Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 02:08:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6suf_10313/07_2023/6suf_10313.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6suf_10313/07_2023/6suf_10313.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/6suf_10313/07_2023/6suf_10313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6suf_10313/07_2023/6suf_10313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6suf_10313/07_2023/6suf_10313.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6suf_10313/07_2023/6suf_10313.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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 330 5.16 5 C 68379 2.51 5 N 18455 2.21 5 O 20948 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 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 PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "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 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 TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1040": "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 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 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 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1508": "OE1" <-> "OE2" Residue "A PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1602": "NH1" <-> "NH2" Residue "A PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1634": "OE1" <-> "OE2" Residue "A PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1725": "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 PHE 1789": "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 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2099": "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 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2377": "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 "B PHE 96": "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 PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "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 PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 604": "OE1" <-> "OE2" 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 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 842": "OD1" <-> "OD2" Residue "B PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1046": "OD1" <-> "OD2" Residue "B ARG 1050": "NH1" <-> "NH2" Residue "B PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1173": "OE1" <-> "OE2" Residue "B TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1194": "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 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1768": "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 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1883": "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 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 TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2469": "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 GLU 121": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "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 346": "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 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 519": "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 TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 842": "OD1" <-> "OD2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 964": "NH1" <-> "NH2" Residue "C ARG 1050": "NH1" <-> "NH2" Residue "C PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1294": "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 PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1760": "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 TYR 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 GLU 2200": "OE1" <-> "OE2" Residue "C TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 842": "OD1" <-> "OD2" Residue "D PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 964": "NH1" <-> "NH2" Residue "D TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 1250": "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 TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1602": "NH1" <-> "NH2" Residue "D PHE 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1703": "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 1805": "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 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 PHE 2147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2402": "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 TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 488": "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 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 912": "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 PHE 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1205": "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 TYR 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 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 1703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1767": "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 1814": "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 PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2402": "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 TYR 2513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 772": "OD1" <-> "OD2" Residue "F PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1010": "NH1" <-> "NH2" Residue "F TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1033": "OD1" <-> "OD2" Residue "F PHE 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1076": "OE1" <-> "OE2" Residue "F PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1764": "OE1" <-> "OE2" Residue "F TYR 1802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1875": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 108112 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: 17127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2147, 17127 Classifications: {'peptide': 2147} Link IDs: {'PTRANS': 115, 'TRANS': 2031} Chain breaks: 1 Time building chain proxies: 36.17, per 1000 atoms: 0.33 Number of scatterers: 108112 At special positions: 0 Unit cell: (233.1, 224.7, 364.35, 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 330 16.00 O 20948 8.00 N 18455 7.00 C 68379 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: 31.68 Conformation dependent library (CDL) restraints added in 11.5 seconds 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25700 Finding SS restraints... Secondary structure from input PDB file: 504 helices and 0 sheets defined 44.