Starting phenix.real_space_refine on Tue Mar 19 13:40:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yey_10797/03_2024/6yey_10797.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yey_10797/03_2024/6yey_10797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yey_10797/03_2024/6yey_10797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yey_10797/03_2024/6yey_10797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yey_10797/03_2024/6yey_10797.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yey_10797/03_2024/6yey_10797.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 335 5.16 5 C 59470 2.51 5 N 15660 2.21 5 O 18035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1614": "NH1" <-> "NH2" Residue "A PHE 1648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1662": "NH1" <-> "NH2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1925": "NH1" <-> "NH2" Residue "A PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2062": "NH1" <-> "NH2" Residue "A PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2189": "NH1" <-> "NH2" Residue "A PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2343": "NH1" <-> "NH2" Residue "A PHE 2365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "A PHE 2481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 562": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1614": "NH1" <-> "NH2" Residue "B PHE 1648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1662": "NH1" <-> "NH2" Residue "B ARG 1677": "NH1" <-> "NH2" Residue "B TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1925": "NH1" <-> "NH2" Residue "B PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2062": "NH1" <-> "NH2" Residue "B PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2189": "NH1" <-> "NH2" Residue "B PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2343": "NH1" <-> "NH2" Residue "B PHE 2365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2452": "NH1" <-> "NH2" Residue "B PHE 2481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C ARG 595": "NH1" <-> "NH2" Residue "C TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 695": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1614": "NH1" <-> "NH2" Residue "C PHE 1648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1662": "NH1" <-> "NH2" Residue "C ARG 1677": "NH1" <-> "NH2" Residue "C TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1925": "NH1" <-> "NH2" Residue "C PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2062": "NH1" <-> "NH2" Residue "C PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2189": "NH1" <-> "NH2" Residue "C PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2343": "NH1" <-> "NH2" Residue "C PHE 2365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2452": "NH1" <-> "NH2" Residue "C PHE 2481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 562": "NH1" <-> "NH2" Residue "D ARG 595": "NH1" <-> "NH2" Residue "D TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 695": "NH1" <-> "NH2" Residue "D ARG 1014": "NH1" <-> "NH2" Residue "D TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1614": "NH1" <-> "NH2" Residue "D PHE 1648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1662": "NH1" <-> "NH2" Residue "D ARG 1677": "NH1" <-> "NH2" Residue "D TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1925": "NH1" <-> "NH2" Residue "D PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2062": "NH1" <-> "NH2" Residue "D PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2189": "NH1" <-> "NH2" Residue "D PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2343": "NH1" <-> "NH2" Residue "D PHE 2365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2452": "NH1" <-> "NH2" Residue "D PHE 2481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 562": "NH1" <-> "NH2" Residue "E ARG 595": "NH1" <-> "NH2" Residue "E TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 695": "NH1" <-> "NH2" Residue "E ARG 1014": "NH1" <-> "NH2" Residue "E TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1614": "NH1" <-> "NH2" Residue "E PHE 1648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1662": "NH1" <-> "NH2" Residue "E ARG 1677": "NH1" <-> "NH2" Residue "E TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1925": "NH1" <-> "NH2" Residue "E PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2062": "NH1" <-> "NH2" Residue "E PHE 2163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2189": "NH1" <-> "NH2" Residue "E PHE 2281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2343": "NH1" <-> "NH2" Residue "E PHE 2365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2452": "NH1" <-> "NH2" Residue "E PHE 2481": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93500 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 35.03, per 1000 atoms: 0.37 Number of scatterers: 93500 At special positions: 0 Unit cell: (185.13, 185.13, 263.78, 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 335 16.00 O 18035 8.00 N 15660 7.00 C 59470 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: 28.46 Conformation dependent library (CDL) restraints added in 12.5 seconds 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22280 Finding SS restraints... Secondary structure from input PDB file: 410 helices and 90 sheets defined 49.0% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.21 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 43 through 69 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.693A pdb=" N ALA A 76 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.587A pdb=" N HIS A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 437 through 456 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.677A pdb=" N GLN A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 550 through 562 Processing helix chain 'A' and resid 564 through 576 Processing helix chain 'A' and resid 586 through 603 removed outlier: 5.023A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 628 through 649 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 669 through 682 Processing helix chain 'A' and resid 688 through 705 removed outlier: 4.221A pdb=" N ILE A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG A 695 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 743 through 766 Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 794 through 812 removed outlier: 3.671A pdb=" N GLY A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.630A pdb=" N LEU A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 836 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 859 through 876 removed outlier: 3.933A pdb=" N ILE A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 901 through 914 Processing helix chain 'A' and resid 917 through 943 removed outlier: 4.204A pdb=" N THR A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 938 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 960 Processing helix chain 'A' and resid 972 through 990 removed outlier: 3.943A pdb=" N ASN A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1002 removed outlier: 3.724A pdb=" N THR A1002 " --> pdb=" O PRO A 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1003 through 1008 Processing helix chain 'A' and resid 1015 through 1028 Processing helix chain 'A' and resid 1029 through 1032 Processing helix chain 'A' and resid 1042 through 1053 Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.577A pdb=" N ALA A1072 " --> pdb=" O ASN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1210 removed outlier: 3.860A pdb=" N LYS A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1272 Processing helix chain 'A' and resid 1582 through 1586 Processing helix chain 'A' and resid 1611 through 1623 removed outlier: 3.630A pdb=" N LYS A1615 " --> pdb=" O LEU A1611 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A1617 " --> pdb=" O SER A1613 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU A1618 " --> pdb=" O ARG A1614 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A1619 " --> pdb=" O LYS A1615 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A1622 " --> pdb=" O GLU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1628 removed outlier: 3.688A pdb=" N LEU A1628 " --> pdb=" O ILE A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1634 removed outlier: 3.735A pdb=" N GLN A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1792 Processing helix chain 'A' and resid 1792 through 1805 Processing helix chain 'A' and resid 1807 through 1817 removed outlier: 3.770A pdb=" N ARG A1813 " --> pdb=" O THR A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1855 through 1863 Processing helix chain 'A' and resid 1864 through 1888 Processing helix chain 'A' and resid 1891 through 1910 removed outlier: 3.845A pdb=" N ASN A1896 " --> pdb=" O ARG A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1930 Processing helix chain 'A' and resid 1931 through 1947 Processing helix chain 'A' and resid 1969 through 1987 removed outlier: 3.787A pdb=" N GLN A1973 " --> pdb=" O ASN A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2120 removed outlier: 3.768A pdb=" N LYS A2089 " --> pdb=" O LYS A2085 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A2107 " --> pdb=" O GLU A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2141 Processing helix chain 'A' and resid 2144 through 2155 Processing helix chain 'A' and resid 2171 through 2260 Processing helix chain 'A' and resid 2263 through 2300 removed outlier: 3.609A pdb=" N TYR A2267 " --> pdb=" O ASN A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2318 Processing helix chain 'A' and resid 2321 through 2341 Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2366 through 2377 removed outlier: 3.840A pdb=" N THR A2372 " --> pdb=" O LYS A2368 " (cutoff:3.500A) Processing helix chain 'A' and resid 2401 through 2406 removed outlier: 3.886A pdb=" N ASN A2406 " --> pdb=" O SER A2403 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2416 removed outlier: 3.846A pdb=" N LEU A2415 " --> pdb=" O PRO A2412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A2416 " --> pdb=" O ASP A2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2412 through 2416' Processing helix chain 'A' and resid 2452 through 2456 removed outlier: 3.509A pdb=" N LYS A2455 " --> pdb=" O ARG A2452 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A2456 " --> pdb=" O GLY A2453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2452 through 2456' Processing helix chain 'A' and resid 2503 through 2509 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 43 through 69 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.693A pdb=" N ALA B 76 " --> pdb=" O PRO B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 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 157 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.587A pdb=" N HIS B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 437 through 456 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.677A pdb=" N GLN B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 518 through 525 Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 564 through 576 Processing helix chain 'B' and resid 586 through 603 removed outlier: 5.022A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 628 through 649 Processing helix chain 'B' and resid 652 through 661 Processing helix chain 'B' and resid 669 through 682 Processing helix chain 'B' and resid 688 through 705 removed outlier: 4.222A pdb=" N ILE B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG B 695 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Proline residue: B 699 - end of helix Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 743 through 766 Processing helix chain 'B' and resid 773 through 780 Processing helix chain 'B' and resid 794 through 812 removed outlier: 3.672A pdb=" N GLY B 812 " --> pdb=" O ILE B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.629A pdb=" N LEU B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 859 through 876 removed outlier: 3.932A pdb=" N ILE B 863 " --> pdb=" O ASN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'B' and resid 901 through 914 Processing helix chain 'B' and resid 917 through 943 removed outlier: 4.204A pdb=" N THR B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 938 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 960 Processing helix chain 'B' and resid 972 through 990 removed outlier: 3.943A pdb=" N ASN B 990 " --> pdb=" O ASN B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1002 removed outlier: 3.724A pdb=" N THR B1002 " --> pdb=" O PRO B 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 999 through 1002' Processing helix chain 'B' and resid 1003 through 1008 Processing helix chain 'B' and resid 1015 through 1028 Processing helix chain 'B' and resid 1029 through 1032 Processing helix chain 'B' and resid 1042 through 1053 Processing helix chain 'B' and resid 1058 through 1078 removed outlier: 3.577A pdb=" N ALA B1072 " --> pdb=" O ASN B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1210 removed outlier: 3.859A pdb=" N LYS B1210 " --> pdb=" O ASN B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1272 Processing helix chain 'B' and resid 1582 through 1586 Processing helix chain 'B' and resid 1611 through 1623 removed outlier: 3.629A pdb=" N LYS B1615 " --> pdb=" O LEU B1611 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B1617 " --> pdb=" O SER B1613 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU B1618 " --> pdb=" O ARG B1614 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG B1619 " --> pdb=" O LYS B1615 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B1622 " --> pdb=" O GLU B1618 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1628 removed outlier: 3.688A pdb=" N LEU B1628 " --> pdb=" O ILE B1624 " (cutoff:3.500A) Processing helix chain 'B' and resid 1629 through 1634 removed outlier: 3.734A pdb=" N GLN B1633 " --> pdb=" O SER B1629 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1792 Processing helix chain 'B' and resid 1792 through 1805 Processing helix chain 'B' and resid 1807 through 1817 removed outlier: 3.770A pdb=" N ARG B1813 " --> pdb=" O THR B1809 " (cutoff:3.500A) Processing helix chain 'B' and resid 1837 through 1842 Processing helix chain 'B' and resid 1855 through 1863 Processing helix chain 'B' and resid 1864 through 1888 Processing helix chain 'B' and resid 1891 through 1910 removed outlier: 3.844A pdb=" N ASN B1896 " --> pdb=" O ARG B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1925 through 1930 Processing helix chain 'B' and resid 1931 through 1947 Processing helix chain 'B' and resid 1969 through 1987 removed outlier: 3.787A pdb=" N GLN B1973 " --> pdb=" O ASN B1969 " (cutoff:3.500A) Processing helix chain 'B' and resid 2034 through 2120 removed outlier: 3.768A pdb=" N LYS B2089 " --> pdb=" O LYS B2085 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B2107 " --> pdb=" O GLU B2103 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2141 Processing helix chain 'B' and resid 2144 through 2155 Processing helix chain 'B' and resid 2171 through 2260 Processing helix chain 'B' and resid 2263 through 2300 removed outlier: 3.610A pdb=" N TYR B2267 " --> pdb=" O ASN B2263 " (cutoff:3.500A) Processing helix chain 'B' and resid 2314 through 2318 Processing helix chain 'B' and resid 2321 through 2341 Processing helix chain 'B' and resid 2353 through 2359 Processing helix chain 'B' and resid 2366 through 2377 removed outlier: 3.840A pdb=" N THR B2372 " --> pdb=" O LYS B2368 " (cutoff:3.500A) Processing helix chain 'B' and resid 2401 through 2406 removed outlier: 3.886A pdb=" N ASN B2406 " --> pdb=" O SER B2403 " (cutoff:3.500A) Processing helix chain 'B' and resid 2412 through 2416 removed outlier: 3.846A pdb=" N LEU B2415 " --> pdb=" O PRO B2412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B2416 " --> pdb=" O ASP B2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2412 through 2416' Processing helix chain 'B' and resid 2452 through 2456 removed outlier: 3.509A pdb=" N LYS B2455 " --> pdb=" O ARG B2452 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B2456 " --> pdb=" O GLY B2453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2452 through 2456' Processing helix chain 'B' and resid 2503 through 2509 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 43 through 69 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.692A pdb=" N ALA C 76 " --> pdb=" O PRO C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 200 through 214 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.587A pdb=" N HIS C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 437 through 456 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.677A pdb=" N GLN C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 518 through 525 Processing helix chain 'C' and resid 550 through 562 Processing helix chain 'C' and resid 564 through 576 Processing helix chain 'C' and resid 586 through 603 removed outlier: 5.023A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 616 Processing helix chain 'C' and resid 628 through 649 Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 669 through 682 Processing helix chain 'C' and resid 688 through 705 removed outlier: 4.222A pdb=" N ILE C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG C 695 " --> pdb=" O ASP C 691 " (cutoff:3.500A) Proline residue: C 699 - end of helix Processing helix chain 'C' and resid 709 through 722 Processing helix chain 'C' and resid 724 through 728 Processing helix chain 'C' and resid 743 through 766 Processing helix chain 'C' and resid 773 through 780 Processing helix chain 'C' and resid 794 through 812 removed outlier: 3.672A pdb=" N GLY C 812 " --> pdb=" O ILE C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.630A pdb=" N LEU C 824 " --> pdb=" O THR C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 836 Processing helix chain 'C' and resid 839 through 851 Processing helix chain 'C' and resid 859 through 876 removed outlier: 3.932A pdb=" N ILE C 863 " --> pdb=" O ASN C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 888 Processing helix chain 'C' and resid 901 through 914 Processing helix chain 'C' and resid 917 through 943 removed outlier: 4.205A pdb=" N THR C 934 " --> pdb=" O GLU C 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 938 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 960 Processing helix chain 'C' and resid 972 through 990 removed outlier: 3.943A pdb=" N ASN C 990 " --> pdb=" O ASN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1002 removed outlier: 3.724A pdb=" N THR C1002 " --> pdb=" O PRO C 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 999 through 1002' Processing helix chain 'C' and resid 1003 through 1008 Processing helix chain 'C' and resid 1015 through 1028 Processing helix chain 'C' and resid 1029 through 1032 Processing helix chain 'C' and resid 1042 through 1053 Processing helix chain 'C' and resid 1058 through 1078 removed outlier: 3.577A pdb=" N ALA C1072 " --> pdb=" O ASN C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1210 removed outlier: 3.859A pdb=" N LYS C1210 " --> pdb=" O ASN C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1261 through 1272 Processing helix chain 'C' and resid 1582 through 1586 Processing helix chain 'C' and resid 1611 through 1623 removed outlier: 3.629A pdb=" N LYS C1615 " --> pdb=" O LEU C1611 