded: chain D residue 2246 SER Chi-restraints excluded: chain D residue 2319 ASP Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain D residue 2409 ILE Chi-restraints excluded: chain D residue 2463 ASP Chi-restraints excluded: chain D residue 2481 THR Chi-restraints excluded: chain D residue 2491 MET Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 640 TRP Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 897 LEU Chi-restraints excluded: chain E residue 906 MET Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 988 GLU Chi-restraints excluded: chain E residue 1022 ASP Chi-restraints excluded: chain E residue 1164 LYS Chi-restraints excluded: chain E residue 1199 LYS Chi-restraints excluded: chain E residue 1242 GLU Chi-restraints excluded: chain E residue 1264 MET Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1603 THR Chi-restraints excluded: chain E residue 1627 MET Chi-restraints excluded: chain E residue 1628 GLU Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1726 VAL Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1761 SER Chi-restraints excluded: chain E residue 1827 TRP Chi-restraints excluded: chain E residue 1873 ARG Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 2022 MET Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2177 ASP Chi-restraints excluded: chain E residue 2194 ILE Chi-restraints excluded: chain E residue 2267 ASP Chi-restraints excluded: chain E residue 2270 VAL Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 659 THR Chi-restraints excluded: chain F residue 663 GLN Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 777 GLU Chi-restraints excluded: chain F residue 823 THR Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 855 ASP Chi-restraints excluded: chain F residue 912 SER Chi-restraints excluded: chain F residue 926 SER Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1260 MET Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1568 THR Chi-restraints excluded: chain F residue 1590 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 811 optimal weight: 3.9990 chunk 523 optimal weight: 7.9990 chunk 783 optimal weight: 1.9990 chunk 395 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 833 optimal weight: 0.9980 chunk 893 optimal weight: 1.9990 chunk 648 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 1031 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1529 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 GLN B2497 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN C1289 ASN C1842 GLN C1951 GLN C2113 GLN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1499 GLN D1842 GLN ** D2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 110643 Z= 0.239 Angle : 0.571 15.550 150332 Z= 0.292 Chirality : 0.041 0.491 16589 Planarity : 0.004 0.057 19578 Dihedral : 4.766 32.466 14891 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 2.01 % Allowed : 10.39 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.07), residues: 13592 helix: 1.60 (0.07), residues: 5345 sheet: 0.22 (0.11), residues: 2382 loop : -0.63 (0.08), residues: 5865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 810 HIS 0.011 0.001 HIS F 219 PHE 0.026 0.001 PHE D2167 TYR 0.033 0.001 TYR C 912 ARG 0.012 0.000 ARG B1358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1018 time to evaluate : 8.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.7502 (t0) cc_final: 0.6682 (m110) REVERT: A 603 ASP cc_start: 0.8564 (m-30) cc_final: 0.8180 (t70) REVERT: A 654 MET cc_start: 0.7770 (mpp) cc_final: 0.7504 (mpp) REVERT: A 764 MET cc_start: 0.8797 (mtm) cc_final: 0.8369 (tpt) REVERT: A 839 MET cc_start: 0.7397 (mtp) cc_final: 0.6823 (tmm) REVERT: A 1099 ASP cc_start: 0.7879 (t0) cc_final: 0.7556 (t0) REVERT: A 1229 ASN cc_start: 0.7342 (p0) cc_final: 0.6800 (p0) REVERT: A 1529 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.7009 (m-40) REVERT: A 1570 PHE cc_start: 0.8462 (m-80) cc_final: 0.8112 (m-10) REVERT: A 1793 ASN cc_start: 0.8696 (t0) cc_final: 0.8339 (t0) REVERT: A 1881 MET cc_start: 0.8748 (tmm) cc_final: 0.8287 (tmm) REVERT: A 2311 MET cc_start: 