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 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 removed outlier: 3.644A pdb=" N GLN A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.445A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 453 through 463 Processing helix chain 'A' and resid 471 through 488 removed outlier: 4.109A pdb=" N LYS A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 499 removed outlier: 3.939A pdb=" N ILE A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.535A pdb=" N THR A 549 " --> pdb=" O ASP A 545 " (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 612 removed outlier: 4.090A pdb=" N ILE A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 645 removed outlier: 3.797A pdb=" N TRP A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 Processing helix chain 'A' and resid 664 through 681 removed outlier: 5.168A pdb=" N LEU A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N HIS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 Proline residue: A 694 - end of helix removed outlier: 4.207A pdb=" N ALA A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 719 Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.585A pdb=" N ASP A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 770 removed outlier: 3.855A pdb=" N HIS A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 782 removed outlier: 4.106A pdb=" N PHE A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 797 through 815 Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 842 through 856 Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 870 through 888 Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'A' and resid 911 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'A' and resid 927 through 954 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 985 through 1002 removed outlier: 3.791A pdb=" N ALA A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 5.469A 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: 3.902A pdb=" N GLN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 4.362A 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 Processing helix chain 'A' and resid 1153 through 1157 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 1291 removed outlier: 3.623A pdb=" N VAL A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1379 removed outlier: 3.614A pdb=" N LYS A1377 " --> pdb=" O ASN A1373 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A1379 " --> pdb=" O MET A1375 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1620 through 1625 Processing helix chain 'A' and resid 1628 through 1632 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 removed outlier: 3.954A pdb=" N PHE A1768 " --> pdb=" O ASN A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1785 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 1844 removed outlier: 4.334A pdb=" N GLN A1842 " --> pdb=" O ASP A1838 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A1843 " --> pdb=" O ALA A1839 " (cutoff:3.500A) 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: 4.043A pdb=" N TYR A1959 " --> pdb=" O VAL A1955 " (cutoff:3.500A) removed outlier: 4.237A 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: 3.656A pdb=" N GLU A2024 " --> pdb=" O PRO A2020 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2145 removed outlier: 4.002A pdb=" N ASP A2139 " --> pdb=" O GLY A2135 " (cutoff:3.500A) Proline residue: A2142 - end of helix Processing helix chain 'A' and resid 2150 through 2153 Processing helix chain 'A' and resid 2154 through 2167 Processing helix chain 'A' and resid 2167 through 2244 Processing helix chain 'A' and resid 2247 through 2284 Processing helix chain 'A' and resid 2293 through 2297 removed outlier: 4.204A pdb=" N ALA A2296 " --> pdb=" O LYS A2293 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP A2297 " --> pdb=" O PRO A2294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2293 through 2297' Processing helix chain 'A' and resid 2299 through 2304 removed outlier: 4.427A pdb=" N GLY A2303 " --> pdb=" O THR A2300 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2325 Processing helix chain 'A' and resid 2337 through 2343 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2352 through 2363 Processing helix chain 'A' and resid 2394 through 2397 Processing helix chain 'A' and resid 2398 through 2402 Processing helix chain 'A' and resid 2403 through 2407 Processing helix chain 'A' and resid 2490 through 2494 Processing helix chain 'A' and resid 2497 through 2502 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 151 through 155 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 removed outlier: 3.847A pdb=" N ARG B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 214 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: 3.656A pdb=" N LEU B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 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 removed outlier: 3.567A pdb=" N LYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.986A pdb=" N ARG B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 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 451 Processing helix chain 'B' and resid 453 through 463 removed outlier: 5.096A pdb=" N GLY B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) 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 555 removed outlier: 3.522A pdb=" N THR B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 598 Processing helix chain 'B' and resid 601 through 613 removed outlier: 3.863A 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: 3.502A pdb=" N THR B 636 " --> pdb=" O ARG B 632 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER B 639 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TRP B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 655 Processing helix chain 'B' and resid 664 through 678 removed outlier: 5.806A pdb=" N LEU B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 671 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'B' and resid 726 through 736 Processing helix chain 'B' and resid 748 through 770 Processing helix chain 'B' and resid 772 through 781 Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 802 through 815 Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 833 through 840 Processing helix chain 'B' and resid 842 through 853 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 Processing helix chain 'B' and resid 911 through 924 Processing helix chain 'B' and resid 927 through 954 removed outlier: 4.218A 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 removed outlier: 4.024A pdb=" N ALA B 991 " --> pdb=" O ALA B 987 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N GLN B 994 " --> pdb=" O ILE B 990 " (cutoff:3.500A) 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: 3.881A pdb=" N VAL B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) removed outlier: 4.276A 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: 4.063A pdb=" N SER B1156 " --> pdb=" O PRO B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1222 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1279 through 1291 removed outlier: 4.201A pdb=" N VAL B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B1289 " --> pdb=" O VAL B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1378 Processing helix chain 'B' and resid 1494 through 1497 Processing helix chain 'B' and resid 1513 through 1517 removed outlier: 3.659A 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 1540 through 1542 No H-bonds generated for 'chain 'B' and resid 1540 through 1542' Processing helix chain 'B' and resid 1609 through 1618 Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1628 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: 3.935A 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 1840 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: 4.026A pdb=" N TYR B1959 " --> pdb=" O VAL B1955 " (cutoff:3.500A) removed outlier: 4.220A 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 2139 Processing helix chain 'B' and resid 2140 through 2145 