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C1617 " --> pdb=" O SER C1613 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU C1618 " --> pdb=" O ARG C1614 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG C1619 " --> pdb=" O LYS C1615 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C1622 " --> pdb=" O GLU C1618 " (cutoff:3.500A) Processing helix chain 'C' and resid 1623 through 1628 removed outlier: 3.689A pdb=" N LEU C1628 " --> pdb=" O ILE C1624 " (cutoff:3.500A) Processing helix chain 'C' and resid 1629 through 1634 removed outlier: 3.736A pdb=" N GLN C1633 " --> pdb=" O SER C1629 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1792 Processing helix chain 'C' and resid 1792 through 1805 Processing helix chain 'C' and resid 1807 through 1817 removed outlier: 3.770A pdb=" N ARG C1813 " --> pdb=" O THR C1809 " (cutoff:3.500A) Processing helix chain 'C' and resid 1837 through 1842 Processing helix chain 'C' and resid 1855 through 1863 Processing helix chain 'C' and resid 1864 through 1888 Processing helix chain 'C' and resid 1891 through 1910 removed outlier: 3.845A pdb=" N ASN C1896 " --> pdb=" O ARG C1892 " (cutoff:3.500A) Processing helix chain 'C' and resid 1925 through 1930 Processing helix chain 'C' and resid 1931 through 1947 Processing helix chain 'C' and resid 1969 through 1987 removed outlier: 3.787A pdb=" N GLN C1973 " --> pdb=" O ASN C1969 " (cutoff:3.500A) Processing helix chain 'C' and resid 2034 through 2120 removed outlier: 3.768A pdb=" N LYS C2089 " --> pdb=" O LYS C2085 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY C2107 " --> pdb=" O GLU C2103 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2141 Processing helix chain 'C' and resid 2144 through 2155 Processing helix chain 'C' and resid 2171 through 2260 Processing helix chain 'C' and resid 2263 through 2300 removed outlier: 3.609A pdb=" N TYR C2267 " --> pdb=" O ASN C2263 " (cutoff:3.500A) Processing helix chain 'C' and resid 2314 through 2318 Processing helix chain 'C' and resid 2321 through 2341 Processing helix chain 'C' and resid 2353 through 2359 Processing helix chain 'C' and resid 2366 through 2377 removed outlier: 3.840A pdb=" N THR C2372 " --> pdb=" O LYS C2368 " (cutoff:3.500A) Processing helix chain 'C' and resid 2401 through 2406 removed outlier: 3.886A pdb=" N ASN C2406 " --> pdb=" O SER C2403 " (cutoff:3.500A) Processing helix chain 'C' and resid 2412 through 2416 removed outlier: 3.846A pdb=" N LEU C2415 " --> pdb=" O PRO C2412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C2416 " --> pdb=" O ASP C2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2412 through 2416' Processing helix chain 'C' and resid 2452 through 2456 removed outlier: 3.508A pdb=" N LYS C2455 " --> pdb=" O ARG C2452 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA C2456 " --> pdb=" O GLY C2453 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2452 through 2456' Processing helix chain 'C' and resid 2503 through 2509 Processing helix chain 'D' and resid 21 through 26 Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 43 through 69 Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.693A pdb=" N ALA D 76 " --> pdb=" O PRO D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 200 through 214 Processing helix chain 'D' and resid 217 through 223 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.587A pdb=" N HIS D 341 " --> pdb=" O PHE D 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 341' Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 437 through 456 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 476 through 493 removed outlier: 3.677A pdb=" N GLN D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'D' and resid 518 through 525 Processing helix chain 'D' and resid 550 through 562 Processing helix chain 'D' and resid 564 through 576 Processing helix chain 'D' and resid 586 through 603 removed outlier: 5.022A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 616 Processing helix chain 'D' and resid 628 through 649 Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 669 through 682 Processing helix chain 'D' and resid 688 through 705 removed outlier: 4.221A pdb=" N ILE D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG D 695 " --> pdb=" O ASP D 691 " (cutoff:3.500A) Proline residue: D 699 - end of helix Processing helix chain 'D' and resid 709 through 722 Processing helix chain 'D' and resid 724 through 728 Processing helix chain 'D' and resid 743 through 766 Processing helix chain 'D' and resid 773 through 780 Processing helix chain 'D' and resid 794 through 812 removed outlier: 3.672A pdb=" N GLY D 812 " --> pdb=" O ILE D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 removed outlier: 3.630A pdb=" N LEU D 824 " --> pdb=" O THR D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 836 Processing helix chain 'D' and resid 839 through 851 Processing helix chain 'D' and resid 859 through 876 removed outlier: 3.932A pdb=" N ILE D 863 " --> pdb=" O ASN D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 888 Processing helix chain 'D' and resid 901 through 914 Processing helix chain 'D' and resid 917 through 943 removed outlier: 4.204A pdb=" N THR D 934 " --> pdb=" O GLU D 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA D 938 " --> pdb=" O THR D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 960 Processing helix chain 'D' and resid 972 through 990 removed outlier: 3.943A pdb=" N ASN D 990 " --> pdb=" O ASN D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 999 through 1002 removed outlier: 3.725A pdb=" N THR D1002 " --> pdb=" O PRO D 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 999 through 1002' Processing helix chain 'D' and resid 1003 through 1008 Processing helix chain 'D' and resid 1015 through 1028 Processing helix chain 'D' and resid 1029 through 1032 Processing helix chain 'D' and resid 1042 through 1053 Processing helix chain 'D' and resid 1058 through 1078 removed outlier: 3.578A pdb=" N ALA D1072 " --> pdb=" O ASN D1068 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1210 removed outlier: 3.859A pdb=" N LYS D1210 " --> pdb=" O ASN D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1272 Processing helix chain 'D' and resid 1582 through 1586 Processing helix chain 'D' and resid 1611 through 1623 removed outlier: 3.629A pdb=" N LYS D1615 " --> pdb=" O LEU D1611 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D1617 " --> pdb=" O SER D1613 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU D1618 " --> pdb=" O ARG D1614 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG D1619 " --> pdb=" O LYS D1615 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D1622 " --> pdb=" O GLU D1618 " (cutoff:3.500A) Processing helix chain 'D' and resid 1623 through 1628 removed outlier: 3.688A pdb=" N LEU D1628 " --> pdb=" O ILE D1624 " (cutoff:3.500A) Processing helix chain 'D' and resid 1629 through 1634 removed outlier: 3.735A pdb=" N GLN D1633 " --> pdb=" O SER D1629 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1792 Processing helix chain 'D' and resid 1792 through 1805 Processing helix chain 'D' and resid 1807 through 1817 removed outlier: 3.770A pdb=" N ARG D1813 " --> pdb=" O THR D1809 " (cutoff:3.500A) Processing helix chain 'D' and resid 1837 through 1842 Processing helix chain 'D' and resid 1855 through 1863 Processing helix chain 'D' and resid 1864 through 1888 Processing helix chain 'D' and resid 1891 through 1910 removed outlier: 3.845A pdb=" N ASN D1896 " --> pdb=" O ARG D1892 " (cutoff:3.500A) Processing helix chain 'D' and resid 1925 through 1930 Processing helix chain 'D' and resid 1931 through 1947 Processing helix chain 'D' and resid 1969 through 1987 removed outlier: 3.786A pdb=" N GLN D1973 " --> pdb=" O ASN D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 2034 through 2120 removed outlier: 3.768A pdb=" N LYS D2089 " --> pdb=" O LYS D2085 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY D2107 " --> pdb=" O GLU D2103 " (cutoff:3.500A) Processing helix chain 'D' and resid 2124 through 2141 Processing helix chain 'D' and resid 2144 through 2155 Processing helix chain 'D' and resid 2171 through 2260 Processing helix chain 'D' and resid 2263 through 2300 removed outlier: 3.609A pdb=" N TYR D2267 " --> pdb=" O ASN D2263 " (cutoff:3.500A) Processing helix chain 'D' and resid 2314 through 2318 Processing helix chain 'D' and resid 2321 through 2341 Processing helix chain 'D' and resid 2353 through 2359 Processing helix chain 'D' and resid 2366 through 2377 removed outlier: 3.839A pdb=" N THR D2372 " --> pdb=" O LYS D2368 " (cutoff:3.500A) Processing helix chain 'D' and resid 2401 through 2406 removed outlier: 3.887A pdb=" N ASN D2406 " --> pdb=" O SER D2403 " (cutoff:3.500A) Processing helix chain 'D' and resid 2412 through 2416 removed outlier: 3.847A pdb=" N LEU D2415 " --> pdb=" O PRO D2412 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D2416 " --> pdb=" O ASP D2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2412 through 2416' Processing helix chain 'D' and resid 2452 through 2456 removed outlier: 3.509A pdb=" N LYS D2455 " --> pdb=" O ARG D2452 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D2456 " --> pdb=" O GLY D2453 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2452 through 2456' Processing helix chain 'D' and resid 2503 through 2509 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 29 through 37 Processing helix chain 'E' and resid 43 through 69 Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.692A pdb=" N ALA E 76 " --> pdb=" O PRO E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 96 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 200 through 214 Processing helix chain 'E' and resid 217 through 223 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 243 through 252 Processing helix chain 'E' and resid 258 through 267 Processing helix chain 'E' and resid 277 through 286 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.587A pdb=" N HIS E 341 " --> pdb=" O PHE E 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 341' Processing helix chain 'E' and resid 402 through 408 Processing helix chain 'E' and resid 437 through 456 Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'E' and resid 476 through 493 removed outlier: 3.677A pdb=" N GLN E 487 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'E' and resid 518 through 525 Processing helix chain 'E' and resid 550 through 562 Processing helix chain 'E' and resid 564 through 576 Processing helix chain 'E' and resid 586 through 603 removed outlier: 5.023A pdb=" N LEU E 592 " --> pdb=" O GLU E 588 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG E 595 " --> pdb=" O SER E 591 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS E 603 " --> pdb=" O LEU E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 616 Processing helix chain 'E' and resid 628 through 649 Processing helix chain 'E' and resid 652 through 661 Processing helix chain 'E' and resid 669 through 682 Processing helix chain 'E' and resid 688 through 705 removed outlier: 4.222A pdb=" N ILE E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG E 695 " --> pdb=" O ASP E 691 " (cutoff:3.500A) Proline residue: E 699 - end of helix Processing helix chain 'E' and resid 709 through 722 Processing helix chain 'E' and resid 724 through 728 Processing helix chain 'E' and resid 743 through 766 Processing helix chain 'E' and resid 773 through 780 Processing helix chain 'E' and resid 794 through 812 removed outlier: 3.672A pdb=" N GLY E 812 " --> pdb=" O ILE E 808 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 824 removed outlier: 3.630A pdb=" N LEU E 824 " --> pdb=" O THR E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 836 Processing helix chain 'E' and resid 839 through 851 Processing helix chain 'E' and resid 859 through 876 removed outlier: 3.932A pdb=" N ILE E 863 " --> pdb=" O ASN E 859 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 888 Processing helix chain 'E' and resid 901 through 914 Processing helix chain 'E' and resid 917 through 943 removed outlier: 4.205A pdb=" N THR E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 938 " --> pdb=" O THR E 934 " (cutoff:3.500A) Processing helix chain 'E' and resid 951 through 960 Processing helix chain 'E' and resid 972 through 990 removed outlier: 3.943A pdb=" N ASN E 990 " --> pdb=" O ASN E 986 " (cutoff:3.500A) Processing helix chain 'E' and resid 999 through 1002 removed outlier: 3.725A pdb=" N THR E1002 " --> pdb=" O PRO E 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 999 through 1002' Processing helix chain 'E' and resid 1003 through 1008 Processing helix chain 'E' and resid 1015 through 1028 Processing helix chain 'E' and resid 1029 through 1032 Processing helix chain 'E' and resid 1042 through 1053 Processing helix chain 'E' and resid 1058 through 1078 removed outlier: 3.577A pdb=" N ALA E1072 " --> pdb=" O ASN E1068 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1210 removed outlier: 3.859A pdb=" N LYS E1210 " --> pdb=" O ASN E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1261 through 1272 Processing helix chain 'E' and resid 1582 through 1586 Processing helix chain 'E' and resid 1611 through 1623 removed outlier: 3.629A pdb=" N LYS E1615 " --> pdb=" O LEU E1611 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA E1617 " --> pdb=" O SER E1613 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU E1618 " --> pdb=" O ARG E1614 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG E1619 " --> pdb=" O LYS E1615 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE E1622 " --> pdb=" O GLU E1618 " (cutoff:3.500A) Processing helix chain 'E' and resid 1623 through 1628 removed outlier: 3.687A pdb=" N LEU E1628 " --> pdb=" O ILE E1624 " (cutoff:3.500A) Processing helix chain 'E' and resid 1629 through 1634 removed outlier: 3.735A pdb=" N GLN E1633 " --> pdb=" O SER E1629 " (cutoff:3.500A) Processing helix chain 'E' and resid 1783 through 1792 Processing helix chain 'E' and resid 1792 through 1805 Processing helix chain 'E' and resid 1807 through 1817 removed outlier: 3.769A pdb=" N ARG E1813 " --> pdb=" O THR E1809 " (cutoff:3.500A) Processing helix chain 'E' and resid 1837 through 1842 Processing helix chain 'E' and resid 1855 through 1863 Processing helix chain 'E' and resid 1864 through 1888 Processing helix chain 'E' and resid 1891 through 1910 removed outlier: 3.845A pdb=" N ASN E1896 " --> pdb=" O ARG E1892 " (cutoff:3.500A) Processing helix chain 'E' and resid 1925 through 1930 Processing helix chain 'E' and resid 1931 through 1947 Processing helix chain 'E' and resid 1969 through 1987 removed outlier: 3.786A pdb=" N GLN E1973 " --> pdb=" O ASN E1969 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2120 removed outlier: 3.768A pdb=" N LYS E2089 " --> pdb=" O LYS E2085 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY E2107 " --> pdb=" O GLU E2103 " (cutoff:3.500A) Processing helix chain 'E' and resid 2124 through 2141 Processing helix chain 'E' and resid 2144 through 2155 Processing helix chain 'E' and resid 2171 through 2260 Processing helix chain 'E' and resid 2263 through 2300 removed outlier: 3.610A pdb=" N TYR E2267 " --> pdb=" O ASN E2263 " (cutoff:3.500A) Processing helix chain 'E' and resid 2314 through 2318 Processing helix chain 'E' and resid 2321 through 2341 Processing helix chain 'E' and resid 2353 through 2359 Processing helix chain 'E' and resid 2366 through 2377 removed outlier: 3.839A pdb=" N THR E2372 " --> pdb=" O LYS E2368 " (cutoff:3.500A) Processing helix chain 'E' and resid 2401 through 2406 removed outlier: 3.886A pdb=" N ASN E2406 " --> pdb=" O SER E2403 " (cutoff:3.500A) Processing helix chain 'E' and resid 2412 through 2416 removed outlier: 3.846A pdb=" N LEU E2415 " --> pdb=" O PRO E2412 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E2416 " --> pdb=" O ASP E2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2412 through 2416' Processing helix chain 'E' and resid 2452 through 2456 removed outlier: 3.509A pdb=" N LYS E2455 " --> pdb=" O ARG E2452 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA E2456 " --> pdb=" O GLY E2453 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2452 through 2456' Processing helix chain 'E' and resid 2503 through 2509 Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 315 removed outlier: 3.560A pdb=" N ARG A 372 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 371 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 383 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 373 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 351 removed outlier: 4.035A pdb=" N TYR A 344 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1080 through 1086 removed outlier: 6.896A pdb=" N ILE A1099 " --> pdb=" O ILE A1082 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A1084 " --> pdb=" O TYR A1097 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR A1097 " --> pdb=" O GLY A1084 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS A1086 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A1095 " --> pdb=" O HIS A1086 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1151 Processing sheet with id=AA5, first strand: chain 'A' and resid 1217 through 1220 Processing sheet with id=AA6, first strand: chain 'A' and resid 1282 through 1283 removed outlier: 4.132A pdb=" N TYR A1282 " --> pdb=" O LEU A1589 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1589 " --> pdb=" O TYR A1282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1292 through 1296 Processing sheet with id=AA8, first strand: chain 'A' and resid 1299 through 1300 removed outlier: 3.526A pdb=" N GLY A1311 " --> pdb=" O ILE A1300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1317 through 1319 Processing sheet with id=AB1, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AB2, first strand: chain 'A' and resid 1693 through 1696 removed outlier: 3.637A pdb=" N VAL A1768 " --> pdb=" O THR A1647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A1766 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1664 through 1668 removed outlier: 6.519A pdb=" N ILE A1668 " --> pdb=" O PRO A1679 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1728 through 1731 Processing sheet with id=AB5, first strand: chain 'A' and resid 1746 through 1749 removed outlier: 6.435A pdb=" N LYS A1756 " --> pdb=" O SER A1747 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A1749 " --> pdb=" O ILE A1754 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A1754 " --> pdb=" O MET A1749 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1825 through 1826 Processing sheet with id=AB7, first strand: chain 'A' and resid 2346 through 2352 removed outlier: 5.650A pdb=" N THR A2520 " --> pdb=" O ILE A2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE A2421 " --> pdb=" O THR A2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG A2522 " --> pdb=" O ARG A2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A2419 " --> pdb=" O ARG A2522 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2346 through 2352 removed outlier: 5.650A pdb=" N THR A2520 " --> pdb=" O ILE A2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE A2421 " --> pdb=" O THR A2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG A2522 " --> pdb=" O ARG A2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A2419 " --> pdb=" O