0.8216 (tpt) cc_final: 0.7695 (tpt) REVERT: A 2324 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: A 2401 ASP cc_start: 0.7347 (m-30) cc_final: 0.7134 (m-30) REVERT: A 2468 LYS cc_start: 0.8939 (mttt) cc_final: 0.8629 (mttm) REVERT: B 496 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8078 (tp) REVERT: B 603 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6316 (t0) REVERT: B 1056 MET cc_start: 0.8241 (mtm) cc_final: 0.7904 (mpp) REVERT: B 1243 ASP cc_start: 0.6840 (t0) cc_final: 0.6520 (t0) REVERT: B 1295 ASP cc_start: 0.7384 (m-30) cc_final: 0.7038 (p0) REVERT: B 1353 ILE cc_start: 0.8387 (mt) cc_final: 0.8082 (pt) REVERT: B 1375 MET cc_start: 0.5809 (ptm) cc_final: 0.5600 (tpt) REVERT: B 1497 LYS cc_start: 0.8297 (tppt) cc_final: 0.7673 (tptm) REVERT: B 1530 TYR cc_start: 0.7691 (m-80) cc_final: 0.7404 (m-10) REVERT: B 1535 LEU cc_start: 0.8880 (mt) cc_final: 0.8601 (mp) REVERT: B 1836 ASP cc_start: 0.7841 (t0) cc_final: 0.7586 (t0) REVERT: B 2463 ASP cc_start: 0.7757 (t0) cc_final: 0.7550 (m-30) REVERT: C 209 GLU cc_start: 0.8389 (tp30) cc_final: 0.8153 (tp30) REVERT: C 231 MET cc_start: 0.7335 (mmm) cc_final: 0.7041 (mmm) REVERT: C 430 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.4985 (tt0) REVERT: C 553 ARG cc_start: 0.7737 (ttm-80) cc_final: 0.7315 (mmp80) REVERT: C 634 LEU cc_start: 0.8974 (tt) cc_final: 0.8577 (mt) REVERT: C 679 GLN cc_start: 0.8477 (tp40) cc_final: 0.7552 (mt0) REVERT: C 1321 ASP cc_start: 0.7534 (t0) cc_final: 0.7271 (t0) REVERT: C 1511 PHE cc_start: 0.7823 (m-80) cc_final: 0.7249 (m-80) REVERT: C 1657 ASP cc_start: 0.6627 (t0) cc_final: 0.5469 (t0) REVERT: C 1658 GLU cc_start: 0.6152 (mp0) cc_final: 0.5717 (mp0) REVERT: C 1975 SER cc_start: 0.9205 (t) cc_final: 0.8957 (p) REVERT: C 2014 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5749 (pmm) REVERT: C 2115 MET cc_start: 0.8901 (ppp) cc_final: 0.8652 (ppp) REVERT: C 2318 GLU cc_start: 0.7816 (tt0) cc_final: 0.7505 (tt0) REVERT: C 2324 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8182 (mtm180) REVERT: C 2426 TYR cc_start: 0.8894 (m-80) cc_final: 0.8673 (m-80) REVERT: D 212 GLN cc_start: 0.8145 (mm110) cc_final: 0.7909 (mp10) REVERT: D 231 MET cc_start: 0.4714 (tpp) cc_final: 0.4322 (tpp) REVERT: D 287 ASN cc_start: 0.8348 (m-40) cc_final: 0.7899 (p0) REVERT: D 341 MET cc_start: 0.1931 (OUTLIER) cc_final: 0.1564 (tpt) REVERT: D 439 LYS cc_start: 0.7214 (tmtt) cc_final: 0.6658 (pttm) REVERT: D 452 LEU cc_start: 0.6996 (pp) cc_final: 0.6773 (pp) REVERT: D 654 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.3870 (mmm) REVERT: D 1229 ASN cc_start: 0.7184 (p0) cc_final: 0.6812 (p0) REVERT: D 1311 GLU cc_start: 0.7743 (mp0) cc_final: 0.7299 (mp0) REVERT: D 1328 TYR cc_start: 0.8400 (m-80) cc_final: 0.8192 (m-80) REVERT: D 1570 PHE cc_start: 0.7290 (m-80) cc_final: 0.6843 (m-80) REVERT: D 1773 TYR cc_start: 0.8874 (t80) cc_final: 0.8490 (t80) REVERT: D 1777 MET cc_start: 0.8633 (mmm) cc_final: 0.8284 (mmm) REVERT: D 2165 MET cc_start: 0.8754 (ppp) cc_final: 0.8473 (tmm) REVERT: D 2267 ASP cc_start: 0.8090 (p0) cc_final: 0.7814 (p0) REVERT: E 264 TYR cc_start: 0.8467 (t80) cc_final: 0.8230 (t80) REVERT: E 341 MET cc_start: 0.7872 (mtp) cc_final: 0.7593 (mtm) REVERT: E 709 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8107 (p90) REVERT: E 766 TYR cc_start: 0.6100 (m-10) cc_final: 0.5484 (m-80) REVERT: E 1003 ASN cc_start: 0.8264 (t0) cc_final: 0.7965 (t0) REVERT: E 1242 GLU cc_start: 0.5366 (OUTLIER) cc_final: 0.4339 (mp0) REVERT: E 1790 ASP cc_start: 0.7983 (p0) cc_final: 0.7712 (p0) REVERT: E 1791 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7331 (mm-30) REVERT: E 2172 MET cc_start: 0.8634 (mtt) cc_final: 0.8289 (mtm) REVERT: F 28 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7438 (mp) REVERT: F 561 ASP cc_start: 0.7466 (t0) cc_final: 0.6889 (t0) REVERT: F 753 ASP cc_start: 0.8160 (t0) cc_final: 0.7878 (t70) REVERT: F 777 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7753 (pm20) outliers start: 235 outliers final: 182 residues processed: 1174 average time/residue: 0.8726 time to fit residues: 1822.3434 Evaluate side-chains 1162 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 967 time to evaluate : 8.