Processing helix chain 'B' and resid 2150 through 2154 Processing helix chain 'B' and resid 2155 through 2167 Processing helix chain 'B' and resid 2167 through 2244 removed outlier: 3.765A 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: 4.017A pdb=" N ALA B2296 " --> pdb=" O LYS B2293 " (cutoff:3.500A) removed outlier: 4.468A 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: 4.480A pdb=" N GLY B2303 " --> pdb=" O THR B2300 " (cutoff:3.500A) Processing helix chain 'B' and resid 2305 through 2325 Processing helix chain 'B' and resid 2337 through 2343 Processing helix chain 'B' and resid 2345 through 2349 Processing helix chain 'B' and resid 2352 through 2363 Processing helix chain 'B' and resid 2394 through 2402 removed outlier: 3.720A pdb=" N LYS B2397 " --> pdb=" O ALA B2394 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE B2398 " --> pdb=" O ASP B2395 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B2399 " --> pdb=" O LEU B2396 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR B2402 " --> pdb=" O ARG B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2403 through 2407 Processing helix chain 'B' and resid 2499 through 2504 Processing helix chain 'C' and resid 114 through 127 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 189 through 193 removed outlier: 3.522A pdb=" N ARG C 193 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 removed outlier: 4.004A pdb=" N GLU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) 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: 3.652A pdb=" N LEU C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 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 removed outlier: 3.730A pdb=" N LYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) 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 451 Processing helix chain 'C' and resid 453 through 465 removed outlier: 3.518A pdb=" N SER C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 488 Processing helix chain 'C' and resid 491 through 499 removed outlier: 4.267A pdb=" N ILE C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.512A pdb=" N GLY C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 612 removed outlier: 3.520A pdb=" N LEU C 607 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 645 Processing helix chain 'C' and resid 647 through 656 Processing helix chain 'C' and resid 664 through 679 removed outlier: 4.358A 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 removed outlier: 4.262A pdb=" N ALA C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 719 Processing helix chain 'C' and resid 726 through 736 Processing helix chain 'C' and resid 747 through 769 Processing helix chain 'C' and resid 774 through 782 removed outlier: 5.068A pdb=" N VAL C 780 " --> pdb=" O PHE C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 786 Processing helix chain 'C' and resid 797 through 815 Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 833 through 839 Processing helix chain 'C' and resid 842 through 854 Processing helix chain 'C' and resid 863 through 867 Processing helix chain 'C' and resid 870 through 887 removed outlier: 5.841A pdb=" N THR C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN C 879 " --> pdb=" O ASN C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 899 removed outlier: 3.672A pdb=" N GLY C 893 " --> pdb=" O VAL C 889 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 897 " --> pdb=" O GLY C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 924 Processing helix chain 'C' and resid 927 through 954 Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 984 through 1002 removed outlier: 3.897A pdb=" N ALA C 991 " --> pdb=" O ALA C 987 " (cutoff:3.500A) removed outlier: 5.571A 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 1066 Processing helix chain 'C' and resid 1070 through 1090 removed outlier: 3.930A pdb=" N GLN C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) removed outlier: 4.532A 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 1153 through 1156 Processing helix chain 'C' and resid 1217 through 1223 removed outlier: 3.656A pdb=" N GLU C1223 " --> pdb=" O LYS C1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 1256 through 1260 Processing helix chain 'C' and resid 1279 through 1291 removed outlier: 4.181A pdb=" N VAL C1285 " --> pdb=" O GLU C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1379 removed outlier: 3.631A pdb=" N GLY C1379 " --> pdb=" O MET C1375 " (cutoff:3.500A) 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 1620 Processing helix chain 'C' and resid 1620 through 1625 Processing helix chain 'C' and resid 1627 through 1631 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: 3.873A 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 1841 Processing helix chain 'C' and resid 1845 through 1869 removed outlier: 3.891A pdb=" N ILE C1861 " --> pdb=" O LEU C1857 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY C1864 " --> pdb=" O LEU C1860 " (cutoff:3.500A) Processing helix chain 'C' and resid 1872 through 1891 Processing helix chain 'C' and resid 1906 through 1911 Processing helix chain 'C' and resid 1953 through 1972 removed outlier: 4.088A pdb=" N TYR C1959 " --> pdb=" O VAL C1955 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP C1960 " --> pdb=" O MET C1956 " (cutoff:3.500A) Processing helix chain 'C' and resid 1991 through 2004 Processing helix chain 'C' and resid 2018 through 2105 Processing helix chain 'C' and resid 2108 through 2145 removed outlier: 3.745A pdb=" N ASP C2139 " --> pdb=" O GLY C2135 " (cutoff:3.500A) Proline residue: C2142 - end of helix 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 2299 through 2304 removed outlier: 3.806A 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 2342 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 2401 removed outlier: 6.178A pdb=" N ILE C2398 " --> pdb=" O ASP C2395 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG C2399 " --> pdb=" O LEU C2396 " (cutoff:3.500A) 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 removed outlier: 3.924A pdb=" N LYS C2502 " --> pdb=" O ALA C2498 " (cutoff:3.500A) 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 152 through 157 Processing helix chain 'D' and resid 162 through 175 Processing helix chain 'D' and resid 176 through 179 removed outlier: 4.024A pdb=" N LEU D 179 " --> pdb=" O GLU D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 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 223 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.574A pdb=" N LEU D 236 " --> pdb=" O HIS D 232 " (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: 4.072A 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 437 through 450 Processing helix chain 'D' and resid 453 through 462 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 583 through 598 Processing helix chain 'D' and resid 601 through 608 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: 5.485A pdb=" N LEU D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) removed outlier: 3.916A 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 693 through 696 Processing helix chain 'D' and resid 704 through 719 removed outlier: 4.520A pdb=" N SER D 710 " --> pdb=" O ASN D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 735 Processing helix chain 'D' and resid 748 through 770 Processing helix