Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 21:31:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/04_2023/6sue_10312.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/04_2023/6sue_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_10312/04_2023/6sue_10312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/04_2023/6sue_10312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/04_2023/6sue_10312.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sue_10312/04_2023/6sue_10312.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 38.45, per 1000 atoms: 0.36 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: 31.32 Conformation dependent library (CDL) restraints added in 11.2 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: 3.93 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: 33.36 Time building geometry restraints manager: 34.56 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: 2.350 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: 17.740 Check model and map are aligned: 1.160 Set scattering table: 0.690 Process input model: 191.110 Find NCS groups from input model: 5.670 Set up NCS constraints: 0.490 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: 0.030 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.770 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 9.103 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 outliers start: 1 outliers final: 1 residues processed: 2368 average time/residue: 0.9996 time to fit residues: 4010.3647 Evaluate side-chains 1162 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1161 time to evaluate : 9.130 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7322 time to fit residues: 13.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 319 ASN A 587 ASN A 679 GLN A 709 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 C1520 GLN C1671 ASN C2021 HIS C2035 GLN D 130 HIS D 580 ASN D 587 ASN D 848 GLN D1068 GLN D1132 ASN D1189 GLN D1499 GLN D1520 GLN D1842 GLN D1951 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 F1274 GLN F1342 GLN F1530 HIS F1546 GLN F1558 GLN F1564 ASN F1671 GLN F1946 ASN F1954 GLN F2003 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 110643 Z= 0.256 Angle : 0.667 11.240 150332 Z= 0.356 Chirality : 0.043 0.243 16589 Planarity : 0.005 0.072 19578 Dihedral : 5.169 34.439 14891 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer Outliers : 1.61 % 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: 1.16 (0.07), residues: 5248 sheet: 0.69 (0.10), residues: 2351 loop : -0.05 (0.08), residues: 5993 *********************** 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 1610 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1422 time to evaluate : 9.300 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 outliers start: 188 outliers final: 101 residues processed: 1528 average time/residue: 0.9257 time to fit residues: 2473.1434 Evaluate side-chains 1140 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1039 time to evaluate : 8.240 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 0.7195 time to fit residues: 148.1622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 686 optimal weight: 5.9990 chunk 383 optimal weight: 10.0000 chunk 1028 optimal weight: 4.9990 chunk 841 optimal weight: 9.9990 chunk 340 optimal weight: 6.9990 chunk 1238 optimal weight: 5.9990 chunk 1337 optimal weight: 0.0970 chunk 1102 optimal weight: 10.0000 chunk 1227 optimal weight: 3.9990 chunk 422 optimal weight: 50.0000 chunk 993 optimal weight: 2.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1341 ASN A1764 ASN A1793 ASN A1877 ASN A1916 GLN A2021 HIS A2461 GLN B 93 ASN B1087 GLN B2032 GLN ** B2414 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 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS C 709 HIS ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN C1303 ASN C1764 ASN C1812 GLN C1961 GLN C2195 GLN D 340 GLN D 361 ASN D 642 HIS D1174 GLN D1202 HIS D1303 ASN D1499 GLN D1793 ASN 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 E1951 GLN E2059 GLN E2195 GLN ** E2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2427 GLN E2505 ASN F 5 GLN ** 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** F1126 HIS F1252 GLN ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1650 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.094 110643 Z= 0.400 Angle : 0.662 14.979 150332 Z= 0.346 Chirality : 0.044 0.261 16589 Planarity : 0.005 0.067 19578 Dihedral : 5.049 33.501 14891 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.79 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: 0.64 (0.07), residues: 13592 helix: 1.29 (0.07), residues: 5309 sheet: 0.53 (0.11), residues: 2372 loop : -0.35 (0.08), residues: 5911 *********************** 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 1301 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1128 time to evaluate : 9.132 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 outliers start: 173 outliers final: 96 residues processed: 1241 average time/residue: 0.9159 time to fit residues: 2002.0829 Evaluate side-chains 1053 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 957 time to evaluate : 9.154 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.7734 time to fit residues: 152.3396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1223 optimal weight: 0.8980 chunk 930 optimal weight: 7.9990 chunk 642 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 590 optimal weight: 8.9990 chunk 831 optimal weight: 8.9990 chunk 1242 optimal weight: 7.9990 chunk 1315 optimal weight: 20.0000 chunk 649 optimal weight: 20.0000 chunk 1177 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1202 HIS A1292 GLN A1529 ASN A1599 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 644 GLN B1210 ASN B1252 GLN B1303 ASN B1951 GLN ** B2414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2497 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1520 GLN C1961 GLN C2455 ASN C2479 GLN D 295 GLN D 812 ASN D 866 ASN D 886 GLN D1499 GLN D1842 GLN D2459 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 866 ASN E1748 ASN E1951 GLN E1972 HIS ** E2278 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 377 HIS ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 790 HIS ** F1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1303 GLN F1359 HIS F1859 GLN F1870 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.125 110643 Z= 0.553 Angle : 0.736 18.053 150332 Z= 0.381 Chirality : 0.046 0.219 16589 Planarity : 0.005 0.079 19578 Dihedral : 5.323 34.782 14891 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.01 % 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: 