ARG A2522 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A2484 " --> pdb=" O ILE A2421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2389 through 2392 Processing sheet with id=AC1, first strand: chain 'B' and resid 313 through 315 removed outlier: 3.560A pdb=" N ARG B 372 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE B 371 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN B 383 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 373 " --> pdb=" O ILE B 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 342 through 351 removed outlier: 4.036A pdb=" N TYR B 344 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1080 through 1086 removed outlier: 6.896A pdb=" N ILE B1099 " --> pdb=" O ILE B1082 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B1084 " --> pdb=" O TYR B1097 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR B1097 " --> pdb=" O GLY B1084 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS B1086 " --> pdb=" O LEU B1095 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B1095 " --> pdb=" O HIS B1086 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1146 through 1151 Processing sheet with id=AC5, first strand: chain 'B' and resid 1217 through 1220 Processing sheet with id=AC6, first strand: chain 'B' and resid 1282 through 1283 removed outlier: 4.132A pdb=" N TYR B1282 " --> pdb=" O LEU B1589 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1589 " --> pdb=" O TYR B1282 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1292 through 1296 Processing sheet with id=AC8, first strand: chain 'B' and resid 1299 through 1300 removed outlier: 3.526A pdb=" N GLY B1311 " --> pdb=" O ILE B1300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1317 through 1319 Processing sheet with id=AD1, first strand: chain 'B' and resid 1335 through 1337 Processing sheet with id=AD2, first strand: chain 'B' and resid 1693 through 1696 removed outlier: 3.638A pdb=" N VAL B1768 " --> pdb=" O THR B1647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B1766 " --> pdb=" O LYS B1649 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1664 through 1668 removed outlier: 6.519A pdb=" N ILE B1668 " --> pdb=" O PRO B1679 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1728 through 1731 Processing sheet with id=AD5, first strand: chain 'B' and resid 1746 through 1749 removed outlier: 6.436A pdb=" N LYS B1756 " --> pdb=" O SER B1747 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET B1749 " --> pdb=" O ILE B1754 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B1754 " --> pdb=" O MET B1749 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1825 through 1826 Processing sheet with id=AD7, first strand: chain 'B' and resid 2346 through 2352 removed outlier: 5.649A pdb=" N THR B2520 " --> pdb=" O ILE B2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE B2421 " --> pdb=" O THR B2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG B2522 " --> pdb=" O ARG B2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG B2419 " --> pdb=" O ARG B2522 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 2346 through 2352 removed outlier: 5.649A pdb=" N THR B2520 " --> pdb=" O ILE B2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE B2421 " --> pdb=" O THR B2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG B2522 " --> pdb=" O ARG B2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG B2419 " --> pdb=" O ARG B2522 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B2484 " --> pdb=" O ILE B2421 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 2389 through 2392 Processing sheet with id=AE1, first strand: chain 'C' and resid 313 through 315 removed outlier: 3.560A pdb=" N ARG C 372 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE C 371 " --> pdb=" O GLN C 383 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN C 383 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 373 " --> pdb=" O ILE C 381 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 342 through 351 removed outlier: 4.035A pdb=" N TYR C 344 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1080 through 1086 removed outlier: 6.896A pdb=" N ILE C1099 " --> pdb=" O ILE C1082 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY C1084 " --> pdb=" O TYR C1097 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C1097 " --> pdb=" O GLY C1084 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS C1086 " --> pdb=" O LEU C1095 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C1095 " --> pdb=" O HIS C1086 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1146 through 1151 Processing sheet with id=AE5, first strand: chain 'C' and resid 1217 through 1220 Processing sheet with id=AE6, first strand: chain 'C' and resid 1282 through 1283 removed outlier: 4.132A pdb=" N TYR C1282 " --> pdb=" O LEU C1589 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C1589 " --> pdb=" O TYR C1282 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1292 through 1296 Processing sheet with id=AE8, first strand: chain 'C' and resid 1299 through 1300 removed outlier: 3.527A pdb=" N GLY C1311 " --> pdb=" O ILE C1300 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1317 through 1319 Processing sheet with id=AF1, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AF2, first strand: chain 'C' and resid 1693 through 1696 removed outlier: 3.637A pdb=" N VAL C1768 " --> pdb=" O THR C1647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS C1766 " --> pdb=" O LYS C1649 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1664 through 1668 removed outlier: 6.519A pdb=" N ILE C1668 " --> pdb=" O PRO C1679 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1728 through 1731 Processing sheet with id=AF5, first strand: chain 'C' and resid 1746 through 1749 removed outlier: 6.436A pdb=" N LYS C1756 " --> pdb=" O SER C1747 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET C1749 " --> pdb=" O ILE C1754 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE C1754 " --> pdb=" O MET C1749 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1825 through 1826 Processing sheet with id=AF7, first strand: chain 'C' and resid 2346 through 2352 removed outlier: 5.649A pdb=" N THR C2520 " --> pdb=" O ILE C2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C2421 " --> pdb=" O THR C2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG C2522 " --> pdb=" O ARG C2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG C2419 " --> pdb=" O ARG C2522 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 2346 through 2352 removed outlier: 5.649A pdb=" N THR C2520 " --> pdb=" O ILE C2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE C2421 " --> pdb=" O THR C2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG C2522 " --> pdb=" O ARG C2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG C2419 " --> pdb=" O ARG C2522 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C2484 " --> pdb=" O ILE C2421 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 2389 through 2392 Processing sheet with id=AG1, first strand: chain 'D' and resid 313 through 315 removed outlier: 3.560A pdb=" N ARG D 372 " --> pdb=" O TRP D 415 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE D 371 " --> pdb=" O GLN D 383 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN D 383 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 373 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 342 through 351 removed outlier: 4.035A pdb=" N TYR D 344 " --> pdb=" O SER D 360 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 1080 through 1086 removed outlier: 6.896A pdb=" N ILE D1099 " --> pdb=" O ILE D1082 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY D1084 " --> pdb=" O TYR D1097 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR D1097 " --> pdb=" O GLY D1084 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS D1086 " --> pdb=" O LEU D1095 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D1095 " --> pdb=" O HIS D1086 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 1146 through 1151 Processing sheet with id=AG5, first strand: chain 'D' and resid 1217 through 1220 Processing sheet with id=AG6, first strand: chain 'D' and resid 1282 through 1283 removed outlier: 4.133A pdb=" N TYR D1282 " --> pdb=" O LEU D1589 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D1589 " --> pdb=" O TYR D1282 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 1292 through 1296 Processing sheet with id=AG8, first strand: chain 'D' and resid 1299 through 1300 removed outlier: 3.526A pdb=" N GLY D1311 " --> pdb=" O ILE D1300 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 1317 through 1319 Processing sheet with id=AH1, first strand: chain 'D' and resid 1335 through 1337 Processing sheet with id=AH2, first strand: chain 'D' and resid 1693 through 1696 removed outlier: 3.638A pdb=" N VAL D1768 " --> pdb=" O THR D1647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS D1766 " --> pdb=" O LYS D1649 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 1664 through 1668 removed outlier: 6.520A pdb=" N ILE D1668 " --> pdb=" O PRO D1679 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 1728 through 1731 Processing sheet with id=AH5, first strand: chain 'D' and resid 1746 through 1749 removed outlier: 6.435A pdb=" N LYS D1756 " --> pdb=" O SER D1747 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET D1749 " --> pdb=" O ILE D1754 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D1754 " --> pdb=" O MET D1749 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 1825 through 1826 Processing sheet with id=AH7, first strand: chain 'D' and resid 2346 through 2352 removed outlier: 5.650A pdb=" N THR D2520 " --> pdb=" O ILE D2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE D2421 " --> pdb=" O THR D2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG D2522 " --> pdb=" O ARG D2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D2419 " --> pdb=" O ARG D2522 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 2346 through 2352 removed outlier: 5.650A pdb=" N THR D2520 " --> pdb=" O ILE D2421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE D2421 " --> pdb=" O THR D2520 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG D2522 " --> pdb=" O ARG D2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG D2419 " --> pdb=" O ARG D2522 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D2484 " --> pdb=" O ILE D2421 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 2389 through 2392 Processing sheet with id=AI1, first strand: chain 'E' and resid 313 through 315 removed outlier: 3.560A pdb=" N ARG E 372 " --> pdb=" O TRP E 415 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE E 371 " --> pdb=" O GLN E 383 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN E 383 " --> pdb=" O PHE E 371 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU E 373 " --> pdb=" O ILE E 381 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 342 through 351 removed outlier: 4.035A pdb=" N TYR E 344 " --> pdb=" O SER E 360 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 1080 through 1086 removed outlier: 6.897A pdb=" N ILE E1099 " --> pdb=" O ILE E1082 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY E1084 " --> pdb=" O TYR E1097 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR E1097 " --> pdb=" O GLY E1084 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS E1086 " --> pdb=" O LEU E1095 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU E1095 " --> pdb=" O HIS E1086 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 1146 through 1151 Processing sheet with id=AI5, first strand: chain 'E' and resid 1217 through 1220 Processing sheet with id=AI6, first strand: chain 'E' and resid 1282 through 1283 removed outlier: 4.132A pdb=" N TYR E1282 " --> pdb=" O LEU E1589 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E1589 " --> pdb=" O TYR E1282 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 1292 through 1296 Processing sheet with id=AI8, first strand: chain 'E' and resid 1299 through 1300 removed outlier: 3.526A pdb=" N GLY E1311 " --> pdb=" O ILE E1300 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 1317 through 1319 Processing sheet with id=AJ1, first strand: chain 'E' and resid 1335 through 1337 Processing sheet with id=AJ2, first strand: chain 'E' and resid 1693 through 1696 removed outlier: 3.638A pdb=" N VAL E1768 " --> pdb=" O THR E1647 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS E1766 " --> pdb=" O LYS E1649 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 1664 through 1668 removed outlier: 6.519A pdb=" N ILE E1668 " --> pdb=" O PRO E1679 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 1728 through 1731 Processing sheet with id=AJ5, first strand: chain 'E' and resid 1746 through 1749 removed outlier: 6.437A pdb=" N LYS E1756 " --> pdb=" O SER E1747 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET E1749 " --> pdb=" O ILE E1754 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E1754 " --> pdb=" O MET E1749 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 1825 through 1826 Processing sheet with id=AJ7, first strand: chain 'E' and resid 2346 through 2352 removed outlier: 5.649A pdb=" N THR E2520 " --> pdb=" O ILE E2421 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE E2421 " --> pdb=" O THR E2520 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG E2522 " --> pdb=" O ARG E2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG E2419 " --> pdb=" O ARG E2522 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 2346 through 2352 removed outlier: 5.649A pdb=" N THR E2520 " --> pdb=" O ILE E2421 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE E2421 " --> pdb=" O THR E2520 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG E2522 " --> pdb=" O ARG E2419 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG E2419 " --> pdb=" O ARG E2522 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E2484 " --> pdb=" O ILE E2421 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 2389 through 2392 4840 hydrogen bonds defined for protein. 13980 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: 56.00 Time building geometry restraints manager: 31.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 30329 1.34 - 1.46: 18476 1.46 - 1.57: 46075 1.57 - 1.69: 0 1.69 - 1.81: 620 Bond restraints: 95500 Sorted by residual: bond pdb=" CG LEU D2049 " pdb=" CD1 LEU D2049 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CG LEU E2049 " pdb=" CD1 LEU E2049 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.36e+00 bond pdb=" CG LEU A2049 " pdb=" CD1 LEU A2049 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" CG LEU B2049 " pdb=" CD1 LEU B2049 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.34e+00 bond pdb=" CG LEU C2049 " pdb=" CD1 LEU C2049 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.28e+00 ... (remaining 95495 not shown) Histogram of bond angle deviations from ideal: 98.86 - 106.48: 2296 106.48 - 114.10: 55336 114.10 - 121.72: 51492 121.72 - 129.34: 19911 129.34 - 136.96: 655 Bond angle restraints: 129690 Sorted by residual: angle pdb=" C THR D 161 " pdb=" N LEU D 162 " pdb=" CA LEU D 162 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 angle pdb=" C THR A 161 " pdb=" N LEU A 162 " pdb=" CA LEU A 162 " ideal model delta sigma weight residual 121.54 132.19 -10.65 1.91e+00 2.74e-01 3.11e+01 angle pdb=" C THR E 161 " pdb=" N LEU E 162 " pdb=" CA LEU E 162 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C THR C 161 " pdb=" N LEU C 162 " pdb=" CA LEU C 162 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C THR B 161 " pdb=" N LEU B 162 " pdb=" CA LEU B 162 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.06e+01 ... (remaining 129685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 51263 17.33 - 34.66: 4693 34.66 - 51.99: 1084 51.99 - 69.32: 305 69.32 - 86.65: 25 Dihedral angle restraints: 57370 sinusoidal: 22845 harmonic: 34525 Sorted by residual: dihedral pdb=" CA ALA E2344 " pdb=" C ALA E2344 " pdb=" N LEU E2345 " pdb=" CA LEU E2345 " ideal model delta harmonic sigma weight residual 180.00 145.38 34.62 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA ALA D2344 " pdb=" C ALA D2344 " pdb=" N LEU D2345 " pdb=" CA LEU D2345 " ideal model delta harmonic sigma weight residual 180.00 145.39 34.61 0 5.00e+00 4.00e-02 4.79e+01 dihedral pdb=" CA ALA B2344 " pdb=" C ALA B2344 " pdb=" N LEU B2345 " pdb=" CA LEU B2345 " ideal model delta harmonic sigma weight residual 180.00 145.39 34.61 0 5.00e+00 4.00e-02 4.79e+01 ... (remaining 57367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 10025 0.043 - 0.085: 3122 0.085 - 0.128: 1246 0.128 - 0.171: 138 0.171 - 0.213: 34 Chirality restraints: 14565 Sorted by residual: chirality pdb=" CA PRO A2451 " pdb=" N PRO A2451 " pdb=" C PRO A2451 " pdb=" CB PRO A2451 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PRO C2451 " pdb=" N PRO C2451 " pdb=" C PRO C2451 " pdb=" CB PRO C2451 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO B2451 " pdb=" N PRO B2451 " pdb=" C PRO B2451 " pdb=" CB PRO B2451 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 14562 not shown) Planarity restraints: 16710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1558 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ILE A1558 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE A1558 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A1559 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D1558 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE D1558 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE D1558 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS D1559 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1558 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ILE C1558 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE C1558 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS C1559 " -0.019 2.00e-02 2.50e+03 ... (remaining 16707 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 23913 2.78 - 3.31: 85751 3.31 - 3.84: 164624 3.84 - 4.37: 184523 4.37 - 4.90: 317676 Nonbonded interactions: 776487 Sorted by model distance: nonbonded pdb=" OH TYR B1151 " pdb=" O ASP B1225 " model vdw 2.255 2.440 nonbonded pdb=" OH TYR E1151 " pdb=" O ASP E1225 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR C1151 " pdb=" O ASP C1225 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR D1151 " pdb=" O ASP D1225 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR A1151 " pdb=" O ASP A1225 " model vdw 2.257 2.440 ... (remaining 776482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 16.230 Check model and map are aligned: 1.070 Set scattering table: 0.660 Process input model: 210.230 Find NCS groups from input model: 5.050 Set up NCS constraints: 0.450 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 243.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.006 0.087 95500 Z= 0.379 Angle : 0.813 10.659 129690 Z= 0.470 Chirality : 0.048 0.213 14565 Planarity : 0.006 0.072 16710 Dihedral : 14.558 86.653 35090 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.62 % Rotamer: Outliers : 8.11 % Allowed : 10.85 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.07 (0.07), residues: 11655 helix: -1.33 (0.06), residues: 5400 sheet: -2.31 (0.11), residues: 1735 loop : -2.66 (0.08), residues: 4520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E1835 HIS 0.007 0.001 HIS D 368 PHE 0.014 0.002 PHE D1644 TYR 0.016 0.002 TYR E1703 ARG 0.005 0.001 ARG A2343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1939 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 831 poor density : 1108 time to evaluate : 8.