chain 'D' and resid 772 through 782 removed outlier: 4.190A pdb=" N VAL D 780 " --> pdb=" O PHE D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 786 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 840 Processing helix chain 'D' and resid 842 through 856 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 removed outlier: 3.633A pdb=" N ALA D 896 " --> pdb=" O GLN D 892 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 897 " --> pdb=" O GLY D 893 " (cutoff:3.500A) 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: 3.810A pdb=" N ALA D 991 " --> pdb=" O ALA D 987 " (cutoff:3.500A) removed outlier: 5.515A 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: 3.814A pdb=" N GLN D1087 " --> pdb=" O THR D1083 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) removed outlier: 4.441A 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 1153 through 1156 removed outlier: 3.949A pdb=" N SER D1156 " --> pdb=" O PRO D1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1153 through 1156' Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1279 through 1291 removed outlier: 4.326A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1366 through 1379 removed outlier: 3.508A pdb=" N LYS D1377 " --> pdb=" O ASN D1373 " (cutoff:3.500A) Processing helix chain 'D' and resid 1513 through 1517 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 removed outlier: 3.915A pdb=" N PHE D1768 " --> pdb=" O ASN D1764 " (cutoff:3.500A) 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: 4.159A pdb=" N GLN D1842 " --> pdb=" O ASP D1838 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D1843 " --> pdb=" O ALA D1839 " (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: 3.999A pdb=" N TYR D1959 " --> pdb=" O VAL D1955 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TRP D1960 " --> pdb=" O MET D1956 " (cutoff:3.500A) Processing helix chain 'D' and resid 1991 through 2005 removed outlier: 3.760A pdb=" N GLY D2005 " --> pdb=" O ALA D2001 " (cutoff:3.500A) 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 2153 Processing helix chain 'D' and resid 2154 through 2167 Processing helix chain 'D' and resid 2167 through 2244 Processing helix chain 'D' and resid 2247 through 2284 Processing helix chain 'D' and resid 2293 through 2297 removed outlier: 4.017A pdb=" N ALA D2296 " --> pdb=" O LYS D2293 " (cutoff:3.500A) removed outlier: 4.384A 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: 4.413A pdb=" N GLY D2303 " --> pdb=" O THR D2300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2305 through 2323 Processing helix chain 'D' and resid 2337 through 2342 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 2490 through 2494 Processing helix chain 'D' and resid 2497 through 2502 removed outlier: 3.813A pdb=" N LYS D2502 " --> pdb=" O ALA D2498 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 127 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: 4.133A pdb=" N ARG E 208 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE E 211 " --> pdb=" O VAL E 207 " (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: 3.903A pdb=" N LEU E 236 " --> pdb=" O HIS E 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 237 " --> pdb=" O GLN E 233 " (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 removed outlier: 3.609A pdb=" N LYS E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 3.537A pdb=" N LEU E 276 " --> pdb=" O GLU E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.960A pdb=" N ARG E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) 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 465 Processing helix chain 'E' and resid 471 through 488 removed outlier: 3.770A pdb=" N LYS E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 498 Processing helix chain 'E' and resid 513 through 520 removed outlier: 3.678A pdb=" N LEU E 518 " --> pdb=" O GLN E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 556 removed outlier: 3.592A 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 601 through 613 removed outlier: 4.084A pdb=" N ASP E 606 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 607 " --> pdb=" O ASP E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 645 removed outlier: 3.647A pdb=" N SER E 639 " --> pdb=" O ASN E 635 " (cutoff:3.500A) removed outlier: 4.191A 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: 5.318A 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: 3.946A pdb=" N ALA E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 699 " --> pdb=" O TYR E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 719 removed outlier: 3.507A pdb=" N ALA E 715 " --> pdb=" O VAL E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 738 removed outlier: 3.552A pdb=" N TYR E 738 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 770 removed outlier: 3.924A pdb=" N VAL E 753 " --> pdb=" O GLN E 749 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN E 754 " --> pdb=" O GLU E 750 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR E 755 " --> pdb=" O HIS E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 782 removed outlier: 3.528A pdb=" N ARG E 777 " --> pdb=" O GLU E 773 " (cutoff:3.500A) removed outlier: 4.210A 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 856 Processing helix chain 'E' and resid 863 through 867 Processing helix chain 'E' and resid 870 through 888 Processing helix chain 'E' and resid 889 through 896 removed outlier: 3.550A pdb=" N GLY E 893 " --> pdb=" O VAL E 889 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA E 896 " --> pdb=" O GLN E 892 " (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: 3.834A pdb=" N ALA E 991 " --> pdb=" O ALA E 987 " (cutoff:3.500A) removed outlier: 5.507A 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 1038 Processing helix chain 'E' and resid 1040 through 1044 Processing helix chain 'E' and resid 1054 through 1065 Processing helix chain 'E' and resid 1070 through 1090 removed outlier: 3.814A pdb=" N VAL E1088 " --> pdb=" O SER E1084 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN E1090 " --> pdb=" O GLU E1086 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 1217 through 1222 Processing helix chain 'E' and resid 1255 through 1260 Processing helix chain 'E' and resid 1279 through 1288 removed outlier: 4.296A pdb=" N VAL E1285 " --> pdb=" O GLU E1281 " (cutoff:3.500A) Processing helix chain 'E' and resid 1366 through 1378 removed outlier: 3.502A pdb=" N ASN E1370 " --> pdb=" O GLY E1366 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1517 removed outlier: 3.560A pdb=" N VAL E1517 " --> pdb=" O ALA E1513 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1513 through 1517' Processing helix chain 'E' and resid 1540 through 1542 No H-bonds generated for 'chain 'E' and resid 1540 through 1542' Processing helix chain 'E' and resid 1609 through 1619 Processing helix chain 'E' and resid 1620 through 1625 Processing helix chain 'E' and resid 1627 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: 3.871A 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: 4.320A pdb=" N GLN E1842 " --> pdb=" O ASP E1838 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E1843 " --> pdb=" O ALA E1839 " (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: 3.985A pdb=" N TYR E1959 " --> pdb=" O VAL E1955 " (cutoff:3.500A) removed outlier: 4.262A 