0.24 (0.07), residues: 13592 helix: 1.13 (0.07), residues: 5295 sheet: 0.18 (0.11), residues: 2348 loop : -0.67 (0.08), residues: 5949 *********************** 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 1242 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1034 time to evaluate : 9.346 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 outliers start: 208 outliers final: 109 residues processed: 1166 average time/residue: 0.9218 time to fit residues: 1892.2678 Evaluate side-chains 1014 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 905 time to evaluate : 8.242 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.7999 time to fit residues: 174.0375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1095 optimal weight: 0.9990 chunk 746 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 979 optimal weight: 20.0000 chunk 542 optimal weight: 2.9990 chunk 1122 optimal weight: 3.9990 chunk 909 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 671 optimal weight: 0.9980 chunk 1180 optimal weight: 1.9990 chunk 331 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN A1261 ASN A1951 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1189 GLN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1289 ASN ** C1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1951 GLN C1961 GLN C2264 GLN D 854 GLN D1842 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 HIS ** 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 E1293 GLN E1667 HIS E1842 GLN E2021 HIS ** E2278 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 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 HIS ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1337 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 110643 Z= 0.193 Angle : 0.562 14.517 150332 Z= 0.291 Chirality : 0.041 0.282 16589 Planarity : 0.004 0.057 19578 Dihedral : 4.882 32.752 14891 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.08 % Favored : 96.85 % Rotamer Outliers : 0.96 % 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: 0.55 (0.07), residues: 13592 helix: 1.47 (0.07), residues: 5344 sheet: 0.26 (0.11), residues: 2374 loop : -0.59 (0.08), residues: 5874 *********************** 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 1209 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1097 time to evaluate : 9.282 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 outliers start: 112 outliers final: 53 residues processed: 1160 average time/residue: 0.9323 time to fit residues: 1913.2414 Evaluate side-chains 1014 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 961 time to evaluate : 9.138 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.8172 time to fit residues: 93.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 260 optimal weight: 10.0000 chunk 772 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 1316 optimal weight: 10.0000 chunk 1093 optimal weight: 8.9990 chunk 609 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 chunk 435 optimal weight: 2.9990 chunk 691 optimal weight: 0.3980 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A1951 GLN A1961 GLN ** 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** B1240 GLN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1289 ASN C2455 ASN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2278 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 ASN ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1842 GLN ** E2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS ** 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** F 681 HIS ** F1281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1337 GLN F1394 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 110643 Z= 0.190 Angle : 0.546 17.416 150332 Z= 0.281 Chirality : 0.040 0.289 16589 Planarity : 0.004 0.057 19578 Dihedral : 4.679 32.752 14891 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.68 (0.07), residues: 13592 helix: 1.63 (0.07), residues: 5347 sheet: 0.30 (0.11), residues: 2399 loop : -0.54 (0.08), residues: 5846 *********************** 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 1118 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1036 time to evaluate : 8.233 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 outliers start: 82 outliers final: 40 residues processed: 1083 average time/residue: 0.9494 time to fit residues: 1821.9086 Evaluate side-chains 1006 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 966 time to evaluate : 9.117 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.8194 time to fit residues: 73.6964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1269 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 750 optimal weight: 6.9990 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: 7.9990 chunk 820 optimal weight: 6.9990 chunk 799 optimal weight: 5.9990 chunk 605 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 306 GLN A1292 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B1007 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 ASN B1547 ASN B1951 GLN B2032 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1951 GLN D 527 GLN D 571 HIS ** D 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1842 GLN ** 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** ** E 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 866 ASN E1007 ASN E1293 GLN ** E2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 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 412 GLN ** 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** F1992 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.112 110643 Z= 0.519 Angle : 0.687 16.284 150332 Z= 0.353 Chirality : 0.045 0.218 16589 Planarity : 0.005 0.085 19578 Dihedral : 5.012 31.180 14891 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.50 % Favored : 95.45 % Rotamer Outliers : 1.01 % 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: 0.36 (0.07), residues: 13592 helix: 1.39 (0.07), residues: 5311 sheet: 0.07 (0.11), residues: 2406 loop : -0.71 (0.08), residues: 5875 *********************** 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 1079 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 961 time to evaluate : 9.