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1913 ILE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2078 LEU Chi-restraints excluded: chain A residue 2324 ARG Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1555 PHE Chi-restraints excluded: chain B residue 1570 PHE Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2038 SER Chi-restraints excluded: chain B residue 2043 ILE Chi-restraints excluded: chain B residue 2064 ILE Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2385 THR Chi-restraints excluded: chain B residue 2454 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 649 PHE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 965 ASP Chi-restraints excluded: chain C residue 1069 LEU Chi-restraints excluded: chain C residue 1087 GLN Chi-restraints excluded: chain C residue 1102 ASN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1291 TYR Chi-restraints excluded: chain C residue 1299 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1347 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1554 THR Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1710 THR Chi-restraints excluded: chain C residue 1728 ASP Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 2003 SER Chi-restraints excluded: chain C residue 2014 MET Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2413 LYS Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 96 PHE Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 871 TRP Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 926 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1278 MET Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1655 HIS Chi-restraints excluded: chain D residue 1683 ASP Chi-restraints excluded: chain D residue 1758 MET Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1790 ASP Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1901 THR Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 2016 LEU Chi-restraints excluded: chain D residue 2022 MET Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2319 ASP Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain D residue 2409 ILE Chi-restraints excluded: chain D residue 2463 ASP Chi-restraints excluded: chain D residue 2491 MET Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 640 TRP Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 922 LEU Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1072 ASP Chi-restraints excluded: chain E residue 1199 LYS Chi-restraints excluded: chain E residue 1242 GLU Chi-restraints excluded: chain E residue 1264 MET Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1627 MET Chi-restraints excluded: chain E residue 1628 GLU Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1726 VAL Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1785 HIS Chi-restraints excluded: chain E residue 1827 TRP Chi-restraints excluded: chain E residue 1873 ARG Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 1945 THR Chi-restraints excluded: chain E residue 2022 MET Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2177 ASP Chi-restraints excluded: chain E residue 2267 ASP Chi-restraints excluded: chain E residue 2270 VAL Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 663 GLN Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 777 GLU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 855 ASP Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1193 optimal weight: 0.9990 chunk 1256 optimal weight: 7.9990 chunk 1146 optimal weight: 5.9990 chunk 1222 optimal weight: 0.4980 chunk 735 optimal weight: 30.0000 chunk 532 optimal weight: 20.0000 chunk 959 optimal weight: 5.9990 chunk 375 optimal weight: 0.8980 chunk 1104 optimal weight: 3.9990 chunk 1156 optimal weight: 0.8980 chunk 1218 optimal weight: 0.9980 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 220 GLN A 287 ASN ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1529 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN C 287 ASN ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1793 ASN C1972 HIS C2264 GLN D 679 GLN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1499 GLN D2143 ASN ** D2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 HIS ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1972 HIS E2465 ASN F 324 HIS ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 HIS ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 110643 Z= 0.159 Angle : 0.548 19.133 150332 Z= 0.279 Chirality : 0.040 0.275 16589 Planarity : 0.003 0.054 19578 Dihedral : 4.541 33.619 14891 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.56 % Allowed : 10.99 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.07), residues: 13592 helix: 1.76 (0.07), residues: 5338 sheet: 0.30 (0.11), residues: 2389 loop : -0.57 (0.08), residues: 5865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 640 HIS 0.009 0.001 HIS A 767 PHE 0.029 0.001 PHE D2167 TYR 0.027 0.001 TYR B1205 ARG 0.010 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1063 time to evaluate : 8.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.8530 (m-30) cc_final: 0.8148 (t70) REVERT: A 654 MET cc_start: 0.7730 (mpp) cc_final: 0.7433 (mpp) REVERT: A 764 MET cc_start: 0.8729 (mtm) cc_final: 0.8351 (tpt) REVERT: A 839 MET cc_start: 0.7403 (mtp) cc_final: 0.6757 (tmm) REVERT: A 1099 ASP cc_start: 0.7830 (t0) cc_final: 0.7531 (t0) REVERT: A 1229 ASN cc_start: 0.7294 (p0) cc_final: 0.6734 (p0) REVERT: A 1529 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6922 (m-40) REVERT: A 1793 ASN cc_start: 0.8655 (t0) cc_final: 0.8309 (t0) REVERT: A 1881 MET cc_start: 0.8745 (tmm) cc_final: 0.8304 (tmm) REVERT: A 2311 MET cc_start: 0.8106 (tpt) cc_final: 0.7586 (tpt) REVERT: A 2324 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7832 (mtm-85) REVERT: A 2397 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8309 (ttmm) REVERT: A 2401 ASP cc_start: 0.7317 (m-30) cc_final: 0.6969 (m-30) REVERT: A 2468 LYS cc_start: 0.8964 (mttt) cc_final: 0.8680 (mttm) REVERT: B 496 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8042 (tp) REVERT: B 603 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6305 (t0) REVERT: B 1056 MET cc_start: 0.8262 (mtm) cc_final: 0.7905 (mpp) REVERT: B 1243 ASP cc_start: 0.6755 (t0) cc_final: 0.6411 (t0) REVERT: B 1295 ASP cc_start: 0.7231 (m-30) cc_final: 0.6933 (p0) REVERT: B 1353 ILE cc_start: 0.8363 (mt) cc_final: 0.8056 (pt) REVERT: B 1375 MET cc_start: 0.5919 (ptm) cc_final: 0.5609 (tpt) REVERT: B 1497 LYS cc_start: 0.8213 (tppt) cc_final: 0.7609 (tptm) REVERT: B 1501 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8405 (mm) REVERT: B 1530 TYR cc_start: 0.7638 (m-80) cc_final: 0.7404 (m-10) REVERT: B 1535 LEU cc_start: 0.8773 (mt) cc_final: 0.8525 (mp) REVERT: B 1836 ASP cc_start: 0.7763 (t0) cc_final: 0.7380 (t0) REVERT: B 1963 LEU cc_start: 0.9476 (mt) cc_final: 0.9247 (mt) REVERT: B 2275 MET cc_start: 0.8297 (mtp) cc_final: 0.8043 (mtt) REVERT: B 2463 ASP cc_start: 0.7717 (t0) cc_final: 0.7514 (m-30) REVERT: C 209 GLU cc_start: 0.8394 (tp30) cc_final: 0.8130 (tp30) REVERT: C 231 MET cc_start: 0.7338 (mmm) cc_final: 0.7058 (mmm) REVERT: C 430 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5197 (tt0) REVERT: C 553 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7312 (mmp80) REVERT: C 634 LEU cc_start: 0.8960 (tt) cc_final: 0.8587 (mt) REVERT: C 679 GLN cc_start: 0.8408 (tp40) cc_final: 0.7488 (mt0) REVERT: C 803 MET cc_start: 0.8468 (ptp) cc_final: 0.8220 (ptp) REVERT: C 1321 ASP cc_start: 0.7489 (t0) cc_final: 0.7181 (t0) REVERT: C 1511 PHE cc_start: 0.7850 (m-80) cc_final: 0.7182 (m-80) REVERT: C 1709 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7017 (ttp) REVERT: C 1782 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.8000 (mtp85) REVERT: C 2014 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5593 (pmm) REVERT: C 2172 MET cc_start: 0.8355 (mtt) cc_final: 0.8082 (mtm) REVERT: C 2318 GLU cc_start: 0.7864 (tt0) cc_final: 0.7422 (tt0) REVERT: C 2324 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8072 (mtm180) REVERT: D 212 GLN cc_start: 