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 2008 removed outlier: 3.593A pdb=" N LYS E2008 " --> pdb=" O GLY E2005 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2005 through 2008' Processing helix chain 'E' and resid 2018 through 2105 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 2153 Processing helix chain 'E' and resid 2154 through 2167 Processing helix chain 'E' and resid 2167 through 2242 removed outlier: 3.844A pdb=" N GLN E2230 " --> pdb=" O SER E2226 " (cutoff:3.500A) Processing helix chain 'E' and resid 2247 through 2284 Processing helix chain 'E' and resid 2299 through 2304 removed outlier: 4.476A pdb=" N GLY E2303 " --> pdb=" O THR E2300 " (cutoff:3.500A) Processing helix chain 'E' and resid 2305 through 2323 Processing helix chain 'E' and resid 2337 through 2343 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 2496 through 2501 removed outlier: 4.310A pdb=" N MET E2500 " --> pdb=" O LYS E2496 " (cutoff:3.500A) Processing helix chain 'E' and resid 2502 through 2504 No H-bonds generated for 'chain 'E' and resid 2502 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 220 Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.849A 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 400 through 404 removed outlier: 3.977A pdb=" N GLU F 404 " --> pdb=" O LEU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 Processing helix chain 'F' and resid 606 through 608 No H-bonds generated for 'chain 'F' and resid 606 through 608' Processing helix chain 'F' and resid 717 through 730 Processing helix chain 'F' and resid 820 through 825 Processing helix chain 'F' and resid 854 through 864 removed outlier: 3.699A pdb=" N ALA F 864 " --> pdb=" O TRP F 860 " (cutoff:3.500A) Processing helix chain 'F' and resid 972 through 976 Processing helix chain 'F' and resid 978 through 982 Processing helix chain 'F' and resid 1017 through 1021 Processing helix chain 'F' and resid 1027 through 1032 Processing helix chain 'F' and resid 1084 through 1089 Processing helix chain 'F' and resid 1093 through 1104 Processing helix chain 'F' and resid 1235 through 1241 removed outlier: 3.905A pdb=" N GLU F1241 " --> pdb=" O ASN F1237 " (cutoff:3.500A) Processing helix chain 'F' and resid 1264 through 1272 Processing helix chain 'F' and resid 1274 through 1282 removed outlier: 3.560A 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: 3.849A pdb=" N SER F1311 " --> pdb=" O GLN F1308 " (cutoff:3.500A) Processing helix chain 'F' and resid 1414 through 1422 removed outlier: 3.801A pdb=" N GLN F1420 " --> pdb=" O ASP F1416 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS F1422 " --> pdb=" O ALA F1418 " (cutoff:3.500A) Processing helix chain 'F' and resid 1465 through 1469 Processing helix chain 'F' and resid 1484 through 1489 Processing helix chain 'F' and resid 1538 through 1546 Processing helix chain 'F' and resid 1635 through 1641 Processing helix chain 'F' and resid 1688 through 1694 removed outlier: 3.731A pdb=" N ASN F1694 " --> pdb=" O THR F1690 " (cutoff:3.500A) Processing helix chain 'F' and resid 1865 through 1869 removed outlier: 3.837A pdb=" N ASN F1869 " --> pdb=" O PRO F1866 " (cutoff:3.500A) Processing helix chain 'F' and resid 1925 through 1930 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 3901 hydrogen bonds defined for protein. 11175 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: 34.62 Time building geometry restraints manager: 34.89 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: 18849 1.30 - 1.44: 31997 1.44 - 1.58: 58830 1.58 - 1.71: 215 1.71 - 1.85: 592 Bond restraints: 110483 Sorted by residual: bond pdb=" CB HIS E1098 " pdb=" CG HIS E1098 " ideal model delta sigma weight residual 1.497 1.338 0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" CB HIS D1098 " pdb=" CG HIS D1098 " ideal model delta sigma weight residual 1.497 1.361 0.136 1.40e-02 5.10e+03 9.42e+01 bond pdb=" CB HIS B1843 " pdb=" CG HIS B1843 " ideal model delta sigma weight residual 1.497 1.365 0.132 1.40e-02 5.10e+03 8.85e+01 bond pdb=" CB HIS E1843 " pdb=" CG HIS E1843 " ideal model delta sigma weight residual 1.497 1.366 0.131 1.40e-02 5.10e+03 8.70e+01 bond pdb=" CB HIS F 744 " pdb=" CG HIS F 744 " ideal model delta sigma weight residual 1.497 1.368 0.129 1.40e-02 5.10e+03 8.53e+01 ... (remaining 110478 not shown) Histogram of bond angle deviations from ideal: 91.29 - 99.96: 76 99.96 - 108.62: 12575 108.62 - 117.28: 67467 117.28 - 125.94: 68249 125.94 - 134.61: 1749 Bond angle restraints: 150116 Sorted by residual: angle pdb=" N HIS B1843 " pdb=" CA HIS B1843 " pdb=" C HIS B1843 " ideal model delta sigma weight residual 114.04 100.53 13.51 1.24e+00 6.50e-01 1.19e+02 angle pdb=" N LEU C1860 " pdb=" CA LEU C1860 " pdb=" C LEU C1860 " ideal model delta sigma weight residual 110.41 97.17 13.24 1.23e+00 6.61e-01 1.16e+02 angle pdb=" N PHE D 436 " pdb=" CA PHE D 436 " pdb=" C PHE D 436 " ideal model delta sigma weight residual 114.04 100.72 13.32 1.24e+00 6.50e-01 1.15e+02 angle pdb=" N SER A1600 " pdb=" CA SER A1600 " pdb=" C SER A1600 " ideal model delta sigma weight residual 113.97 100.38 13.59 1.28e+00 6.10e-01 1.13e+02 angle pdb=" N ILE E1952 " pdb=" CA ILE E1952 " pdb=" C ILE E1952 " ideal model delta sigma weight residual 110.62 121.04 -10.42 1.02e+00 9.61e-01 1.04e+02 ... (remaining 150111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 63690 17.96 - 35.91: 1665 35.91 - 53.87: 389 53.87 - 71.82: 310 71.82 - 89.78: 59 Dihedral angle restraints: 66113 sinusoidal: 26142 harmonic: 39971 Sorted by residual: dihedral pdb=" C ARG B1124 " pdb=" N ARG B1124 " pdb=" CA ARG B1124 " pdb=" CB ARG B1124 " ideal model delta harmonic sigma weight residual -122.60 -111.09 -11.51 0 2.50e+00 1.60e-01 2.12e+01 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 -111.50 -11.10 0 2.50e+00 1.60e-01 1.97e+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 -111.88 -10.72 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 66110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 11049 0.092 - 0.184: 4526 0.184 - 0.276: 874 0.276 - 0.368: 104 0.368 - 0.460: 7 Chirality restraints: 16560 Sorted by residual: chirality pdb=" CA ASN B 311 " pdb=" N ASN B 311 " pdb=" C ASN B 311 " pdb=" CB ASN B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+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 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CG LEU A 670 " pdb=" CB LEU A 670 " pdb=" CD1 LEU A 670 " pdb=" CD2 LEU A 670 " both_signs ideal model delta sigma weight residual False -2.59 -3.00 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 16557 not shown) Planarity restraints: 19553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 766 " 0.102 2.00e-02 2.50e+03 5.70e-02 6.50e+01 pdb=" CG TYR E 766 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 766 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR E 766 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 766 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR E 766 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR E 766 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 766 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 902 " -0.094 2.00e-02 2.50e+03 5.43e-02 5.90e+01 pdb=" CG TYR D 902 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 902 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR D 902 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR D 902 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 902 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR D 902 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 902 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 766 " -0.104 2.00e-02 2.50e+03 5.37e-02 5.76e+01 pdb=" CG TYR D 766 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR D 766 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 766 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 766 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 766 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR D 766 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 766 " -0.068 2.00e-02 2.50e+03 ... (remaining 19550 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 17222 2.73 - 3.27: 110378 3.27 - 3.81: 187601 3.81 - 4.36: 245061 4.36 - 4.90: 386221 Nonbonded interactions: 946483 Sorted by model distance: nonbonded pdb=" N ILE B 990 " pdb=" O ILE B 990 " model vdw 2.186 2.496 nonbonded pdb=" OG1 THR E 252 " pdb=" OG1 THR E 472 " model vdw 2.235 2.440 nonbonded pdb=" N LEU C1860 " pdb=" O LEU C1860 " model vdw 2.247 2.496 nonbonded pdb=" OH TYR D1774 " pdb=" OH TYR D1848 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR A1774 " pdb=" OH TYR A1848 " model vdw 2.277 2.440 ... (remaining 946478 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: 2.920 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: 21.450 Check model and map are aligned: 1.210 Set scattering table: 0.740 Process input model: 196.360 Find NCS groups from input model: 5.450 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.205 110483 Z= 1.390 Angle : 1.769 18.781 150116 Z= 1.212 Chirality : 0.097 0.460 16560 Planarity : 0.012 0.151 19553 Dihedral : 10.779 89.777 40413 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.40 % Favored : 97.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.07), residues: 13573 helix: -1.19 (0.06), residues: 5161 sheet: 0.94 (0.10), residues: 2297 loop : 0.24 (0.08), residues: 6115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2447 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2447 time to evaluate : 9.043 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 outliers start: 0 outliers final: 0 residues processed: 2447 average time/residue: 1.0031 time to fit residues: 4176.8633 Evaluate side-chains 1148 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1148 time to evaluate : 8.989 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.4936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 1147 optimal weight: 4.9990 chunk 1030 optimal weight: 1.9990 chunk 571 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 694 optimal weight: 0.7980 chunk 550 optimal weight: 0.9990 chunk 1065 optimal weight: 5.9990 chunk 412 optimal weight: 0.8980 chunk 647 optimal weight: 6.9990 chunk 792 optimal weight: 2.9990 chunk 1234 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 812 ASN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 ASN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1189 GLN ** A1289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1764 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN B 644 GLN B 679 GLN B 761 GLN B 879 GLN B 927 ASN B 953 GLN B1139 ASN B1189 GLN B1265 GLN B1651 ASN B1671 ASN B1787 GLN B1810 GLN B1842 GLN B1951 GLN B1961 GLN B2021 HIS B2129 GLN B2173 ASN B2190 GLN B2223 GLN C 130 HIS C 259 ASN C 735 ASN ** C 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN C1547 ASN C1671 ASN C1842 GLN C2170 ASN C2461 GLN D 130 HIS D 340 GLN D 361 ASN D 580 ASN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN D 914 GLN D1087 GLN ** D1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1531 GLN D1636 GLN ** D1724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2021 HIS D2205 GLN D2497 GLN D2505 ASN E 130 HIS E 222 ASN ** E 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1174 GLN E1240 GLN E1671 ASN ** E1751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1810 GLN E1885 GLN E2021 HIS E2248 GLN E2278 GLN E2459 GLN E2461 GLN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 ASN F 89 HIS F 230 HIS F 336 ASN F 391 ASN F 448 GLN F 457 ASN F 461 GLN F 591 GLN F 609 GLN F 668 GLN F 794 GLN F 933 ASN ** F 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1558 GLN ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 110483 Z= 0.248 Angle : 0.653 11.902 150116 Z= 0.350 Chirality : 0.044 0.399 16560 Planarity : 0.005 0.066 19553 Dihedral : 5.216 33.153 14871 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.19 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % 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: 0.54 (0.07), residues: 13573 helix: 0.89 (0.07), residues: 5189 sheet: 0.63 (0.10), residues: 2409 loop : -0.11 (0.08), residues: 5975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1371 time to evaluate : 9.041 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 outliers start: 180 outliers final: 98 residues processed: 1497 average time/residue: 0.9573 time to fit residues: 2476.0235 Evaluate side-chains 1097 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 999 time to evaluate : 9.050 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.7751 time to fit residues: 155.7638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 685 optimal weight: 3.9990 chunk 383 optimal weight: 9.9990 chunk 1027 optimal weight: 8.9990 chunk 840 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 1236 optimal weight: 8.9990 chunk 1335 optimal weight: 2.9990 chunk 1101 optimal weight: 8.9990 chunk 1226 optimal weight: 0.0670 chunk 421 optimal weight: 7.9990 chunk 991 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 854 GLN A 856 HIS ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1743 HIS A2237 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN B 486 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1674 HIS B2059 GLN ** B2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2237 GLN B2510 HIS C 220 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C 848 GLN C 882 ASN C 885 GLN C 917 ASN C1252 GLN ** C1700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1842 GLN C1972 HIS C2248 GLN C2285 ASN C2461 GLN D 587 ASN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1341 ASN D1588 HIS ** D1724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2113 GLN E 222 ASN E 650 GLN E 749 GLN ** E 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1068 GLN E1240 GLN ** E1751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1916 GLN E2042 ASN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2505 ASN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 GLN F 600 GLN F 658 HIS F 686 HIS F 974 ASN ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1089 ASN F1147 GLN ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1415 ASN ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1650 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 110483 Z= 0.429 Angle : 0.686 13.641 150116 Z= 0.359 Chirality : 0.046 0.234 16560 Planarity : 0.005 0.092 19553 Dihedral : 5.253 32.925 14871 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.57 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.07), residues: 13573 helix: 0.93 (0.07), residues: 5281 sheet: 0.37 (0.10), residues: 2397 loop : -0.44 (0.08), residues: 