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 72 residues processed: 1020 average time/residue: 0.9372 time to fit residues: 1693.0964 Evaluate side-chains 980 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 908 time to evaluate : 9.164 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.7967 time to fit residues: 119.2765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 811 optimal weight: 5.9990 chunk 523 optimal weight: 0.2980 chunk 783 optimal weight: 0.9980 chunk 395 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 833 optimal weight: 0.9980 chunk 893 optimal weight: 2.9990 chunk 648 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 1031 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1289 ASN B1547 ASN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1951 GLN ** B2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN C1174 GLN C1289 ASN ** C1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1951 GLN C2455 ASN D 679 GLN ** D 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2143 ASN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 HIS ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1293 GLN ** E2278 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** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 110643 Z= 0.177 Angle : 0.565 20.943 150332 Z= 0.288 Chirality : 0.040 0.219 16589 Planarity : 0.004 0.054 19578 Dihedral : 4.729 33.603 14891 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer Outliers : 0.39 % 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: 0.58 (0.07), residues: 13592 helix: 1.61 (0.07), residues: 5350 sheet: 0.16 (0.11), residues: 2420 loop : -0.63 (0.08), residues: 5822 *********************** 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 1057 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1012 time to evaluate : 9.686 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 outliers start: 45 outliers final: 24 residues processed: 1031 average time/residue: 0.9643 time to fit residues: 1761.1622 Evaluate side-chains 963 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 939 time to evaluate : 9.145 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.8630 time to fit residues: 50.5816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 1193 optimal weight: 0.6980 chunk 1256 optimal weight: 8.9990 chunk 1146 optimal weight: 8.9990 chunk 1222 optimal weight: 0.9980 chunk 735 optimal weight: 30.0000 chunk 532 optimal weight: 20.0000 chunk 959 optimal weight: 10.0000 chunk 375 optimal weight: 5.9990 chunk 1104 optimal weight: 7.9990 chunk 1156 optimal weight: 0.0770 chunk 1218 optimal weight: 0.9980 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 GLN ** 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** B1631 ASN B2032 GLN B2497 GLN C 240 ASN C 761 GLN C 875 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2113 GLN D 287 ASN ** D 866 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2479 GLN F 163 GLN ** 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** F1366 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 110643 Z= 0.223 Angle : 0.567 17.288 150332 Z= 0.289 Chirality : 0.041 0.250 16589 Planarity : 0.004 0.059 19578 Dihedral : 4.623 32.316 14891 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer Outliers : 0.33 % 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: 0.66 (0.07), residues: 13592 helix: 1.69 (0.07), residues: 5322 sheet: 0.19 (0.11), residues: 2410 loop : -0.59 (0.08), residues: 5860 *********************** 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 1015 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 977 time to evaluate : 9.201 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 outliers start: 38 outliers final: 29 residues processed: 996 average time/residue: 0.9516 time to fit residues: 1681.9118 Evaluate side-chains 974 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 945 time to evaluate : 9.116 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.7961 time to fit residues: 55.6727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 802 optimal weight: 5.9990 chunk 1292 optimal weight: 7.9990 chunk 788 optimal weight: 2.9990 chunk 613 optimal weight: 9.9990 chunk 898 optimal weight: 4.9990 chunk 1355 optimal weight: 0.0010 chunk 1247 optimal weight: 4.9990 chunk 1079 optimal weight: 0.0570 chunk 112 optimal weight: 0.9980 chunk 833 optimal weight: 5.9990 chunk 662 optimal weight: 1.9990 overall best weight: 1.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** A 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2237 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1631 ASN ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN B2059 GLN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2455 ASN ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2278 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 110643 Z= 0.181 Angle : 0.559 17.882 150332 Z= 0.284 Chirality : 0.040 0.276 16589 Planarity : 0.003 0.051 19578 Dihedral : 4.532 32.934 14891 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.07), residues: 13592 helix: 1.74 (0.07), residues: 5335 sheet: 0.26 (0.11), residues: 2387 loop : -0.56 (0.08), residues: 5870 ********************** 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 1021 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 998 time to evaluate : 9.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 1004 average time/residue: 0.9503 time to fit residues: 1694.8039 Evaluate side-chains 963 residues out of total 11682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 952 time to evaluate : 9.147 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.8520 time to fit residues: 29.3978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1361 random chunks: chunk 857 optimal weight: 0.4980 chunk 1150 optimal weight: 0.0870 chunk 330 optimal weight: 0.1980 chunk 995 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 1081 optimal weight: 1.9990 chunk 452 optimal weight: 1.9990 chunk 1110 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1655 HIS ** B1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2032 GLN C 259 ASN C 875 ASN ** C 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1103 ASN ** E2278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2479 GLN ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079000 restraints weight = 302166.173| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.92 r_work: 0.3021 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 110643 Z= 0.165 Angle : 0.554 17.597 150332 Z= 0.281 Chirality : 0.040 0.268 16589 Planarity : 0.003 0.056 19578 Dihedral : 4.429 33.400 14891 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.39 % Rotamer Outliers : 0.19 % 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: 0.81 (0.07), residues: 13592 helix: 1.84 (0.07), residues: 5286 sheet: 0.33 (0.11), residues: 2364 loop : -0.54 (0.08), residues: 5942 =============================================================================== Job complete usr+sys time: 30594.42 seconds wall clock time: 534 minutes 7.97 seconds (32047.97 seconds total)