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8641 (ptp) cc_final: 0.8391 (ptp) REVERT: A 65 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8939 (mp) REVERT: A 433 MET cc_start: 0.8473 (ptm) cc_final: 0.8103 (ttm) REVERT: A 694 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9002 (mt) REVERT: A 899 MET cc_start: 0.8833 (mmm) cc_final: 0.8557 (mmp) REVERT: A 968 GLN cc_start: 0.8891 (mp10) cc_final: 0.8516 (mp10) REVERT: A 1032 TYR cc_start: 0.8661 (m-80) cc_final: 0.8300 (m-80) REVERT: A 1067 LYS cc_start: 0.9074 (mttt) cc_final: 0.8590 (mtmt) REVERT: A 1134 LYS cc_start: 0.8926 (tttm) cc_final: 0.8666 (tttm) REVERT: A 1323 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7886 (p0) REVERT: A 1334 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: A 1770 MET cc_start: 0.7998 (mmp) cc_final: 0.7768 (mmm) REVERT: A 1811 SER cc_start: 0.9557 (OUTLIER) cc_final: 0.9350 (t) REVERT: A 1845 SER cc_start: 0.8886 (m) cc_final: 0.8536 (p) REVERT: A 1984 TYR cc_start: 0.8778 (t80) cc_final: 0.8264 (t80) REVERT: A 2291 MET cc_start: 0.8782 (mtm) cc_final: 0.8435 (mtm) REVERT: A 2308 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8742 (mt) REVERT: A 2390 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8459 (t0) REVERT: A 2448 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8175 (p) REVERT: A 2463 MET cc_start: 0.8988 (tpt) cc_final: 0.8709 (tpp) REVERT: B 65 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8860 (mt) REVERT: B 433 MET cc_start: 0.8379 (ptm) cc_final: 0.8091 (ttp) REVERT: B 592 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8946 (pp) REVERT: B 646 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9056 (mt) REVERT: B 795 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8940 (tp) REVERT: B 809 MET cc_start: 0.8888 (mmt) cc_final: 0.8531 (mmm) REVERT: B 899 MET cc_start: 0.8975 (mmm) cc_final: 0.8745 (mmm) REVERT: B 968 GLN cc_start: 0.8959 (mp10) cc_final: 0.8613 (mp10) REVERT: B 1067 LYS cc_start: 0.9105 (mttt) cc_final: 0.8545 (mtmt) REVERT: B 1134 LYS cc_start: 0.8895 (tttm) cc_final: 0.8441 (tttm) REVERT: B 1323 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 1845 SER cc_start: 0.9051 (m) cc_final: 0.8601 (p) REVERT: B 2291 MET cc_start: 0.8715 (mtm) cc_final: 0.8420 (mtm) REVERT: B 2308 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8748 (mt) REVERT: B 2390 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 2448 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8475 (p) REVERT: B 2463 MET cc_start: 0.8864 (tpt) cc_final: 0.8649 (tpp) REVERT: C 28 MET cc_start: 0.8833 (ptp) cc_final: 0.8509 (ptp) REVERT: C 65 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8624 (mt) REVERT: C 226 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9157 (p) REVERT: C 453 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8764 (ttpt) REVERT: C 592 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8717 (pp) REVERT: C 613 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8978 (tt) REVERT: C 809 MET cc_start: 0.9060 (mmt) cc_final: 0.8643 (mmm) REVERT: C 1044 MET cc_start: 0.8830 (ptp) cc_final: 0.8616 (ptp) REVERT: C 1069 TYR cc_start: 0.8831 (t80) cc_final: 0.8402 (t80) REVERT: C 1137 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9090 (pt) REVERT: C 1323 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7779 (p0) REVERT: C 1334 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8369 (mmm) REVERT: C 1554 SER cc_start: 0.8040 (OUTLIER) cc_final: 0.7782 (p) REVERT: C 1684 MET cc_start: 0.7990 (ttp) cc_final: 0.7761 (ttm) REVERT: C 1875 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8262 (tpp) REVERT: C 2025 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8445 (mt) REVERT: C 2102 GLN cc_start: 0.8095 (mt0) cc_final: 0.7641 (mt0) REVERT: C 2160 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8576 (mt) REVERT: C 2308 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8653 (mp) REVERT: C 2333 MET cc_start: 0.8622 (ttp) cc_final: 0.8401 (ttp) REVERT: C 2390 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8297 (t0) REVERT: C 2486 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8644 (t) REVERT: D 28 MET cc_start: 0.8595 (ptp) cc_final: 0.8243 (ptp) REVERT: D 65 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8884 (mt) REVERT: D 433 MET cc_start: 0.8565 (ptm) cc_final: 0.8154 (ttp) REVERT: D 483 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9481 (tt) REVERT: D 592 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8943 (pp) REVERT: D 630 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8900 (p) REVERT: D 694 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9094 (mt) REVERT: D 775 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8629 (m) REVERT: D 809 MET cc_start: 0.9263 (mmt) cc_final: 0.8732 (mmm) REVERT: D 899 MET cc_start: 0.8878 (mmm) cc_final: 0.8625 (mmp) REVERT: D 968 GLN cc_start: 0.9063 (mp10) cc_final: 0.8762 (mp10) REVERT: D 1067 LYS cc_start: 0.9121 (mttt) cc_final: 0.8296 (mtmm) REVERT: D 1323 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7865 (p0) REVERT: D 1334 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8218 (mtp) REVERT: D 1554 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (p) REVERT: D 1619 ARG cc_start: 0.8305 (mmt180) cc_final: 0.7968 (mtt90) REVERT: D 1811 SER cc_start: 0.9567 (OUTLIER) cc_final: 0.9317 (t) REVERT: D 1845 SER cc_start: 0.8799 (m) cc_final: 0.8325 (p) REVERT: D 2030 MET cc_start: 0.9248 (tpt) cc_final: 0.8893 (tpp) REVERT: D 2032 MET cc_start: 0.7523 (mmm) cc_final: 0.7255 (tpp) REVERT: D 2109 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7951 (tp40) REVERT: D 2113 ASP cc_start: 0.7756 (m-30) cc_final: 0.7345 (m-30) REVERT: D 2131 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.7954 (mmt) REVERT: D 2220 LYS cc_start: 0.9078 (mttt) cc_final: 0.8740 (mtmt) REVERT: D 2270 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8849 (mp) REVERT: D 2291 MET cc_start: 0.8752 (mtm) cc_final: 0.8454 (mtm) REVERT: D 2308 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8762 (mt) REVERT: D 2390 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8364 (t0) REVERT: D 2463 MET cc_start: 0.8863 (tpt) cc_final: 0.8495 (tpp) REVERT: E 28 MET cc_start: 0.8773 (ptp) cc_final: 0.8471 (ptp) REVERT: E 54 HIS cc_start: 0.8709 (t-90) cc_final: 0.8116 (t-170) REVERT: E 65 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8891 (mt) REVERT: E 433 MET cc_start: 0.8470 (ptm) cc_final: 0.8149 (ttt) REVERT: E 694 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8878 (mt) REVERT: E 763 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9036 (tt) REVERT: E 775 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8739 (m) REVERT: E 795 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8929 (tp) REVERT: E 899 MET cc_start: 0.9008 (mmm) cc_final: 0.8694 (mmp) REVERT: E 968 GLN cc_start: 0.8778 (mp10) cc_final: 0.8536 (mp10) REVERT: E 1067 LYS cc_start: 0.9086 (mttt) cc_final: 0.8246 (mtmm) REVERT: E 1134 LYS cc_start: 0.9001 (tttm) cc_final: 0.8636 (tttm) REVERT: E 1137 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9272 (pt) REVERT: E 1218 CYS cc_start: 0.7745 (m) cc_final: 0.7382 (m) REVERT: E 1334 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: E 1554 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8267 (p) REVERT: E 1619 ARG cc_start: 0.8305 (mmt180) cc_final: 0.7881 (mpt180) REVERT: E 1749 MET cc_start: 0.9408 (tpp) cc_final: 0.9160 (tpt) REVERT: E 1811 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9287 (t) REVERT: E 1845 SER cc_start: 0.9023 (m) cc_final: 0.8619 (p) REVERT: E 2113 ASP cc_start: 0.7754 (m-30) cc_final: 0.7382 (m-30) REVERT: E 2220 LYS cc_start: 0.9108 (mttt) cc_final: 0.8882 (mtmt) REVERT: E 2291 MET cc_start: 0.8803 (mtm) cc_final: 0.8533 (mtp) REVERT: E 2308 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8650 (mt) REVERT: E 2390 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8331 (t0) REVERT: E 2448 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8487 (p) REVERT: E 2463 MET cc_start: 0.8852 (tpt) cc_final: 0.8603 (tpp) outliers start: 831 outliers final: 197 residues processed: 1859 average time/residue: 0.8699 time to fit residues: 2827.5502 Evaluate side-chains 838 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 584 time to evaluate : 8.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1334 MET Chi-restraints excluded: chain A residue 1500 ASP Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1712 VAL Chi-restraints excluded: chain A residue 1811 SER Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 1999 LEU Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2259 SER Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2360 LEU Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2448 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1323 ASN Chi-restraints excluded: chain B residue 1500 ASP Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1712 VAL Chi-restraints excluded: chain B residue 1893 ASP Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2017 THR Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2142 THR Chi-restraints excluded: chain B residue 2259 SER Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2363 ASN Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2448 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 453 LYS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 1011 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1323 ASN Chi-restraints excluded: chain C residue 1334 MET Chi-restraints excluded: chain C residue 1500 ASP Chi-restraints excluded: chain C residue 1545 ILE Chi-restraints excluded: chain C residue 1554 SER Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1803 LEU Chi-restraints excluded: chain C residue 1875 MET Chi-restraints excluded: chain C residue 1893 ASP Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1991 THR Chi-restraints excluded: chain C residue 2025 LEU Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2142 THR Chi-restraints excluded: chain C residue 2160 ILE Chi-restraints excluded: chain C residue 2259 SER Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 487 GLN Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 630 THR Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 879 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1323 ASN Chi-restraints excluded: chain D residue 1334 MET Chi-restraints excluded: chain D residue 1500 ASP Chi-restraints excluded: chain D residue 1554 SER Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1811 SER Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1854 VAL Chi-restraints excluded: chain D residue 1893 ASP Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2131 MET Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2259 SER Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2363 ASN Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 478 ASN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 487 GLN Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 763 ILE Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain E residue 795 LEU Chi-restraints excluded: chain E residue 879 THR Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 1047 ASN Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1137 ILE Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1256 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1334 MET Chi-restraints excluded: chain E residue 1500 ASP Chi-restraints excluded: chain E residue 1554 SER Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1712 VAL Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1811 SER Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 1999 LEU Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2259 SER Chi-restraints excluded: chain E residue 2308 ILE Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2363 ASN Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2448 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 983 optimal weight: 4.9990 chunk 883 optimal weight: 9.9990 chunk 489 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 595 optimal weight: 3.9990 chunk 471 optimal weight: 6.9990 chunk 913 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 555 optimal weight: 0.7980 chunk 679 optimal weight: 0.6980 chunk 1057 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 55 GLN A 77 ASN A 139 ASN A 171 HIS A 172 ASN A 200 HIS A 213 GLN A 216 ASN A 341 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 487 GLN A 519 HIS A 681 ASN A 766 ASN A1041 GLN A1051 GLN A1056 GLN A1080 GLN A1167 ASN A1197 ASN A1206 ASN A1502 ASN ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1540 GLN A1670 ASN A1804 GLN A1866 HIS A1939 GLN A2102 GLN A2159 ASN A2197 GLN A2221 GLN A2251 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2461 HIS A2516 HIS B 24 ASN B 55 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 139 ASN B 171 HIS B 172 ASN B 200 HIS B 213 GLN B 216 ASN B 306 ASN B 341 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN B 420 ASN B 478 ASN B 487 GLN B 519 HIS B 681 ASN B 759 GLN B 766 ASN ** B1031 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 GLN B1047 ASN B1050 GLN B1051 GLN B1056 GLN B1080 GLN B1167 ASN ** B1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1206 ASN B1502 ASN ** B1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1540 GLN B1626 ASN B1634 ASN B1670 ASN B1735 ASN B1804 GLN B1939 GLN ** B2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2159 ASN B2197 GLN B2221 GLN B2239 GLN B2251 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2461 HIS B2516 HIS C 24 ASN C 55 GLN C 72 ASN C 74 GLN C 80 ASN C 139 ASN C 171 HIS C 172 ASN C 200 HIS C 213 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 519 HIS C 681 ASN C 722 GLN C 755 GLN C 766 ASN C 785 GLN C1041 GLN C1054 GLN C1056 GLN C1080 GLN C1167 ASN ** C1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1206 ASN C1502 ASN ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1540 GLN C1670 ASN C1735 ASN ** C1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1866 HIS C1939 GLN ** C2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2159 ASN C2221 GLN C2251 GLN ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2468 GLN C2516 HIS D 24 ASN D 55 GLN D 77 ASN D 139 ASN D 172 ASN D 200 HIS D 213 GLN ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 ASN D 420 ASN D 478 ASN D 487 GLN D 519 HIS D 681 ASN D 766 ASN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1041 GLN D1051 GLN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1056 GLN D1068 ASN D1080 GLN D1167 ASN D1197 ASN D1206 ASN D1502 ASN ** D1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1540 GLN ** D1634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 ASN D1804 GLN D1939 GLN D2102 GLN D2159 ASN D2221 GLN D2251 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2461 HIS D2516 HIS E 24 ASN E 55 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 80 ASN E 139 ASN E 171 HIS E 172 ASN E 200 HIS E 213 GLN E 216 ASN E 306 ASN E 341 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 ASN E 478 ASN E 487 GLN E 519 HIS E 634 GLN E 681 ASN E 766 ASN E1041 GLN E1051 GLN E1056 GLN E1080 GLN E1167 ASN E1197 ASN E1206 ASN E1502 ASN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1540 GLN E1626 ASN E1670 ASN E1735 ASN E1804 GLN E1939 GLN ** E2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2159 ASN E2197 GLN E2221 GLN E2239 GLN E2251 GLN ** E2294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2461 HIS E2468 GLN E2516 HIS Total number of N/Q/H flips: 186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 95500 Z= 0.246 Angle : 0.606 8.970 129690 Z= 0.318 Chirality : 0.042 0.185 14565 Planarity : 0.004 0.053 16710 Dihedral : 7.702 89.629 13120 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.50 % Allowed : 15.67 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.08), residues: 11655 helix: 0.69 (0.07), residues: 5445 sheet: -1.83 (0.12), residues: 1715 loop : -2.25 (0.09), residues: 4495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 463 HIS 0.005 0.001 HIS C1116 PHE 0.015 0.001 PHE A1872 TYR 0.017 0.001 TYR C1984 ARG 0.008 0.000 ARG D1888 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 461 poor density : 626 time to evaluate : 8.054 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: A 28 MET cc_start: 0.8576 (ptp) cc_final: 0.8305 (ptp) REVERT: A 65 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8849 (mt) REVERT: A 263 MET cc_start: 0.9494 (tpp) cc_final: 0.8918 (tpp) REVERT: A 490 MET cc_start: 0.8477 (ptp) cc_final: 0.7953 (ptp) REVERT: A 659 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8683 (ttm) REVERT: A 899 MET cc_start: 0.8871 (mmm) cc_final: 0.8612 (mmp) REVERT: A 968 GLN cc_start: 0.8667 (mp10) cc_final: 0.8439 (mp10) REVERT: A 1297 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8849 (ttpp) REVERT: A 1770 MET cc_start: 0.8210 (mmp) cc_final: 0.7778 (mmm) REVERT: A 1845 SER cc_start: 0.8762 (m) cc_final: 0.8500 (p) REVERT: A 1936 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8403 (t70) REVERT: A 2032 MET cc_start: 0.7835 (tpp) cc_final: 0.7379 (tpp) REVERT: A 2289 CYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8560 (t) REVERT: A 2291 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8587 (mtm) REVERT: A 2390 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8529 (t0) REVERT: B 65 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8740 (mt) REVERT: B 263 MET cc_start: 0.9549 (tpp) cc_final: 0.9254 (tpp) REVERT: B 809 MET cc_start: 0.8926 (mmt) cc_final: 0.8669 (mmm) REVERT: B 968 GLN cc_start: 0.8682 (mp10) cc_final: 0.8386 (mp10) REVERT: B 976 GLU cc_start: 0.8824 (tp30) cc_final: 0.8540 (tm-30) REVERT: B 1323 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7699 (p0) REVERT: B 1328 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9012 (tp) REVERT: B 1749 MET cc_start: 0.9540 (tpt) cc_final: 0.9297 (tpp) REVERT: B 1796 MET cc_start: 0.8777 (tpp) cc_final: 0.8565 (mmm) REVERT: B 1845 SER cc_start: 0.8997 (m) cc_final: 0.8676 (p) REVERT: B 2091 MET cc_start: 0.7015 (tmm) cc_final: 0.6776 (tmm) REVERT: B 2131 MET cc_start: 0.8606 (mmm) cc_final: 0.8377 (mmt) REVERT: B 2182 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 2233 ARG cc_start: 0.7929 (ttt90) cc_final: 0.7234 (tpt-90) REVERT: B 2289 CYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8379 (t) REVERT: B 2291 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8610 (mtp) REVERT: B 2390 ASN cc_start: 0.8951 (OUTLIER) cc_final: 0.8492 (t0) REVERT: C 28 MET cc_start: 0.8771 (ptp) cc_final: 0.8517 (ptp) REVERT: C 65 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8691 (mt) REVERT: C 176 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8672 (pp) REVERT: C 434 MET cc_start: 0.8414 (mpp) cc_final: 0.8193 (mpp) REVERT: C 584 MET cc_start: 0.8715 (mmm) cc_final: 0.7960 (mmm) REVERT: C 1137 ILE cc_start: 0.9447 (OUTLIER) cc_final: 0.9218 (pt) REVERT: C 1225 ASP cc_start: 0.7506 (p0) cc_final: 0.7217 (p0) REVERT: C 1323 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7837 (p0) REVERT: C 1684 MET cc_start: 0.8182 (ttp) cc_final: 0.7920 (ttm) REVERT: C 1875 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8313 (tpp) REVERT: C 2124 ASN cc_start: 0.8175 (t0) cc_final: 0.7836 (t0) REVERT: C 2160 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8778 (mt) REVERT: C 2390 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8141 (t0) REVERT: C 2472 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8270 (p0) REVERT: C 2486 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8780 (t) REVERT: C 2499 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8664 (pt) REVERT: D 28 MET cc_start: 0.8509 (ptp) cc_final: 0.8237 (ptp) REVERT: D 65 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8869 (mt) REVERT: D 155 MET cc_start: 0.8773 (ttm) cc_final: 0.8571 (ttp) REVERT: D 694 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8887 (mt) REVERT: D 775 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8659 (m) REVERT: D 809 MET cc_start: 0.9145 (mmt) cc_final: 0.8856 (mmm) REVERT: D 899 MET cc_start: 0.8902 (mmm) cc_final: 0.8645 (mmp) REVERT: D 968 GLN cc_start: 0.8886 (mp10) cc_final: 0.8608 (mp10) REVERT: D 1045 MET cc_start: 0.8754 (mmm) cc_final: 0.8533 (mmm) REVERT: D 1323 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8141 (p0) REVERT: D 1334 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7948 (mtp) REVERT: D 1749 MET cc_start: 0.9380 (tpt) cc_final: 0.9155 (tpp) REVERT: D 1811 SER cc_start: 0.9576 (OUTLIER) cc_final: 0.9362 (t) REVERT: D 1845 SER cc_start: 0.8724 (m) cc_final: 0.8370 (p) REVERT: D 1865 MET cc_start: 0.8397 (tmm) cc_final: 0.8023 (tmm) REVERT: D 2010 MET cc_start: 0.8174 (tpt) cc_final: 0.7851 (tpt) REVERT: D 2032 MET cc_start: 0.7636 (mmm) cc_final: 0.7408 (tpp) REVERT: D 2131 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7964 (mmt) REVERT: D 2291 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8607 (mtm) REVERT: D 2390 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8135 (t0) REVERT: E 28 MET cc_start: 0.8711 (ptp) cc_final: 0.8446 (ptp) REVERT: E 54 HIS cc_start: 0.8706 (t-90) cc_final: 0.8122 (t-170) REVERT: E 65 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8838 (mt) REVERT: E 155 MET cc_start: 0.8897 (tpp) cc_final: 0.8585 (ttm) REVERT: E 230 MET cc_start: 0.7828 (mtt) cc_final: 0.7595 (mtt) REVERT: E 263 MET cc_start: 0.9443 (tpp) cc_final: 0.8931 (tpp) REVERT: E 490 MET cc_start: 0.8822 (ptm) cc_final: 0.8433 (ptp) REVERT: E 584 MET cc_start: 0.8350 (mmm) cc_final: 0.8013 (mmm) REVERT: E 694 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8882 (mt) REVERT: E 775 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8746 (m) REVERT: E 899 MET cc_start: 0.8998 (mmm) cc_final: 0.8717 (mmp) REVERT: E 968 GLN cc_start: 0.8746 (mp10) cc_final: 0.8463 (mp10) REVERT: E 1050 GLN cc_start: 0.8319 (mt0) cc_final: 0.8102 (mt0) REVERT: E 1250 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7439 (t) REVERT: E 1334 MET cc_start: 0.8486 (tpp) cc_final: 0.7843 (tpp) REVERT: E 1749 MET cc_start: 0.9464 (tpp) cc_final: 0.9160 (tpp) REVERT: E 1845 SER cc_start: 0.8944 (m) cc_final: 0.8653 (p) REVERT: E 1936 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8430 (t70) REVERT: E 2032 MET cc_start: 0.8041 (tpp) cc_final: 0.7761 (tpp) REVERT: E 2109 GLN cc_start: 0.8502 (tp40) cc_final: 0.8253 (tp40) REVERT: E 2113 ASP cc_start: 0.7710 (m-30) cc_final: 0.6978 (m-30) REVERT: E 2291 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8622 (mtp) REVERT: E 2390 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8424 (t0) outliers start: 461 outliers final: 243 residues processed: 1037 average time/residue: 0.8040 time to fit residues: 1476.9135 Evaluate side-chains 794 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 512 time to evaluate : 8.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1297 LYS Chi-restraints excluded: chain A residue 1500 ASP Chi-restraints excluded: chain A residue 1545 ILE Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1712 VAL Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2289 CYS Chi-restraints excluded: chain A residue 2291 MET Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2372 THR Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2448 THR Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1323 ASN Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1690 THR Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1712 VAL Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1818 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1893 ASP Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 1951 LEU Chi-restraints excluded: chain B residue 1956 THR Chi-restraints excluded: chain B residue 1991 THR Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2289 CYS Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2372 THR Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2448 THR Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 830 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 972 THR Chi-restraints excluded: chain C residue 1011 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1137 ILE Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1323 ASN Chi-restraints excluded: chain C residue 1543 VAL Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1785 ILE Chi-restraints excluded: chain C residue 1803 LEU Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1875 MET Chi-restraints excluded: chain C residue 1893 ASP Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2010 MET Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2142 THR Chi-restraints excluded: chain C residue 2145 THR Chi-restraints excluded: chain C residue 2160 ILE Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2289 CYS Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2372 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2499 ILE Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 879 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1323 ASN Chi-restraints excluded: chain D residue 1334 MET Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1785 ILE Chi-restraints excluded: chain D residue 1811 SER Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1893 ASP Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 1956 THR Chi-restraints excluded: chain D residue 1991 THR Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2103 GLU Chi-restraints excluded: chain D residue 2131 MET Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2181 ILE Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2291 MET Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2372 THR Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 745 ASN Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 771 GLU Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 879 THR Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1047 ASN Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1256 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1500 ASP Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1712 VAL Chi-restraints excluded: chain E residue 1785 ILE Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2181 ILE Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2326 LEU Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 587 optimal weight: 6.9990 chunk 328 optimal weight: 4.9990 chunk 880 optimal weight: 6.9990 chunk 720 optimal weight: 2.9990 chunk 291 optimal weight: 0.0570 chunk 1059 optimal weight: 9.9990 chunk 1144 optimal weight: 7.9990 chunk 943 optimal weight: 7.9990 chunk 1051 optimal weight: 0.9980 chunk 361 optimal weight: 7.9990 chunk 850 optimal weight: 0.5980 overall best weight: 1.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN A 135 GLN A 171 HIS A 306 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN A 755 GLN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1575 HIS A2148 HIS ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2468 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 GLN B 755 GLN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1031 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN B1197 ASN ** B1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1575 HIS ** B2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1197 ASN ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2148 HIS ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 ASN D 171 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 722 GLN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1626 ASN ** D1634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2148 HIS D2239 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 722 GLN E 759 GLN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1050 GLN E1051 GLN E1068 ASN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1735 ASN ** E2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2148 HIS E2211 GLN ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 95500 Z= 0.211 Angle : 0.564 11.511 129690 Z= 0.293 Chirality : 0.041 0.165 14565 Planarity : 0.004 0.050 16710 Dihedral : 6.716 88.026 12970 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.07 % Allowed : 16.35 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.44 (0.08), residues: 11655 helix: 1.45 (0.07), residues: 5450 sheet: -1.53 (0.12), residues: 1695 loop : -2.00 (0.09), residues: 4510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1846 HIS 0.004 0.001 HIS D2516 PHE 0.012 0.001 PHE C1872 TYR 0.012 0.001 TYR A2242 ARG 0.008 0.000 ARG D1888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 562 time to evaluate : 8.188 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: A 28 MET cc_start: 0.8558 (ptp) cc_final: 0.8272 (ptp) REVERT: A 65 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8853 (mt) REVERT: A 187 MET cc_start: 0.8317 (tmm) cc_final: 0.8033 (tmm) REVERT: A 263 MET cc_start: 0.9546 (tpp) cc_final: 0.8918 (tpp) REVERT: A 522 MET cc_start: 0.9031 (tmm) cc_final: 0.8703 (tmm) REVERT: A 557 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8921 (ttm) REVERT: A 659 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8792 (ttm) REVERT: A 669 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 694 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8919 (mt) REVERT: A 899 MET cc_start: 0.8961 (mmm) cc_final: 0.8611 (mmp) REVERT: A 1045 MET cc_start: 0.8655 (mmm) cc_final: 0.8401 (mmm) REVERT: A 1050 GLN cc_start: 0.8102 (mt0) cc_final: 0.7890 (mt0) REVERT: A 1293 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9237 (mt) REVERT: A 1684 MET cc_start: 0.8976 (ttm) cc_final: 0.8661 (tpp) REVERT: A 1770 MET cc_start: 0.8118 (mmp) cc_final: 0.7852 (mmm) REVERT: A 1845 SER cc_start: 0.8703 (m) cc_final: 0.8403 (p) REVERT: A 1846 TRP cc_start: 0.8076 (t60) cc_final: 0.7541 (t60) REVERT: A 1934 MET cc_start: 0.9151 (tmm) cc_final: 0.8823 (tmm) REVERT: A 1936 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8427 (t70) REVERT: A 2032 MET cc_start: 0.8173 (tpp) cc_final: 0.7424 (tpp) REVERT: A 2106 HIS cc_start: 0.7985 (m170) cc_final: 0.7491 (m90) REVERT: A 2291 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8679 (mtm) REVERT: A 2390 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8360 (t0) REVERT: B 65 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8743 (mt) REVERT: B 230 MET cc_start: 0.7802 (mtt) cc_final: 0.7491 (mtt) REVERT: B 263 MET cc_start: 0.9531 (tpp) cc_final: 0.9192 (tpp) REVERT: B 669 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 809 MET cc_start: 0.8961 (mmt) cc_final: 0.8760 (mmm) REVERT: B 830 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: B 968 GLN cc_start: 0.8621 (mp10) cc_final: 0.8176 (mp10) REVERT: B 1061 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9073 (t) REVERT: B 1293 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9276 (mt) REVERT: B 1845 SER cc_start: 0.8970 (m) cc_final: 0.8624 (p) REVERT: B 2182 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 2233 ARG cc_start: 0.7892 (ttt90) cc_final: 0.7266 (tpt-90) REVERT: B 2289 CYS cc_start: 0.8960 (m) cc_final: 0.8378 (t) REVERT: B 2291 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8680 (mtm) REVERT: B 2390 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8431 (t0) REVERT: C 65 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8729 (mt) REVERT: C 434 MET cc_start: 0.8530 (mpp) cc_final: 0.8261 (mpp) REVERT: C 518 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8820 (t) REVERT: C 522 MET cc_start: 0.9086 (tmm) cc_final: 0.8882 (tmm) REVERT: C 584 MET cc_start: 0.8689 (mmm) cc_final: 0.8248 (mmm) REVERT: C 707 MET cc_start: 0.8199 (mpp) cc_final: 0.7919 (mpp) REVERT: C 976 GLU cc_start: 0.8643 (tp30) cc_final: 0.8343 (tp30) REVERT: C 1069 TYR cc_start: 0.9018 (t80) cc_final: 0.8649 (t80) REVERT: C 1225 ASP cc_start: 0.7377 (p0) cc_final: 0.6972 (p0) REVERT: C 1323 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7722 (p0) REVERT: C 1334 MET cc_start: 0.8534 (mmm) cc_final: 0.8319 (mmm) REVERT: C 1684 MET cc_start: 0.8296 (ttp) cc_final: 0.7996 (ttm) REVERT: C 1875 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8398 (tpp) REVERT: C 1936 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8560 (t70) REVERT: C 2032 MET cc_start: 0.8021 (tpp) cc_final: 0.7617 (tpp) REVERT: C 2390 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8106 (t0) REVERT: D 28 MET cc_start: 0.8507 (ptp) cc_final: 0.8252 (ptp) REVERT: D 65 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 411 THR cc_start: 0.9419 (OUTLIER) cc_final: 0.9174 (m) REVERT: D 694 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8976 (mt) REVERT: D 775 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8636 (m) REVERT: D 809 MET cc_start: 0.9112 (mmt) cc_final: 0.8900 (mmm) REVERT: D 899 MET cc_start: 0.8888 (mmm) cc_final: 0.8617 (mmp) REVERT: D 968 GLN cc_start: 0.8858 (mp10) cc_final: 0.8587 (mp10) REVERT: D 1045 MET cc_start: 0.8611 (mmm) cc_final: 0.8395 (mmm) REVERT: D 1845 SER cc_start: 0.8651 (m) cc_final: 0.8310 (p) REVERT: D 1865 MET cc_start: 0.8503 (tmm) cc_final: 0.8117 (tmm) REVERT: D 1888 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: D 1970 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8486 (ttmm) REVERT: D 2032 MET cc_start: 0.7583 (mmm) cc_final: 0.7353 (tpp) REVERT: D 2109 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8008 (tp40) REVERT: D 2113 ASP cc_start: 0.8026 (m-30) cc_final: 0.6727 (m-30) REVERT: D 2291 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: D 2390 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8166 (t0) REVERT: E 28 MET cc_start: 0.8686 (ptp) cc_final: 0.8401 (ptp) REVERT: E 54 HIS cc_start: 0.8738 (t-90) cc_final: 0.8138 (t70) REVERT: E 65 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8803 (mt) REVERT: E 224 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8165 (p) REVERT: E 230 MET cc_start: 0.7696 (mtt) cc_final: 0.7415 (mtt) REVERT: E 263 MET cc_start: 0.9483 (tpp) cc_final: 0.8888 (tpp) REVERT: E 584 MET cc_start: 0.8405 (mmm) cc_final: 0.7934 (mmm) REVERT: E 694 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8789 (mt) REVERT: E 775 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8727 (m) REVERT: E 899 MET cc_start: 0.9026 (mmm) cc_final: 0.8735 (mmp) REVERT: E 968 GLN cc_start: 0.8796 (mp10) cc_final: 0.8496 (mp10) REVERT: E 1061 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8947 (t) REVERT: E 1225 ASP cc_start: 0.6907 (p0) cc_final: 0.6543 (p0) REVERT: E 1250 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.7740 (t) REVERT: E 1334 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8066 (tpp) REVERT: E 1749 MET cc_start: 0.9492 (tpp) cc_final: 0.9141 (tpp) REVERT: E 1838 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8228 (ptm-80) REVERT: E 1845 SER cc_start: 0.8892 (m) cc_final: 0.8586 (p) REVERT: E 1934 MET cc_start: 0.9080 (ppp) cc_final: 0.8840 (ppp) REVERT: E 1936 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8470 (t70) REVERT: E 2030 MET cc_start: 0.9255 (tpp) cc_final: 0.8818 (tpp) REVERT: E 2032 MET cc_start: 0.8498 (tpp) cc_final: 0.7884 (tpp) REVERT: E 2291 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8642 (mtp) REVERT: E 2390 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8457 (t0) outliers start: 417 outliers final: 229 residues processed: 927 average time/residue: 0.8137 time to fit residues: 1342.7456 Evaluate side-chains 783 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 515 time to evaluate : 7.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1658 HIS Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1712 VAL Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2291 MET Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2372 THR Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2448 THR Chi-restraints excluded: chain A residue 2499 ILE Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1061 THR Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1630 MET Chi-restraints excluded: chain B residue 1658 HIS Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1712 VAL Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2142 THR Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2372 THR Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2448 THR Chi-restraints excluded: chain B residue 2499 ILE Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 830 GLU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 972 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1222 TYR Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1259 ILE Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1323 ASN Chi-restraints excluded: chain C residue 1543 VAL Chi-restraints excluded: chain C residue 1658 HIS Chi-restraints excluded: chain C residue 1690 THR Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1785 ILE Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1875 MET Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2010 MET Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 879 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1053 SER Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1060 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1656 GLU Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2291 MET Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2366 ILE Chi-restraints excluded: chain D residue 2372 THR Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2499 ILE Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 288 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 771 GLU Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1047 ASN Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1061 THR Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1334 MET Chi-restraints excluded: chain E residue 1500 ASP Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1712 VAL Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2103 GLU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2181 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2448 THR Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 1047 optimal weight: 8.9990 chunk 796 optimal weight: 0.9990 chunk 550 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 505 optimal weight: 6.9990 chunk 711 optimal weight: 9.9990 chunk 1063 optimal weight: 5.9990 chunk 1126 optimal weight: 7.9990 chunk 555 optimal weight: 6.9990 chunk 1008 optimal weight: 0.8980 chunk 303 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1634 ASN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1031 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 GLN B1047 ASN B1050 GLN ** B2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 HIS ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2221 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2468 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN E 171 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1050 GLN ** E1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2503 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 95500 Z= 0.198 Angle : 0.548 9.159 129690 Z= 0.284 Chirality : 0.040 0.166 14565 Planarity : 0.004 0.049 16710 Dihedral : 6.336 84.367 12917 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.96 % Allowed : 16.61 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.07 (0.08), residues: 11655 helix: 1.78 (0.07), residues: 5455 sheet: -1.33 (0.12), residues: 1690 loop : -1.87 (0.09), residues: 4510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D1835 HIS 0.005 0.001 HIS D2148 PHE 0.010 0.001 PHE E2473 TYR 0.012 0.001 TYR C1230 ARG 0.008 0.000 ARG A2189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 406 poor density : 551 time to evaluate : 8.