5895 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1082 time to evaluate : 9.079 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 outliers start: 167 outliers final: 94 residues processed: 1193 average time/residue: 0.9204 time to fit residues: 1925.4128 Evaluate side-chains 1012 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 918 time to evaluate : 9.025 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.7647 time to fit residues: 148.5962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 1221 optimal weight: 0.9990 chunk 929 optimal weight: 10.0000 chunk 641 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 590 optimal weight: 6.9990 chunk 830 optimal weight: 0.8980 chunk 1240 optimal weight: 8.9990 chunk 1313 optimal weight: 6.9990 chunk 648 optimal weight: 30.0000 chunk 1175 optimal weight: 0.8980 chunk 354 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 866 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN A1293 GLN A1304 ASN A1655 HIS A2059 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1842 GLN B1916 GLN B2129 GLN B2170 ASN B2459 GLN C 486 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 882 ASN C 917 ASN ** C1700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2278 GLN D 598 HIS ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1341 ASN D1842 GLN D2248 GLN ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 HIS ** E 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2237 GLN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 391 ASN F 790 HIS ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1136 GLN F1216 ASN ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1744 GLN F1891 GLN ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 110483 Z= 0.233 Angle : 0.552 11.939 150116 Z= 0.289 Chirality : 0.041 0.191 16560 Planarity : 0.004 0.063 19553 Dihedral : 4.920 33.162 14871 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.80 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.07), residues: 13573 helix: 1.25 (0.07), residues: 5261 sheet: 0.37 (0.11), residues: 2420 loop : -0.50 (0.08), residues: 5892 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1074 time to evaluate : 9.198 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: 110 outliers final: 65 residues processed: 1137 average time/residue: 0.9495 time to fit residues: 1891.6825 Evaluate side-chains 998 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 933 time to evaluate : 9.123 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.7910 time to fit residues: 109.7468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 1094 optimal weight: 0.3980 chunk 745 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 978 optimal weight: 10.0000 chunk 542 optimal weight: 8.9990 chunk 1120 optimal weight: 1.9990 chunk 908 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 670 optimal weight: 2.9990 chunk 1179 optimal weight: 0.7980 chunk 331 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 GLN A1655 HIS A1965 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1292 GLN C 486 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 855 ASN C 917 ASN C1066 GLN C1529 ASN C1700 ASN C1951 GLN C2459 GLN D 95 GLN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 ASN ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1341 ASN D1842 GLN D2059 GLN D2113 GLN E 222 ASN ** E 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 ASN ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 110483 Z= 0.184 Angle : 0.520 11.904 150116 Z= 0.272 Chirality : 0.040 0.186 16560 Planarity : 0.004 0.056 19553 Dihedral : 4.661 33.415 14871 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.19 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.07), residues: 13573 helix: 1.44 (0.07), residues: 5292 sheet: 0.40 (0.11), residues: 2424 loop : -0.53 (0.08), residues: 5857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1024 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: 91 outliers final: 41 residues processed: 1088 average time/residue: 0.9576 time to fit residues: 1832.0375 Evaluate side-chains 958 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 917 time to evaluate : 9.067 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.7834 time to fit residues: 74.2379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 441 optimal weight: 0.9980 chunk 1182 optimal weight: 2.9990 chunk 259 optimal weight: 30.0000 chunk 771 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 1314 optimal weight: 10.0000 chunk 1091 optimal weight: 0.6980 chunk 608 optimal weight: 10.0000 chunk 109 optimal weight: 0.0270 chunk 434 optimal weight: 4.9990 chunk 690 optimal weight: 2.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1655 HIS B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1958 ASN B2042 ASN C 287 ASN C 486 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 ASN C1951 GLN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1341 ASN ** D1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1059 ASN ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 110483 Z= 0.172 Angle : 0.512 11.838 150116 Z= 0.265 Chirality : 0.040 0.178 16560 Planarity : 0.004 0.056 19553 Dihedral : 4.515 33.777 14871 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer Outliers : 0.68 % 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: 0.71 (0.07), residues: 13573 helix: 1.58 (0.07), residues: 5277 sheet: 0.45 (0.11), residues: 2417 loop : -0.49 (0.08), residues: 5879 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 994 time to evaluate : 9.206 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 outliers start: 79 outliers final: 40 residues processed: 1038 average time/residue: 0.9188 time to fit residues: 1680.0673 Evaluate side-chains 951 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 911 time to evaluate : 9.097 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.7719 time to fit residues: 71.3435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 1267 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 749 optimal weight: 5.9990 chunk 960 optimal weight: 6.9990 chunk 743 optimal weight: 10.0000 chunk 1106 optimal weight: 20.0000 chunk 734 optimal weight: 20.0000 chunk 1309 optimal weight: 9.9990 chunk 819 optimal weight: 6.9990 chunk 798 optimal weight: 3.9990 chunk 604 optimal weight: 0.8980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS A 774 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN A1303 ASN A1636 GLN B 240 ASN B 642 HIS B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1842 GLN B2093 GLN B2488 ASN C 287 ASN C 486 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 882 ASN C 930 GLN C1951 GLN C2278 GLN D 340 GLN D 361 ASN D 587 ASN ** D 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 855 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 ASN D1174 GLN D1293 GLN D1304 ASN D1341 ASN D1680 GLN D1951 GLN D2059 GLN ** D2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 HIS E1062 GLN E1098 HIS ** E1751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2461 GLN E2488 ASN E2497 GLN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1136 GLN ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1674 GLN F1693 GLN ** F1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.093 110483 Z= 0.474 Angle : 0.678 14.728 150116 Z= 0.349 