0.8142 (mm110) cc_final: 0.7843 (mp10) REVERT: D 231 MET cc_start: 0.4825 (tpp) cc_final: 0.4483 (tpp) REVERT: D 439 LYS cc_start: 0.7140 (tmtt) cc_final: 0.6580 (pttm) REVERT: D 452 LEU cc_start: 0.7041 (pp) cc_final: 0.6813 (pp) REVERT: D 654 MET cc_start: 0.4089 (OUTLIER) cc_final: 0.3519 (mtm) REVERT: D 1311 GLU cc_start: 0.7712 (mp0) cc_final: 0.7268 (mp0) REVERT: D 1328 TYR cc_start: 0.8366 (m-80) cc_final: 0.7969 (m-80) REVERT: D 1375 MET cc_start: 0.8132 (pmm) cc_final: 0.7517 (ttt) REVERT: D 1528 MET cc_start: 0.5657 (tpp) cc_final: 0.4540 (tmm) REVERT: D 2165 MET cc_start: 0.8733 (ppp) cc_final: 0.8438 (tmm) REVERT: E 341 MET cc_start: 0.7914 (mtp) cc_final: 0.7640 (mtm) REVERT: E 709 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8098 (p90) REVERT: E 763 GLU cc_start: 0.6370 (tp30) cc_final: 0.6039 (mm-30) REVERT: E 766 TYR cc_start: 0.6270 (m-10) cc_final: 0.5345 (m-80) REVERT: E 1003 ASN cc_start: 0.8238 (t0) cc_final: 0.7898 (t0) REVERT: E 1242 GLU cc_start: 0.5169 (OUTLIER) cc_final: 0.4181 (mp0) REVERT: E 1336 ASP cc_start: 0.7719 (p0) cc_final: 0.7271 (t0) REVERT: E 1790 ASP cc_start: 0.7943 (p0) cc_final: 0.7664 (p0) REVERT: E 1791 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7415 (mm-30) REVERT: E 2193 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7445 (tp30) REVERT: F 91 ASP cc_start: 0.7529 (p0) cc_final: 0.7161 (p0) REVERT: F 561 ASP cc_start: 0.7358 (t0) cc_final: 0.6717 (t0) REVERT: F 753 ASP cc_start: 0.8211 (t0) cc_final: 0.7776 (t70) REVERT: F 777 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: F 1297 ARG cc_start: 0.7338 (mmm160) cc_final: 0.7053 (mmm160) REVERT: F 2158 MET cc_start: 0.5263 (mtp) cc_final: 0.4659 (mtp) outliers start: 182 outliers final: 134 residues processed: 1181 average time/residue: 0.8853 time to fit residues: 1855.2291 Evaluate side-chains 1135 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 988 time to evaluate : 8.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1529 ASN Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2324 ARG Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1555 PHE Chi-restraints excluded: chain B residue 1570 PHE Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2454 MET Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1087 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1291 TYR Chi-restraints excluded: chain C residue 1299 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1728 ASP Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 2014 MET Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2382 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1278 MET Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1655 HIS Chi-restraints excluded: chain D residue 1758 MET Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 640 TRP Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 897 LEU Chi-restraints excluded: chain E residue 922 LEU Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1072 ASP Chi-restraints excluded: chain E residue 1242 GLU Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1627 MET Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1726 VAL Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1761 SER Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2267 ASP Chi-restraints excluded: chain E residue 2270 VAL Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 377 HIS Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 663 GLN Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 777 GLU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 961 ASN Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 802 optimal weight: 0.9990 chunk 1292 optimal weight: 5.9990 chunk 788 optimal weight: 5.9990 chunk 613 optimal weight: 5.9990 chunk 898 optimal weight: 5.9990 chunk 1355 optimal weight: 10.0000 chunk 1247 optimal weight: 7.9990 chunk 1079 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 833 optimal weight: 4.9990 chunk 662 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 361 ASN ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1529 ASN ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 GLN ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1240 GLN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2479 GLN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 HIS ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1366 GLN ** F1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 110643 Z= 0.236 Angle : 0.571 17.739 150332 Z= 0.290 Chirality : 0.041 0.411 16589 Planarity : 0.004 0.056 19578 Dihedral : 4.522 31.643 14891 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 1.55 % Allowed : 11.35 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.19 % Twisted General : 0.03 % 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: 0.74 (0.07), residues: 13592 helix: 1.75 (0.07), residues: 5352 sheet: 0.29 (0.11), residues: 2391 loop : -0.58 (0.08), residues: 5849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP E 810 HIS 0.010 0.001 HIS F 377 PHE 0.040 0.001 PHE A1555 TYR 0.032 0.001 TYR E 264 ARG 0.008 0.000 ARG B1358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27184 Ramachandran restraints generated. 13592 Oldfield, 0 Emsley, 13592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1003 time to evaluate : 8.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.8557 (m-30) cc_final: 0.8145 (t70) REVERT: A 654 MET cc_start: 0.7657 (mpp) cc_final: 0.7314 (mpp) REVERT: A 764 MET cc_start: 0.8701 (mtm) cc_final: 0.8306 (tpt) REVERT: A 839 MET cc_start: 0.7399 (mtp) cc_final: 0.6794 (tmm) REVERT: A 1099 ASP cc_start: 0.7889 (t0) cc_final: 0.7553 (t0) REVERT: A 1229 ASN cc_start: 0.7295 (p0) cc_final: 0.6859 (t0) REVERT: A 1292 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: A 1793 ASN cc_start: 0.8680 (t0) cc_final: 0.8329 (t0) REVERT: A 1881 MET cc_start: 0.8756 (tmm) cc_final: 0.8319 (tmm) REVERT: A 1997 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8686 (m) REVERT: A 2311 MET cc_start: 0.8183 (tpt) cc_final: 0.7699 (tpt) REVERT: A 2324 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7847 (mtm-85) REVERT: A 2397 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8317 (ttmm) REVERT: A 2401 ASP cc_start: 0.7394 (m-30) cc_final: 0.7030 (m-30) REVERT: A 2468 LYS cc_start: 0.8951 (mttt) cc_final: 0.8676 (mttm) REVERT: B 457 LEU cc_start: 0.8665 (mt) cc_final: 0.8294 (pp) REVERT: B 496 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8082 (tp) REVERT: B 603 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6305 (t0) REVERT: B 1243 ASP cc_start: 0.6905 (t0) cc_final: 0.6704 (t0) REVERT: B 1295 ASP cc_start: 0.7383 (m-30) cc_final: 0.7037 (p0) REVERT: B 1353 ILE cc_start: 0.8372 (mt) cc_final: 0.8071 (pt) REVERT: B 1375 MET cc_start: 0.5920 (ptm) cc_final: 0.5665 (tpt) REVERT: B 1535 LEU cc_start: 0.8734 (mt) cc_final: 0.8504 (mp) REVERT: B 1836 ASP cc_start: 0.7743 (t0) cc_final: 0.7328 (t0) REVERT: C 209 GLU cc_start: 0.8413 (tp30) cc_final: 0.8162 (tp30) REVERT: C 231 MET cc_start: 0.7427 (mmm) cc_final: 0.7068 (mmm) REVERT: C 430 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5206 (tt0) REVERT: C 553 ARG cc_start: 0.7679 (ttm-80) cc_final: 0.7316 (mmp80) REVERT: C 634 LEU cc_start: 0.8961 (tt) cc_final: 0.8669 (mt) REVERT: C 654 MET cc_start: 0.6562 (ptp) cc_final: 0.6202 (ptp) REVERT: C 679 GLN cc_start: 0.8433 (tp40) cc_final: 0.7542 (mt0) REVERT: C 803 MET cc_start: 0.8545 (ptp) cc_final: 0.8202 (ptp) REVERT: C 1321 ASP cc_start: 0.7492 (t0) cc_final: 0.7209 (t0) REVERT: C 1511 PHE cc_start: 0.7849 (m-80) cc_final: 0.7164 (m-80) REVERT: C 1709 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7133 (ttp) REVERT: C 1782 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.8000 (mtp85) REVERT: C 2014 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.5667 (pmm) REVERT: C 2172 MET cc_start: 0.8367 (mtt) cc_final: 0.8096 (mtm) REVERT: C 2318 GLU cc_start: 0.7884 (tt0) cc_final: 0.7525 (tt0) REVERT: C 2324 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8127 (mtm180) REVERT: D 212 GLN cc_start: 0.8140 (mm110) cc_final: 0.7813 (mp10) REVERT: D 231 MET cc_start: 0.4770 (tpp) cc_final: 0.4298 (tpp) REVERT: D 439 LYS cc_start: 0.7141 (tmtt) cc_final: 0.6618 (pttm) REVERT: D 1311 GLU cc_start: 0.7755 (mp0) cc_final: 0.7311 (mp0) REVERT: D 1328 TYR cc_start: 0.8361 (m-80) cc_final: 0.7941 (m-80) REVERT: D 1375 MET cc_start: 0.8143 (pmm) cc_final: 0.7545 (ttt) REVERT: D 1528 MET cc_start: 0.5652 (tpp) cc_final: 0.4545 (tmm) REVERT: D 1570 PHE cc_start: 0.7309 (m-80) cc_final: 0.6925 (m-80) REVERT: D 1773 TYR cc_start: 0.8910 (t80) cc_final: 0.8519 (t80) REVERT: D 2165 MET cc_start: 0.8718 (ppp) cc_final: 0.8422 (tmm) REVERT: D 2267 ASP cc_start: 0.8125 (p0) cc_final: 0.7870 (p0) REVERT: E 709 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8102 (p90) REVERT: E 763 GLU cc_start: 0.6382 (tp30) cc_final: 0.6052 (mm-30) REVERT: E 766 TYR cc_start: 0.6245 (m-10) cc_final: 0.5324 (m-80) REVERT: E 1003 ASN cc_start: 0.8241 (t0) cc_final: 0.7945 (t0) REVERT: E 1242 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4321 (mp0) REVERT: E 1336 ASP cc_start: 0.7733 (p0) cc_final: 0.7278 (t0) REVERT: E 1790 ASP cc_start: 0.7977 (p0) cc_final: 0.7688 (p0) REVERT: E 1791 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7420 (mm-30) REVERT: E 1881 MET cc_start: 0.8696 (tmm) cc_final: 0.8163 (ttp) REVERT: E 2193 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7484 (tp30) REVERT: F 28 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6676 (pt) REVERT: F 561 ASP cc_start: 0.7363 (t0) cc_final: 0.6742 (t0) REVERT: F 752 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 753 ASP cc_start: 0.8214 (t0) cc_final: 0.8012 (t70) REVERT: F 777 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7758 (pm20) outliers start: 181 outliers final: 146 residues processed: 1116 average time/residue: 0.8866 time to fit residues: 1754.4199 Evaluate side-chains 1134 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 975 time to evaluate : 8.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1157 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1554 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1603 THR Chi-restraints excluded: chain A residue 1885 GLN Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2016 LEU Chi-restraints excluded: chain A residue 2324 ARG Chi-restraints excluded: chain A residue 2326 LYS Chi-restraints excluded: chain A residue 2357 ILE Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1351 ILE Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1555 PHE Chi-restraints excluded: chain B residue 1570 PHE Chi-restraints excluded: chain B residue 1634 GLU Chi-restraints excluded: chain B residue 1682 THR Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1945 THR Chi-restraints excluded: chain B residue 2016 LEU Chi-restraints excluded: chain B residue 2382 ASP Chi-restraints excluded: chain B residue 2454 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 603 ASP Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 772 ASN Chi-restraints excluded: chain C residue 805 THR Chi-restraints excluded: chain C residue 833 GLU Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 1087 GLN Chi-restraints excluded: chain C residue 1129 SER Chi-restraints excluded: chain C residue 1148 ASP Chi-restraints excluded: chain C residue 1291 TYR Chi-restraints excluded: chain C residue 1299 VAL Chi-restraints excluded: chain C residue 1314 SER Chi-restraints excluded: chain C residue 1347 SER Chi-restraints excluded: chain C residue 1353 ILE Chi-restraints excluded: chain C residue 1357 LEU Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1603 THR Chi-restraints excluded: chain C residue 1709 MET Chi-restraints excluded: chain C residue 1742 THR Chi-restraints excluded: chain C residue 1874 ASP Chi-restraints excluded: chain C residue 1892 ASP Chi-restraints excluded: chain C residue 2014 MET Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2163 TYR Chi-restraints excluded: chain C residue 2324 ARG Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2382 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 874 ILE Chi-restraints excluded: chain D residue 897 LEU Chi-restraints excluded: chain D residue 1278 