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8589 (ptp) cc_final: 0.8360 (ptp) REVERT: A 65 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8794 (mt) REVERT: A 263 MET cc_start: 0.9555 (tpp) cc_final: 0.8888 (tpp) REVERT: A 433 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8000 (tpp) REVERT: A 659 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8828 (ttm) REVERT: A 694 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8931 (mt) REVERT: A 899 MET cc_start: 0.8943 (mmm) cc_final: 0.8570 (mmp) REVERT: A 1293 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9238 (mt) REVERT: A 1684 MET cc_start: 0.8991 (ttm) cc_final: 0.8721 (tpp) REVERT: A 1770 MET cc_start: 0.8099 (mmp) cc_final: 0.7859 (mmm) REVERT: A 1845 SER cc_start: 0.8695 (m) cc_final: 0.8399 (p) REVERT: A 1846 TRP cc_start: 0.8048 (t60) cc_final: 0.7582 (t60) REVERT: A 1934 MET cc_start: 0.9137 (tmm) cc_final: 0.8807 (tmm) REVERT: A 1936 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8396 (t70) REVERT: A 2032 MET cc_start: 0.8332 (tpp) cc_final: 0.7479 (tpp) REVERT: A 2106 HIS cc_start: 0.7950 (m170) cc_final: 0.7448 (m90) REVERT: A 2291 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8700 (mtm) REVERT: A 2390 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8394 (t0) REVERT: B 65 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8748 (mt) REVERT: B 263 MET cc_start: 0.9538 (tpp) cc_final: 0.9220 (tpp) REVERT: B 809 MET cc_start: 0.9013 (mmt) cc_final: 0.8797 (mmm) REVERT: B 830 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: B 968 GLN cc_start: 0.8606 (mp10) cc_final: 0.8178 (mp10) REVERT: B 1225 ASP cc_start: 0.7061 (p0) cc_final: 0.6835 (p0) REVERT: B 1250 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7885 (t) REVERT: B 1293 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9278 (mt) REVERT: B 1534 MET cc_start: 0.8057 (mmm) cc_final: 0.7747 (mmm) REVERT: B 1749 MET cc_start: 0.9134 (tpp) cc_final: 0.8870 (tpp) REVERT: B 1845 SER cc_start: 0.8924 (m) cc_final: 0.8604 (p) REVERT: B 2032 MET cc_start: 0.8365 (tpp) cc_final: 0.8117 (tpp) REVERT: B 2182 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 2233 ARG cc_start: 0.7723 (ttt90) cc_final: 0.7522 (tpt-90) REVERT: B 2289 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8462 (t) REVERT: B 2291 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8660 (mtm) REVERT: B 2390 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8424 (t0) REVERT: C 28 MET cc_start: 0.8772 (ptp) cc_final: 0.8559 (ptp) REVERT: C 65 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8743 (mt) REVERT: C 434 MET cc_start: 0.8564 (mpp) cc_final: 0.8267 (mpp) REVERT: C 518 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8932 (t) REVERT: C 522 MET cc_start: 0.9164 (tmm) cc_final: 0.8953 (tmm) REVERT: C 584 MET cc_start: 0.8643 (mmm) cc_final: 0.8155 (mmm) REVERT: C 613 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9055 (tt) REVERT: C 976 GLU cc_start: 0.8622 (tp30) cc_final: 0.8274 (tp30) REVERT: C 1069 TYR cc_start: 0.9037 (t80) cc_final: 0.8681 (t80) REVERT: C 1225 ASP cc_start: 0.7018 (p0) cc_final: 0.6635 (p0) REVERT: C 1314 PHE cc_start: 0.8062 (m-80) cc_final: 0.7505 (m-80) REVERT: C 1323 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7269 (p0) REVERT: C 1334 MET cc_start: 0.8524 (mmm) cc_final: 0.8310 (mmm) REVERT: C 1749 MET cc_start: 0.9158 (tpp) cc_final: 0.8917 (tpp) REVERT: C 1875 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8460 (tpp) REVERT: C 1936 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.8564 (t70) REVERT: C 2030 MET cc_start: 0.9132 (tpp) cc_final: 0.8878 (tpp) REVERT: C 2316 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8762 (t) REVERT: C 2390 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8061 (t0) REVERT: D 28 MET cc_start: 0.8582 (ptp) cc_final: 0.8314 (ptp) REVERT: D 65 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8883 (mt) REVERT: D 104 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9331 (m) REVERT: D 155 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8430 (ttm) REVERT: D 263 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9228 (tpp) REVERT: D 411 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9077 (m) REVERT: D 496 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8345 (p) REVERT: D 669 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9006 (p) REVERT: D 694 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.9006 (mt) REVERT: D 775 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8632 (m) REVERT: D 809 MET cc_start: 0.9151 (mmt) cc_final: 0.8933 (mmm) REVERT: D 899 MET cc_start: 0.8889 (mmm) cc_final: 0.8613 (mmp) REVERT: D 968 GLN cc_start: 0.8778 (mp10) cc_final: 0.8313 (mp10) REVERT: D 1334 MET cc_start: 0.8204 (tpp) cc_final: 0.7711 (tpp) REVERT: D 1534 MET cc_start: 0.7913 (mmm) cc_final: 0.7619 (mmm) REVERT: D 1845 SER cc_start: 0.8610 (m) cc_final: 0.8298 (p) REVERT: D 1865 MET cc_start: 0.8551 (tmm) cc_final: 0.8150 (tmm) REVERT: D 1888 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7913 (mtm-85) REVERT: D 1970 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8455 (ttmm) REVERT: D 2032 MET cc_start: 0.7675 (mmm) cc_final: 0.7394 (tpp) REVERT: D 2109 GLN cc_start: 0.8553 (tp-100) cc_final: 0.7975 (tp40) REVERT: D 2113 ASP cc_start: 0.8074 (m-30) cc_final: 0.6683 (m-30) REVERT: D 2291 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8649 (mtm) REVERT: D 2374 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8601 (mt) REVERT: D 2390 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8192 (t0) REVERT: E 28 MET cc_start: 0.8680 (ptp) cc_final: 0.8394 (ptp) REVERT: E 54 HIS cc_start: 0.8749 (t-90) cc_final: 0.8137 (t70) REVERT: E 65 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8816 (mt) REVERT: E 263 MET cc_start: 0.9500 (tpp) cc_final: 0.8908 (tpp) REVERT: E 487 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7775 (mm-40) REVERT: E 490 MET cc_start: 0.8352 (ptp) cc_final: 0.8147 (ptp) REVERT: E 518 SER cc_start: 0.9401 (OUTLIER) cc_final: 0.9149 (t) REVERT: E 584 MET cc_start: 0.8450 (mmm) cc_final: 0.8187 (mmm) REVERT: E 694 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8796 (mt) REVERT: E 771 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: E 899 MET cc_start: 0.9035 (mmm) cc_final: 0.8697 (mmp) REVERT: E 968 GLN cc_start: 0.8820 (mp10) cc_final: 0.8567 (mp10) REVERT: E 1047 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.6567 (t0) REVERT: E 1225 ASP cc_start: 0.6929 (p0) cc_final: 0.6659 (p0) REVERT: E 1250 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7838 (t) REVERT: E 1257 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9341 (tt) REVERT: E 1334 MET cc_start: 0.8400 (tpp) cc_final: 0.8102 (tpp) REVERT: E 1749 MET cc_start: 0.9456 (tpp) cc_final: 0.9241 (tpt) REVERT: E 1777 MET cc_start: 0.8368 (tpt) cc_final: 0.8086 (tpt) REVERT: E 1838 ARG cc_start: 0.9290 (OUTLIER) cc_final: 0.8222 (ptm-80) REVERT: E 1845 SER cc_start: 0.8884 (m) cc_final: 0.8566 (p) REVERT: E 1934 MET cc_start: 0.9104 (ppp) cc_final: 0.8825 (ppp) REVERT: E 1936 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.8525 (t70) REVERT: E 2032 MET cc_start: 0.8424 (tpp) cc_final: 0.7803 (tpp) REVERT: E 2109 GLN cc_start: 0.8552 (tp40) cc_final: 0.7954 (tp40) REVERT: E 2291 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8638 (mtp) REVERT: E 2374 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8432 (mt) REVERT: E 2390 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8456 (t0) REVERT: E 2503 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8086 (mt0) outliers start: 406 outliers final: 237 residues processed: 900 average time/residue: 0.7891 time to fit residues: 1263.4940 Evaluate side-chains 791 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 506 time to evaluate : 7.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1222 TYR Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1712 VAL Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2291 MET Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2448 THR Chi-restraints excluded: chain A residue 2499 ILE Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1293 LEU Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1630 MET Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1712 VAL Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1818 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2142 THR Chi-restraints excluded: chain B residue 2289 CYS Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2448 THR Chi-restraints excluded: chain B residue 2499 ILE Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 763 ILE Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1222 TYR Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1259 ILE Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1323 ASN Chi-restraints excluded: chain C residue 1690 THR Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1785 ILE Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1875 MET Chi-restraints excluded: chain C residue 1885 SER Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2366 ILE Chi-restraints excluded: chain C residue 2372 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 879 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1053 SER Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2221 GLN Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2291 MET Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2366 ILE Chi-restraints excluded: chain D residue 2372 THR Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2499 ILE Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 771 GLU Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1047 ASN Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1257 LEU Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1658 HIS Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1712 VAL Chi-restraints excluded: chain E residue 1718 ILE Chi-restraints excluded: chain E residue 1785 ILE Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2181 ILE Chi-restraints excluded: chain E residue 2243 LEU Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2374 LEU Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2503 GLN Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 937 optimal weight: 6.9990 chunk 639 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 838 optimal weight: 5.9990 chunk 464 optimal weight: 9.9990 chunk 960 optimal weight: 5.9990 chunk 778 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 575 optimal weight: 7.9990 chunk 1010 optimal weight: 8.9990 chunk 284 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 74 GLN A 171 HIS A 193 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1751 GLN A2221 GLN A2239 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 171 HIS B 193 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 HIS ** B1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1804 GLN B2221 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2503 GLN C 171 HIS C 193 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1751 GLN ** C1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2221 GLN ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2503 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN D 755 GLN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1751 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2503 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 193 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 634 GLN E 755 GLN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 HIS E1050 GLN E1068 ASN ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1634 ASN E1751 GLN ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2503 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 95500 Z= 0.408 Angle : 0.668 10.838 129690 Z= 0.345 Chirality : 0.043 0.165 14565 Planarity : 0.004 0.047 16710 Dihedral : 6.531 75.308 12900 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.68 % Favored : 92.24 % Rotamer: Outliers : 4.85 % Allowed : 16.75 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.10 (0.08), residues: 11655 helix: 1.80 (0.07), residues: 5410 sheet: -1.47 (0.12), residues: 1725 loop : -1.86 (0.09), residues: 4520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D1835 HIS 0.007 0.001 HIS D1862 PHE 0.017 0.001 PHE C1791 TYR 0.019 0.002 TYR B2134 ARG 0.004 0.001 ARG D1888 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 497 poor density : 495 time to evaluate : 8.084 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: A 28 MET cc_start: 0.8671 (ptp) cc_final: 0.8394 (ptp) REVERT: A 65 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8833 (mt) REVERT: A 230 MET cc_start: 0.7950 (mtt) cc_final: 0.7741 (mtt) REVERT: A 263 MET cc_start: 0.9628 (tpp) cc_final: 0.8903 (tpp) REVERT: A 433 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8475 (ttt) REVERT: A 522 MET cc_start: 0.9067 (tmm) cc_final: 0.8748 (tmm) REVERT: A 659 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8883 (ttm) REVERT: A 694 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8956 (mt) REVERT: A 809 MET cc_start: 0.8869 (mmm) cc_final: 0.8212 (mmm) REVERT: A 899 MET cc_start: 0.8908 (mmm) cc_final: 0.8492 (mmp) REVERT: A 1293 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9288 (mm) REVERT: A 1630 MET cc_start: 0.8733 (tpp) cc_final: 0.8214 (tpp) REVERT: A 1684 MET cc_start: 0.8970 (ttm) cc_final: 0.8754 (tpp) REVERT: A 1749 MET cc_start: 0.9332 (tpt) cc_final: 0.9088 (tpp) REVERT: A 1770 MET cc_start: 0.8126 (mmp) cc_final: 0.7770 (mmm) REVERT: A 1845 SER cc_start: 0.8783 (m) cc_final: 0.8549 (p) REVERT: A 1934 MET cc_start: 0.9171 (tmm) cc_final: 0.8846 (tmm) REVERT: A 1936 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.8411 (t70) REVERT: A 2030 MET cc_start: 0.9360 (tpp) cc_final: 0.8601 (ttm) REVERT: A 2032 MET cc_start: 0.8466 (tpp) cc_final: 0.7569 (tpp) REVERT: A 2289 CYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8459 (t) REVERT: A 2291 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8636 (mtm) REVERT: A 2308 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8384 (mp) REVERT: A 2390 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8509 (t0) REVERT: A 2503 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: B 104 VAL cc_start: 0.9561 (OUTLIER) cc_final: 0.9330 (m) REVERT: B 148 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9051 (tt) REVERT: B 263 MET cc_start: 0.9598 (tpp) cc_final: 0.9226 (tpp) REVERT: B 669 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 968 GLN cc_start: 0.8661 (mp10) cc_final: 0.8240 (mp10) REVERT: B 1225 ASP cc_start: 0.7053 (p0) cc_final: 0.6821 (p0) REVERT: B 1250 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7968 (t) REVERT: B 1534 MET cc_start: 0.7950 (mmm) cc_final: 0.7616 (mmm) REVERT: B 1749 MET cc_start: 0.9331 (tpp) cc_final: 0.8992 (tpp) REVERT: B 1845 SER cc_start: 0.8968 (m) cc_final: 0.8641 (p) REVERT: B 1934 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8764 (ppp) REVERT: B 2032 MET cc_start: 0.8503 (tpp) cc_final: 0.8222 (tpp) REVERT: B 2149 MET cc_start: 0.8518 (mmm) cc_final: 0.8225 (mmm) REVERT: B 2182 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 2289 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8365 (t) REVERT: B 2291 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8755 (mtm) REVERT: B 2308 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 2360 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8738 (tt) REVERT: B 2390 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8346 (t0) REVERT: B 2503 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8231 (mt0) REVERT: C 65 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8772 (mt) REVERT: C 434 MET cc_start: 0.8474 (mpp) cc_final: 0.8122 (mpp) REVERT: C 490 MET cc_start: 0.8320 (tpp) cc_final: 0.8040 (tpp) REVERT: C 522 MET cc_start: 0.9152 (tmm) cc_final: 0.8900 (tmm) REVERT: C 584 MET cc_start: 0.8539 (mmm) cc_final: 0.8143 (mmm) REVERT: C 613 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9039 (tt) REVERT: C 707 MET cc_start: 0.8199 (mpp) cc_final: 0.7972 (mpp) REVERT: C 899 MET cc_start: 0.9025 (mmm) cc_final: 0.8678 (mmp) REVERT: C 1225 ASP cc_start: 0.7019 (p0) cc_final: 0.6392 (p0) REVERT: C 1684 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7840 (ttm) REVERT: C 1749 MET cc_start: 0.9263 (tpp) cc_final: 0.9057 (tpp) REVERT: C 1936 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8635 (t70) REVERT: C 2030 MET cc_start: 0.9143 (tpp) cc_final: 0.8854 (tpp) REVERT: C 2032 MET cc_start: 0.8073 (tpp) cc_final: 0.7809 (tpp) REVERT: C 2308 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (mp) REVERT: C 2316 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8890 (t) REVERT: C 2390 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8037 (t0) REVERT: C 2486 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.9010 (t) REVERT: C 2503 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: D 28 MET cc_start: 0.8666 (ptp) cc_final: 0.8418 (ptp) REVERT: D 155 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8453 (ttm) REVERT: D 263 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.9247 (tpp) REVERT: D 490 MET cc_start: 0.8236 (tpp) cc_final: 0.8029 (tpp) REVERT: D 634 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8262 (mp10) REVERT: D 669 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9024 (p) REVERT: D 694 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9060 (mt) REVERT: D 775 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8650 (m) REVERT: D 809 MET cc_start: 0.9144 (mmt) cc_final: 0.8892 (mmm) REVERT: D 899 MET cc_start: 0.8897 (mmm) cc_final: 0.8613 (mmp) REVERT: D 968 GLN cc_start: 0.8831 (mp10) cc_final: 0.8402 (mp10) REVERT: D 1845 SER cc_start: 0.8705 (m) cc_final: 0.8409 (p) REVERT: D 1865 MET cc_start: 0.8633 (tmm) cc_final: 0.8271 (tmm) REVERT: D 2032 MET cc_start: 0.7852 (mmm) cc_final: 0.7589 (tpp) REVERT: D 2109 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8248 (tp40) REVERT: D 2291 MET cc_start: 0.8898 (mtm) cc_final: 0.8678 (mtm) REVERT: D 2308 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8606 (mt) REVERT: D 2341 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8936 (t0) REVERT: D 2374 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8475 (mt) REVERT: D 2390 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8115 (t0) REVERT: D 2503 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: E 28 MET cc_start: 0.8790 (ptp) cc_final: 0.8479 (ptp) REVERT: E 65 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8777 (mp) REVERT: E 263 MET cc_start: 0.9550 (tpp) cc_final: 0.8952 (tpp) REVERT: E 487 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7858 (mm-40) REVERT: E 490 MET cc_start: 0.8477 (ptp) cc_final: 0.8265 (ptp) REVERT: E 518 SER cc_start: 0.9368 (OUTLIER) cc_final: 0.9131 (t) REVERT: E 584 MET cc_start: 0.8404 (mmm) cc_final: 0.8007 (mmm) REVERT: E 694 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8808 (mt) REVERT: E 899 MET cc_start: 0.8999 (mmm) cc_final: 0.8578 (mmp) REVERT: E 968 GLN cc_start: 0.8658 (mp10) cc_final: 0.8369 (mp10) REVERT: E 1225 ASP cc_start: 0.7025 (p0) cc_final: 0.6708 (p0) REVERT: E 1250 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7817 (t) REVERT: E 1334 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8031 (tpp) REVERT: E 1749 MET cc_start: 0.9476 (tpp) cc_final: 0.9070 (tpp) REVERT: E 1838 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8248 (ptm-80) REVERT: E 1845 SER cc_start: 0.8925 (m) cc_final: 0.8636 (p) REVERT: E 1936 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8526 (t70) REVERT: E 2030 MET cc_start: 0.9447 (tpp) cc_final: 0.8645 (ttm) REVERT: E 2032 MET cc_start: 0.8644 (tpp) cc_final: 0.7985 (tpp) REVERT: E 2291 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8587 (mtp) REVERT: E 2390 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8252 (t0) outliers start: 497 outliers final: 300 residues processed: 932 average time/residue: 0.7735 time to fit residues: 1292.4151 Evaluate side-chains 821 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 470 time to evaluate : 8.