Chirality : 0.046 0.224 16560 Planarity : 0.005 0.087 19553 Dihedral : 5.063 38.179 14871 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.46 % Favored : 95.51 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.25 (0.07), residues: 13573 helix: 1.16 (0.07), residues: 5311 sheet: 0.14 (0.10), residues: 2507 loop : -0.70 (0.08), residues: 5755 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 941 time to evaluate : 9.082 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: 92 outliers final: 55 residues processed: 1000 average time/residue: 0.9377 time to fit residues: 1654.7938 Evaluate side-chains 928 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 873 time to evaluate : 9.010 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.7614 time to fit residues: 92.9738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 810 optimal weight: 7.9990 chunk 523 optimal weight: 30.0000 chunk 782 optimal weight: 0.7980 chunk 394 optimal weight: 0.6980 chunk 257 optimal weight: 6.9990 chunk 253 optimal weight: 30.0000 chunk 832 optimal weight: 0.2980 chunk 892 optimal weight: 0.6980 chunk 647 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 1029 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1282 GLN A1303 ASN A1655 HIS A1700 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1842 GLN C 486 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 GLN C 930 GLN ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2497 GLN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1174 GLN D1293 GLN D1533 ASN ** D1842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN ** D2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 772 ASN ** E 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1062 GLN E1174 GLN E1334 ASN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 GLN ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.071 110483 Z= 0.156 Angle : 0.527 14.155 150116 Z= 0.273 Chirality : 0.040 0.213 16560 Planarity : 0.004 0.057 19553 Dihedral : 4.612 36.140 14871 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.56 (0.07), residues: 13573 helix: 1.50 (0.07), residues: 5300 sheet: 0.29 (0.11), residues: 2442 loop : -0.61 (0.08), residues: 5831 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 992 time to evaluate : 9.034 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 outliers start: 39 outliers final: 21 residues processed: 1011 average time/residue: 0.9457 time to fit residues: 1683.5115 Evaluate side-chains 929 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 908 time to evaluate : 9.077 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.7838 time to fit residues: 43.5104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 1191 optimal weight: 0.6980 chunk 1254 optimal weight: 1.9990 chunk 1144 optimal weight: 5.9990 chunk 1220 optimal weight: 0.0470 chunk 734 optimal weight: 8.9990 chunk 531 optimal weight: 5.9990 chunk 958 optimal weight: 9.9990 chunk 374 optimal weight: 2.9990 chunk 1103 optimal weight: 9.9990 chunk 1154 optimal weight: 4.9990 chunk 1216 optimal weight: 1.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1655 HIS B 212 GLN B 240 ASN B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1298 ASN B1842 GLN C 486 GLN C 882 ASN C 917 ASN ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 679 GLN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1341 ASN D1951 GLN ** D2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1174 GLN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 110483 Z= 0.233 Angle : 0.551 12.654 150116 Z= 0.284 Chirality : 0.041 0.257 16560 Planarity : 0.004 0.057 19553 Dihedral : 4.589 40.047 14871 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.55 (0.07), residues: 13573 helix: 1.50 (0.07), residues: 5308 sheet: 0.30 (0.11), residues: 2423 loop : -0.62 (0.08), residues: 5842 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 947 time to evaluate : 9.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 965 average time/residue: 0.9451 time to fit residues: 1602.2628 Evaluate side-chains 913 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 890 time to evaluate : 8.671 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.7783 time to fit residues: 45.8564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 801 optimal weight: 0.7980 chunk 1290 optimal weight: 0.0570 chunk 787 optimal weight: 3.9990 chunk 612 optimal weight: 7.9990 chunk 897 optimal weight: 0.9990 chunk 1353 optimal weight: 3.9990 chunk 1246 optimal weight: 5.9990 chunk 1078 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 832 optimal weight: 2.9990 chunk 661 optimal weight: 3.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1655 HIS A1764 ASN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1842 GLN C 486 GLN C 917 ASN C1979 GLN ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2278 GLN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1798 GLN ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 110483 Z= 0.173 Angle : 0.533 18.310 150116 Z= 0.274 Chirality : 0.040 0.317 16560 Planarity : 0.004 0.053 19553 Dihedral : 4.475 42.347 14871 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer Outliers : 0.10 % 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: 13573 helix: 1.52 (0.07), residues: 5357 sheet: 0.36 (0.11), residues: 2427 loop : -0.65 (0.08), residues: 5789 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27146 Ramachandran restraints generated. 13573 Oldfield, 0 Emsley, 13573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 975 time to evaluate : 9.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 984 average time/residue: 0.9708 time to fit residues: 1672.2881 Evaluate side-chains 930 residues out of total 11664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 925 time to evaluate : 9.099 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.8351 time to fit residues: 20.2490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1359 random chunks: chunk 856 optimal weight: 0.9990 chunk 1148 optimal weight: 5.9990 chunk 330 optimal weight: 4.9990 chunk 994 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 299 optimal weight: 30.0000 chunk 1079 optimal weight: 0.9990 chunk 451 optimal weight: 8.9990 chunk 1108 optimal weight: 20.0000 chunk 136 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 HIS ** B 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 GLN ** C2129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2363 GLN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN D1304 ASN ** D2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 690 HIS ** E 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112935 restraints weight = 190176.692| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.83 r_work: 0.3102 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 110483 Z= 0.249 Angle : 0.570 20.188 150116 Z= 0.292 Chirality : 0.042 0.277 16560 Planarity : 0.004 0.062 19553 Dihedral : 4.552 42.603 14871 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.49 (0.07), residues: 13573 helix: 1.43 (0.07), residues: 5361 sheet: 0.32 (0.11), residues: 2426 loop : -0.69 (0.08), residues: 5786 =============================================================================== Job complete usr+sys time: 31466.39 seconds wall clock time: 548 minutes 18.41 seconds (32898.41 seconds total)