MET Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1655 HIS Chi-restraints excluded: chain D residue 1683 ASP Chi-restraints excluded: chain D residue 1758 MET Chi-restraints excluded: chain D residue 1761 SER Chi-restraints excluded: chain D residue 1827 TRP Chi-restraints excluded: chain D residue 1947 LEU Chi-restraints excluded: chain D residue 2128 VAL Chi-restraints excluded: chain D residue 2391 VAL Chi-restraints excluded: chain D residue 2409 ILE Chi-restraints excluded: chain D residue 2463 ASP Chi-restraints excluded: chain D residue 2511 ILE Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 96 PHE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 640 TRP Chi-restraints excluded: chain E residue 709 HIS Chi-restraints excluded: chain E residue 716 ASP Chi-restraints excluded: chain E residue 796 HIS Chi-restraints excluded: chain E residue 966 ASP Chi-restraints excluded: chain E residue 1072 ASP Chi-restraints excluded: chain E residue 1242 GLU Chi-restraints excluded: chain E residue 1264 MET Chi-restraints excluded: chain E residue 1290 SER Chi-restraints excluded: chain E residue 1339 THR Chi-restraints excluded: chain E residue 1603 THR Chi-restraints excluded: chain E residue 1627 MET Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1696 ASP Chi-restraints excluded: chain E residue 1726 VAL Chi-restraints excluded: chain E residue 1752 ASN Chi-restraints excluded: chain E residue 1874 ASP Chi-restraints excluded: chain E residue 2022 MET Chi-restraints excluded: chain E residue 2024 GLU Chi-restraints excluded: chain E residue 2035 GLN Chi-restraints excluded: chain E residue 2267 ASP Chi-restraints excluded: chain E residue 2270 VAL Chi-restraints excluded: chain E residue 2287 ASP Chi-restraints excluded: chain E residue 2428 ASP Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 560 SER Chi-restraints excluded: chain F residue 571 VAL Chi-restraints excluded: chain F residue 572 GLU Chi-restraints excluded: chain F residue 576 THR Chi-restraints excluded: chain F residue 663 GLN Chi-restraints excluded: chain F residue 672 VAL Chi-restraints excluded: chain F residue 678 SER Chi-restraints excluded: chain F residue 693 ASN Chi-restraints excluded: chain F residue 744 HIS Chi-restraints excluded: chain F residue 777 GLU Chi-restraints excluded: chain F residue 829 ASP Chi-restraints excluded: chain F residue 978 ASP Chi-restraints excluded: chain F residue 1028 LEU Chi-restraints excluded: chain F residue 1033 ASP Chi-restraints excluded: chain F residue 1299 TRP Chi-restraints excluded: chain F residue 1329 ASP Chi-restraints excluded: chain F residue 1568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 857 optimal weight: 0.7980 chunk 1150 optimal weight: 0.9990 chunk 330 optimal weight: 1.9990 chunk 995 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 1081 optimal weight: 2.9990 chunk 452 optimal weight: 0.9990 chunk 1110 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 361 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 HIS ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN C 287 ASN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 767 HIS E1103 ASN ** E1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082135 restraints weight = 301363.769| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.17 r_work: 0.3018 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 110643 Z= 0.172 Angle : 0.553 16.963 150332 Z= 0.280 Chirality : 0.040 0.369 16589 Planarity : 0.003 0.060 19578 Dihedral : 4.416 33.241 14891 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 1.40 % Allowed : 11.65 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.07), residues: 13592 helix: 1.80 (0.07), residues: 5355 sheet: 0.34 (0.11), residues: 2410 loop : -0.56 (0.08), residues: 5827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP E 810 HIS 0.009 0.001 HIS A 767 PHE 0.036 0.001 PHE A 779 TYR 0.028 0.001 TYR B1205 ARG 0.007 0.000 ARG D 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31614.54 seconds wall clock time: 550 minutes 20.36 seconds (33020.36 seconds total)