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1658 HIS Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1712 VAL Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1919 ASN Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2143 SER Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2289 CYS Chi-restraints excluded: chain A residue 2291 MET Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2366 ILE Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2448 THR Chi-restraints excluded: chain A residue 2499 ILE Chi-restraints excluded: chain A residue 2503 GLN Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1658 HIS Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1718 ILE Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1818 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1934 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2142 THR Chi-restraints excluded: chain B residue 2143 SER Chi-restraints excluded: chain B residue 2145 THR Chi-restraints excluded: chain B residue 2289 CYS Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2360 LEU Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2448 THR Chi-restraints excluded: chain B residue 2499 ILE Chi-restraints excluded: chain B residue 2503 GLN Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1259 ILE Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1301 THR Chi-restraints excluded: chain C residue 1658 HIS Chi-restraints excluded: chain C residue 1684 MET Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1785 ILE Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1885 SER Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1953 THR Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1993 ASP Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2143 SER Chi-restraints excluded: chain C residue 2237 VAL Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2289 CYS Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2366 ILE Chi-restraints excluded: chain C residue 2372 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2499 ILE Chi-restraints excluded: chain C residue 2503 GLN Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 634 GLN Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 879 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1919 ASN Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2143 SER Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2181 ILE Chi-restraints excluded: chain D residue 2190 ILE Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2341 ASP Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2499 ILE Chi-restraints excluded: chain D residue 2503 GLN Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1301 THR Chi-restraints excluded: chain E residue 1334 MET Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1658 HIS Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1712 VAL Chi-restraints excluded: chain E residue 1718 ILE Chi-restraints excluded: chain E residue 1729 TYR Chi-restraints excluded: chain E residue 1785 ILE Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1934 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2059 ILE Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2143 SER Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2181 ILE Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2366 ILE Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 378 optimal weight: 0.6980 chunk 1014 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 661 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 1127 optimal weight: 2.9990 chunk 935 optimal weight: 4.9990 chunk 521 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 591 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 GLN A1502 ASN A2221 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1502 ASN B1804 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2468 GLN B2503 GLN C 171 HIS ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1800 GLN C1804 GLN C2221 GLN ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2503 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1502 ASN ** D1634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2221 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2503 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1050 GLN ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 95500 Z= 0.197 Angle : 0.556 12.410 129690 Z= 0.287 Chirality : 0.041 0.164 14565 Planarity : 0.003 0.049 16710 Dihedral : 6.150 72.580 12884 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.59 % Allowed : 18.20 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.13 (0.08), residues: 11655 helix: 1.99 (0.07), residues: 5460 sheet: -1.32 (0.12), residues: 1700 loop : -1.79 (0.10), residues: 4495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1846 HIS 0.004 0.001 HIS C2516 PHE 0.010 0.001 PHE E1872 TYR 0.013 0.001 TYR C1230 ARG 0.006 0.000 ARG D1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 515 time to evaluate : 8.092 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: A 28 MET cc_start: 0.8593 (ptp) cc_final: 0.8370 (ptp) REVERT: A 65 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8826 (mt) REVERT: A 230 MET cc_start: 0.7936 (mtt) cc_final: 0.7716 (mtt) REVERT: A 263 MET cc_start: 0.9594 (tpp) cc_final: 0.8878 (tpp) REVERT: A 433 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8217 (ttt) REVERT: A 659 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8819 (ttm) REVERT: A 694 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8923 (mt) REVERT: A 899 MET cc_start: 0.8952 (mmm) cc_final: 0.8548 (mmp) REVERT: A 1250 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 1630 MET cc_start: 0.8713 (tpp) cc_final: 0.8304 (tpp) REVERT: A 1684 MET cc_start: 0.8995 (ttm) cc_final: 0.8704 (tpp) REVERT: A 1749 MET cc_start: 0.9285 (tpt) cc_final: 0.9027 (tpp) REVERT: A 1770 MET cc_start: 0.8126 (mmp) cc_final: 0.7919 (mmm) REVERT: A 1845 SER cc_start: 0.8718 (m) cc_final: 0.8441 (p) REVERT: A 1934 MET cc_start: 0.9130 (tmm) cc_final: 0.8806 (tmm) REVERT: A 1936 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8389 (t70) REVERT: A 2032 MET cc_start: 0.8558 (tpp) cc_final: 0.7671 (tpp) REVERT: A 2086 MET cc_start: 0.8471 (mmm) cc_final: 0.8195 (mmm) REVERT: A 2291 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8618 (mtm) REVERT: A 2390 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8553 (t0) REVERT: A 2503 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8510 (mt0) REVERT: B 148 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9085 (tt) REVERT: B 263 MET cc_start: 0.9540 (tpp) cc_final: 0.9178 (tpp) REVERT: B 669 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.8926 (p) REVERT: B 968 GLN cc_start: 0.8664 (mp10) cc_final: 0.8262 (mp10) REVERT: B 1225 ASP cc_start: 0.6958 (p0) cc_final: 0.6728 (p0) REVERT: B 1250 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8084 (t) REVERT: B 1534 MET cc_start: 0.8088 (mmm) cc_final: 0.7730 (mmm) REVERT: B 1749 MET cc_start: 0.9288 (tpp) cc_final: 0.8934 (tpp) REVERT: B 1845 SER cc_start: 0.8873 (m) cc_final: 0.8543 (p) REVERT: B 2032 MET cc_start: 0.8540 (tpp) cc_final: 0.8305 (tpp) REVERT: B 2149 MET cc_start: 0.8559 (mmm) cc_final: 0.8319 (mmm) REVERT: B 2182 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 2289 CYS cc_start: 0.8972 (m) cc_final: 0.8475 (t) REVERT: B 2291 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8637 (mtm) REVERT: B 2360 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8745 (tt) REVERT: B 2390 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8400 (t0) REVERT: B 2503 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: C 65 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 411 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9107 (m) REVERT: C 434 MET cc_start: 0.8479 (mpp) cc_final: 0.8123 (mpp) REVERT: C 490 MET cc_start: 0.8271 (tpp) cc_final: 0.7998 (tpp) REVERT: C 522 MET cc_start: 0.9136 (tmm) cc_final: 0.8861 (tmm) REVERT: C 584 MET cc_start: 0.8517 (mmm) cc_final: 0.8243 (mmm) REVERT: C 613 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9024 (tt) REVERT: C 899 MET cc_start: 0.8990 (mmm) cc_final: 0.8646 (mmp) REVERT: C 976 GLU cc_start: 0.8627 (tp30) cc_final: 0.8404 (tp30) REVERT: C 1225 ASP cc_start: 0.6856 (p0) cc_final: 0.6272 (p0) REVERT: C 1314 PHE cc_start: 0.7988 (m-80) cc_final: 0.7408 (m-80) REVERT: C 1684 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7881 (ttm) REVERT: C 1712 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9095 (p) REVERT: C 1749 MET cc_start: 0.9338 (tpp) cc_final: 0.9118 (tpp) REVERT: C 1936 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8675 (t70) REVERT: C 2030 MET cc_start: 0.9178 (tpp) cc_final: 0.8916 (tpp) REVERT: C 2131 MET cc_start: 0.8452 (mmt) cc_final: 0.8214 (mmt) REVERT: C 2183 ILE cc_start: 0.9399 (pt) cc_final: 0.9168 (pt) REVERT: C 2270 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9134 (mp) REVERT: C 2308 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8797 (mp) REVERT: C 2316 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8803 (t) REVERT: C 2390 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8220 (t0) REVERT: C 2486 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8909 (t) REVERT: C 2503 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: D 28 MET cc_start: 0.8608 (ptp) cc_final: 0.8336 (ptp) REVERT: D 65 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8804 (mt) REVERT: D 148 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9180 (tt) REVERT: D 490 MET cc_start: 0.8138 (tpp) cc_final: 0.7920 (tpp) REVERT: D 669 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8985 (p) REVERT: D 694 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9037 (mt) REVERT: D 775 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8654 (m) REVERT: D 809 MET cc_start: 0.9134 (mmt) cc_final: 0.8930 (mmm) REVERT: D 899 MET cc_start: 0.8900 (mmm) cc_final: 0.8619 (mmp) REVERT: D 968 GLN cc_start: 0.8752 (mp10) cc_final: 0.8318 (mp10) REVERT: D 1334 MET cc_start: 0.8213 (tpp) cc_final: 0.7721 (tpp) REVERT: D 1534 MET cc_start: 0.8072 (mmm) cc_final: 0.7737 (mmm) REVERT: D 1845 SER cc_start: 0.8412 (m) cc_final: 0.8144 (p) REVERT: D 1865 MET cc_start: 0.8643 (tmm) cc_final: 0.8200 (tmm) REVERT: D 2032 MET cc_start: 0.7916 (mmm) cc_final: 0.7627 (tpp) REVERT: D 2109 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8165 (tp40) REVERT: D 2390 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8138 (t0) REVERT: D 2499 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8543 (mt) REVERT: D 2503 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: E 28 MET cc_start: 0.8695 (ptp) cc_final: 0.8415 (ptp) REVERT: E 65 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8807 (mp) REVERT: E 263 MET cc_start: 0.9515 (tpp) cc_final: 0.8941 (tpp) REVERT: E 487 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7869 (mm-40) REVERT: E 490 MET cc_start: 0.8522 (ptp) cc_final: 0.8218 (ptp) REVERT: E 518 SER cc_start: 0.9469 (OUTLIER) cc_final: 0.9244 (t) REVERT: E 584 MET cc_start: 0.8411 (mmm) cc_final: 0.8002 (mmm) REVERT: E 694 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8804 (mt) REVERT: E 899 MET cc_start: 0.8974 (mmm) cc_final: 0.8555 (mmp) REVERT: E 968 GLN cc_start: 0.8757 (mp10) cc_final: 0.8482 (mp10) REVERT: E 1225 ASP cc_start: 0.6728 (p0) cc_final: 0.6411 (p0) REVERT: E 1250 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.7873 (t) REVERT: E 1334 MET cc_start: 0.8316 (tpp) cc_final: 0.8042 (tpp) REVERT: E 1749 MET cc_start: 0.9451 (tpp) cc_final: 0.9217 (tpt) REVERT: E 1838 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8311 (ptm-80) REVERT: E 1845 SER cc_start: 0.8854 (m) cc_final: 0.8545 (p) REVERT: E 1936 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8516 (t70) REVERT: E 2030 MET cc_start: 0.9373 (tpp) cc_final: 0.8785 (ttm) REVERT: E 2182 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7901 (tm-30) REVERT: E 2291 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8536 (mtp) REVERT: E 2390 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8366 (t0) outliers start: 368 outliers final: 252 residues processed: 832 average time/residue: 0.7892 time to fit residues: 1176.8158 Evaluate side-chains 789 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 493 time to evaluate : 8.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1222 TYR Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1712 VAL Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1844 THR Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2291 MET Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2503 GLN Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1630 MET Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1718 ILE Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1934 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2142 THR Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2333 MET Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2360 LEU Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2499 ILE Chi-restraints excluded: chain B residue 2503 GLN Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1259 ILE Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1684 MET Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1768 VAL Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1885 SER Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2010 MET Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2145 THR Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2366 ILE Chi-restraints excluded: chain C residue 2372 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2503 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 701 ILE Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1053 SER Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1919 ASN Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2221 GLN Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2366 ILE Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2499 ILE Chi-restraints excluded: chain D residue 2503 GLN Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1045 MET Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1092 ASN Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1301 THR Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1712 VAL Chi-restraints excluded: chain E residue 1729 TYR Chi-restraints excluded: chain E residue 1785 ILE Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1934 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2243 LEU Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2366 ILE Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 1086 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 642 optimal weight: 3.9990 chunk 823 optimal weight: 7.9990 chunk 637 optimal weight: 4.9990 chunk 948 optimal weight: 1.9990 chunk 629 optimal weight: 5.9990 chunk 1122 optimal weight: 0.9990 chunk 702 optimal weight: 10.0000 chunk 684 optimal weight: 2.9990 chunk 518 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1050 GLN A1051 GLN A1068 ASN A1502 ASN A2221 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1502 ASN B1804 GLN B2221 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2503 GLN C 171 HIS ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2329 ASN ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2461 HIS C2503 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 171 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN D 785 GLN D1502 ASN ** D1634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2221 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2503 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 634 GLN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1041 GLN E1050 GLN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 95500 Z= 0.225 Angle : 0.566 10.914 129690 Z= 0.291 Chirality : 0.041 0.164 14565 Planarity : 0.003 0.049 16710 Dihedral : 6.052 69.049 12880 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.78 % Allowed : 18.32 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.21 (0.08), residues: 11655 helix: 2.05 (0.07), residues: 5460 sheet: -1.26 (0.12), residues: 1725 loop : -1.76 (0.10), residues: 4470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E1846 HIS 0.007 0.001 HIS E1522 PHE 0.011 0.001 PHE C1872 TYR 0.012 0.001 TYR C 939 ARG 0.005 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 509 time to evaluate : 8.207 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: A 28 MET cc_start: 0.8591 (ptp) cc_final: 0.8340 (ptp) REVERT: A 65 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8863 (mt) REVERT: A 230 MET cc_start: 0.7953 (mtt) cc_final: 0.7707 (mtt) REVERT: A 263 MET cc_start: 0.9606 (tpp) cc_final: 0.8869 (tpp) REVERT: A 659 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8824 (ttm) REVERT: A 694 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8939 (mt) REVERT: A 809 MET cc_start: 0.8781 (mmm) cc_final: 0.8160 (mmm) REVERT: A 899 MET cc_start: 0.8956 (mmm) cc_final: 0.8550 (mmp) REVERT: A 1250 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8124 (t) REVERT: A 1293 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9262 (mt) REVERT: A 1630 MET cc_start: 0.8665 (tpp) cc_final: 0.8256 (tpp) REVERT: A 1684 MET cc_start: 0.8992 (ttm) cc_final: 0.8698 (tpp) REVERT: A 1749 MET cc_start: 0.9293 (tpt) cc_final: 0.9032 (tpp) REVERT: A 1770 MET cc_start: 0.8150 (mmp) cc_final: 0.7924 (mmm) REVERT: A 1845 SER cc_start: 0.8730 (m) cc_final: 0.8462 (p) REVERT: A 1934 MET cc_start: 0.9133 (tmm) cc_final: 0.8801 (tmm) REVERT: A 1936 HIS cc_start: 0.8861 (OUTLIER) cc_final: 0.8407 (t70) REVERT: A 2032 MET cc_start: 0.8638 (tpp) cc_final: 0.7753 (tpp) REVERT: A 2086 MET cc_start: 0.8494 (mmm) cc_final: 0.8193 (mmm) REVERT: A 2106 HIS cc_start: 0.7971 (m170) cc_final: 0.7472 (m90) REVERT: A 2216 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 2289 CYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8615 (t) REVERT: A 2291 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8626 (mtm) REVERT: A 2308 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 2390 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8619 (t0) REVERT: A 2503 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: B 148 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9077 (tt) REVERT: B 263 MET cc_start: 0.9568 (tpp) cc_final: 0.9167 (tpp) REVERT: B 669 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.8904 (p) REVERT: B 968 GLN cc_start: 0.8645 (mp10) cc_final: 0.8249 (mp10) REVERT: B 1225 ASP cc_start: 0.6994 (p0) cc_final: 0.6742 (p0) REVERT: B 1250 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8032 (t) REVERT: B 1534 MET cc_start: 0.8070 (mmm) cc_final: 0.7703 (mmm) REVERT: B 1749 MET cc_start: 0.9332 (tpp) cc_final: 0.8995 (tpp) REVERT: B 1845 SER cc_start: 0.8810 (m) cc_final: 0.8485 (p) REVERT: B 2032 MET cc_start: 0.8622 (tpp) cc_final: 0.8287 (tpp) REVERT: B 2149 MET cc_start: 0.8566 (mmm) cc_final: 0.8286 (mmm) REVERT: B 2182 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 2289 CYS cc_start: 0.8981 (m) cc_final: 0.8527 (t) REVERT: B 2291 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8742 (mtm) REVERT: B 2308 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 2360 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8769 (tt) REVERT: B 2390 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8420 (t0) REVERT: B 2503 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: C 65 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8760 (mt) REVERT: C 411 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9121 (m) REVERT: C 434 MET cc_start: 0.8491 (mpp) cc_final: 0.8137 (mpp) REVERT: C 490 MET cc_start: 0.8218 (tpp) cc_final: 0.7923 (tpp) REVERT: C 522 MET cc_start: 0.9138 (tmm) cc_final: 0.8774 (tmm) REVERT: C 613 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9013 (tt) REVERT: C 707 MET cc_start: 0.8031 (mpp) cc_final: 0.7787 (mpp) REVERT: C 899 MET cc_start: 0.8978 (mmm) cc_final: 0.8623 (mmp) REVERT: C 976 GLU cc_start: 0.8592 (tp30) cc_final: 0.8369 (tp30) REVERT: C 1225 ASP cc_start: 0.6945 (p0) cc_final: 0.6310 (p0) REVERT: C 1314 PHE cc_start: 0.7986 (m-80) cc_final: 0.7428 (m-80) REVERT: C 1334 MET cc_start: 0.7986 (mmm) cc_final: 0.7785 (mmm) REVERT: C 1684 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7928 (ttm) REVERT: C 1712 VAL cc_start: 0.9455 (OUTLIER) cc_final: 0.9097 (p) REVERT: C 1749 MET cc_start: 0.9464 (tpp) cc_final: 0.9246 (tpp) REVERT: C 1770 MET cc_start: 0.7353 (mpp) cc_final: 0.7046 (mpp) REVERT: C 1936 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8673 (t70) REVERT: C 2030 MET cc_start: 0.9097 (tpp) cc_final: 0.8877 (tpp) REVERT: C 2131 MET cc_start: 0.8501 (mmt) cc_final: 0.8283 (mmt) REVERT: C 2183 ILE cc_start: 0.9381 (pt) cc_final: 0.9162 (pt) REVERT: C 2268 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8234 (t0) REVERT: C 2270 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9103 (mp) REVERT: C 2316 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8809 (t) REVERT: C 2390 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8289 (t0) REVERT: C 2486 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8936 (t) REVERT: C 2503 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: D 28 MET cc_start: 0.8580 (ptp) cc_final: 0.8317 (ptp) REVERT: D 65 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 263 MET cc_start: 0.9438 (tpp) cc_final: 0.9040 (tpp) REVERT: D 411 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9173 (m) REVERT: D 669 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8976 (p) REVERT: D 694 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8968 (mt) REVERT: D 775 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8662 (m) REVERT: D 899 MET cc_start: 0.8910 (mmm) cc_final: 0.8629 (mmp) REVERT: D 968 GLN cc_start: 0.8737 (mp10) cc_final: 0.8306 (mp10) REVERT: D 1045 MET cc_start: 0.8831 (mmm) cc_final: 0.8540 (mmm) REVERT: D 1334 MET cc_start: 0.8170 (tpp) cc_final: 0.7734 (tpp) REVERT: D 1534 MET cc_start: 0.8079 (mmm) cc_final: 0.7736 (mmm) REVERT: D 1845 SER cc_start: 0.8392 (m) cc_final: 0.8117 (p) REVERT: D 1865 MET cc_start: 0.8666 (tmm) cc_final: 0.8208 (tmm) REVERT: D 2032 MET cc_start: 0.7946 (mmm) cc_final: 0.7666 (tpp) REVERT: D 2071 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8946 (tt) REVERT: D 2109 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8179 (tp40) REVERT: D 2308 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (mt) REVERT: D 2390 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8119 (t0) REVERT: D 2503 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: E 28 MET cc_start: 0.8740 (ptp) cc_final: 0.8431 (ptp) REVERT: E 230 MET cc_start: 0.8130 (mpp) cc_final: 0.7880 (mpp) REVERT: E 263 MET cc_start: 0.9525 (tpp) cc_final: 0.8924 (tpp) REVERT: E 518 SER cc_start: 0.9472 (OUTLIER) cc_final: 0.9242 (t) REVERT: E 584 MET cc_start: 0.8395 (mmm) cc_final: 0.7982 (mmm) REVERT: E 694 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8855 (mt) REVERT: E 899 MET cc_start: 0.8977 (mmm) cc_final: 0.8557 (mmp) REVERT: E 968 GLN cc_start: 0.8756 (mp10) cc_final: 0.8491 (mp10) REVERT: E 1225 ASP cc_start: 0.6791 (p0) cc_final: 0.6465 (p0) REVERT: E 1250 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7870 (t) REVERT: E 1334 MET cc_start: 0.8280 (tpp) cc_final: 0.8053 (tpp) REVERT: E 1749 MET cc_start: 0.9440 (tpp) cc_final: 0.9213 (tpt) REVERT: E 1838 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8304 (ptm-80) REVERT: E 1845 SER cc_start: 0.8870 (m) cc_final: 0.8563 (p) REVERT: E 1936 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8492 (t70) REVERT: E 2182 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7883 (tm-30) REVERT: E 2291 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: E 2390 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8282 (t0) REVERT: E 2492 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8784 (mt) outliers start: 387 outliers final: 278 residues processed: 838 average time/residue: 0.7822 time to fit residues: 1175.5242 Evaluate side-chains 819 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 493 time to evaluate : 7.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1222 TYR Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1596 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1785 ILE Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1919 ASN Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2289 CYS Chi-restraints excluded: chain A residue 2291 MET Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2366 ILE Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2503 GLN Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1222 TYR Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1301 THR Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1718 ILE Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1934 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2143 SER Chi-restraints excluded: chain B residue 2145 THR Chi-restraints excluded: chain B residue 2234 GLU Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2333 MET Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2360 LEU Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2499 ILE Chi-restraints excluded: chain B residue 2503 GLN Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 428 ASN Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1059 ILE Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1222 TYR Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1684 MET Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1768 VAL Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1885 SER Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2010 MET Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2142 THR Chi-restraints excluded: chain C residue 2145 THR Chi-restraints excluded: chain C residue 2268 ASN Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2289 CYS Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2372 THR Chi-restraints excluded: chain C residue 2390 ASN Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2503 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 694 ILE Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1064 ASP Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1222 TYR Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1919 ASN Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2071 ILE Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2143 SER Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2181 ILE Chi-restraints excluded: chain D residue 2221 GLN Chi-restraints excluded: chain D residue 2270 LEU Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2503 GLN Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 407 THR Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1045 MET Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1092 ASN Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1256 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1301 THR Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1718 ILE Chi-restraints excluded: chain E residue 1729 TYR Chi-restraints excluded: chain E residue 1768 VAL Chi-restraints excluded: chain E residue 1785 ILE Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1818 ILE Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1900 MET Chi-restraints excluded: chain E residue 1934 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2243 LEU Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2366 ILE Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2492 LEU Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 694 optimal weight: 0.5980 chunk 448 optimal weight: 9.9990 chunk 670 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 713 optimal weight: 0.9990 chunk 765 optimal weight: 5.9990 chunk 555 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 882 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2221 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B1804 GLN B2221 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2503 GLN C 171 HIS ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 HIS ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN C2329 ASN ** C2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2503 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2221 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2503 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 634 GLN E 785 GLN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 95500 Z= 0.170 Angle : 0.549 13.715 129690 Z= 0.280 Chirality : 0.040 0.175 14565 Planarity : 0.003 0.049 16710 Dihedral : 5.850 65.337 12876 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.33 % Allowed : 19.20 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.34 (0.08), residues: 11655 helix: 2.12 (0.07), residues: 5460 sheet: -1.09 (0.13), residues: 1695 loop : -1.70 (0.10), residues: 4500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E1846 HIS 0.007 0.001 HIS E1522 PHE 0.009 0.001 PHE E2469 TYR 0.018 0.001 TYR B1714 ARG 0.005 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 523 time to evaluate : 8.279 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: A 28 MET cc_start: 0.8591 (ptp) cc_final: 0.8358 (ptp) REVERT: A 65 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8858 (mt) REVERT: A 263 MET cc_start: 0.9597 (tpp) cc_final: 0.8852 (tpp) REVERT: A 659 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8762 (ttm) REVERT: A 694 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8936 (mt) REVERT: A 809 MET cc_start: 0.8767 (mmm) cc_final: 0.8135 (mmm) REVERT: A 899 MET cc_start: 0.8950 (mmm) cc_final: 0.8553 (mmp) REVERT: A 1250 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8127 (t) REVERT: A 1293 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9263 (mt) REVERT: A 1630 MET cc_start: 0.8601 (tpp) cc_final: 0.8209 (tpp) REVERT: A 1684 MET cc_start: 0.8991 (ttm) cc_final: 0.8681 (tpp) REVERT: A 1749 MET cc_start: 0.9299 (tpt) cc_final: 0.9051 (tpp) REVERT: A 1845 SER cc_start: 0.8686 (m) cc_final: 0.8423 (p) REVERT: A 1934 MET cc_start: 0.9113 (tmm) cc_final: 0.8785 (tmm) REVERT: A 1936 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.8338 (t70) REVERT: A 1984 TYR cc_start: 0.8530 (t80) cc_final: 0.8032 (t80) REVERT: A 2030 MET cc_start: 0.9049 (tpp) cc_final: 0.8815 (ttm) REVERT: A 2032 MET cc_start: 0.8588 (tpp) cc_final: 0.7720 (tpp) REVERT: A 2086 MET cc_start: 0.8504 (mmm) cc_final: 0.8178 (mmm) REVERT: A 2106 HIS cc_start: 0.7879 (m170) cc_final: 0.7386 (m90) REVERT: A 2216 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 2289 CYS cc_start: 0.9093 (m) cc_final: 0.8611 (t) REVERT: A 2308 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 2390 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8722 (t0) REVERT: B 263 MET cc_start: 0.9568 (tpp) cc_final: 0.9186 (tpp) REVERT: B 669 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.8862 (p) REVERT: B 968 GLN cc_start: 0.8588 (mp10) cc_final: 0.8327 (mp10) REVERT: B 1225 ASP cc_start: 0.6986 (p0) cc_final: 0.6629 (p0) REVERT: B 1250 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8035 (t) REVERT: B 1534 MET cc_start: 0.8119 (mmm) cc_final: 0.7734 (mmm) REVERT: B 1749 MET cc_start: 0.9362 (tpp) cc_final: 0.9036 (tpp) REVERT: B 1845 SER cc_start: 0.8714 (m) cc_final: 0.8364 (p) REVERT: B 2149 MET cc_start: 0.8531 (mmm) cc_final: 0.8264 (mmm) REVERT: B 2182 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 2289 CYS cc_start: 0.8934 (m) cc_final: 0.8588 (t) REVERT: B 2291 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8630 (mtm) REVERT: B 2308 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8170 (mp) REVERT: B 2360 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8777 (tt) REVERT: B 2390 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8448 (t0) REVERT: B 2503 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: C 65 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8728 (mt) REVERT: C 434 MET cc_start: 0.8493 (mpp) cc_final: 0.8145 (mpp) REVERT: C 490 MET cc_start: 0.8192 (tpp) cc_final: 0.7918 (tpp) REVERT: C 522 MET cc_start: 0.9134 (tmm) cc_final: 0.8837 (tmm) REVERT: C 613 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9038 (tt) REVERT: C 734 MET cc_start: 0.8765 (mmm) cc_final: 0.8434 (mmm) REVERT: C 809 MET cc_start: 0.8867 (mmm) cc_final: 0.8614 (mmm) REVERT: C 899 MET cc_start: 0.8965 (mmm) cc_final: 0.8614 (mmp) REVERT: C 976 GLU cc_start: 0.8496 (tp30) cc_final: 0.8285 (tp30) REVERT: C 1225 ASP cc_start: 0.6845 (p0) cc_final: 0.6230 (p0) REVERT: C 1334 MET cc_start: 0.7995 (mmm) cc_final: 0.7775 (mmm) REVERT: C 1612 PHE cc_start: 0.9343 (t80) cc_final: 0.8987 (t80) REVERT: C 1684 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7855 (ttm) REVERT: C 1749 MET cc_start: 0.9459 (tpp) cc_final: 0.9242 (tpp) REVERT: C 1770 MET cc_start: 0.7273 (mpp) cc_final: 0.6770 (mpp) REVERT: C 1936 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8653 (t70) REVERT: C 2030 MET cc_start: 0.9181 (tpp) cc_final: 0.8955 (tpp) REVERT: C 2270 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9156 (mp) REVERT: C 2316 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8730 (t) REVERT: C 2486 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8911 (t) REVERT: C 2503 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8648 (mt0) REVERT: D 28 MET cc_start: 0.8552 (ptp) cc_final: 0.8304 (ptp) REVERT: D 65 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8717 (mt) REVERT: D 263 MET cc_start: 0.9504 (tpp) cc_final: 0.9052 (tpp) REVERT: D 669 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8950 (p) REVERT: D 775 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8662 (m) REVERT: D 899 MET cc_start: 0.8898 (mmm) cc_final: 0.8615 (mmp) REVERT: D 968 GLN cc_start: 0.8700 (mp10) cc_final: 0.8387 (mp10) REVERT: D 1045 MET cc_start: 0.8786 (mmm) cc_final: 0.8421 (mmm) REVERT: D 1053 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8215 (p) REVERT: D 1534 MET cc_start: 0.8012 (mmm) cc_final: 0.7641 (mmm) REVERT: D 1845 SER cc_start: 0.8376 (m) cc_final: 0.8118 (p) REVERT: D 1865 MET cc_start: 0.8637 (tmm) cc_final: 0.8179 (tmm) REVERT: D 2030 MET cc_start: 0.8871 (tpp) cc_final: 0.8667 (tpp) REVERT: D 2032 MET cc_start: 0.7934 (mmm) cc_final: 0.7658 (tpp) REVERT: D 2106 HIS cc_start: 0.7956 (m170) cc_final: 0.7745 (m170) REVERT: D 2308 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8432 (mt) REVERT: D 2390 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8292 (t0) REVERT: D 2503 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8355 (mt0) REVERT: E 28 MET cc_start: 0.8740 (ptp) cc_final: 0.8389 (ptp) REVERT: E 263 MET cc_start: 0.9511 (tpp) cc_final: 0.8905 (tpp) REVERT: E 518 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.9241 (t) REVERT: E 584 MET cc_start: 0.8327 (mmm) cc_final: 0.7950 (mmm) REVERT: E 694 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8893 (mt) REVERT: E 899 MET cc_start: 0.8957 (mmm) cc_final: 0.8534 (mmp) REVERT: E 968 GLN cc_start: 0.8750 (mp10) cc_final: 0.8515 (mp10) REVERT: E 1225 ASP cc_start: 0.6758 (p0) cc_final: 0.6445 (p0) REVERT: E 1250 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7924 (t) REVERT: E 1838 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8348 (ptm-80) REVERT: E 1845 SER cc_start: 0.8869 (m) cc_final: 0.8517 (p) REVERT: E 1936 HIS cc_start: 0.8889 (OUTLIER) cc_final: 0.8496 (t70) REVERT: E 2109 GLN cc_start: 0.8275 (tp40) cc_final: 0.7451 (tp-100) REVERT: E 2182 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7826 (tm-30) REVERT: E 2291 MET cc_start: 0.8864 (mtm) cc_final: 0.8565 (mtp) REVERT: E 2390 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8334 (t0) REVERT: E 2492 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8821 (mt) outliers start: 341 outliers final: 259 residues processed: 810 average time/residue: 0.8168 time to fit residues: 1187.6528 Evaluate side-chains 799 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 503 time to evaluate : 8.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1222 TYR Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1277 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2143 SER Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2366 ILE Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 691 ASP Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1076 VAL Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1222 TYR Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1630 MET Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1934 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2142 THR Chi-restraints excluded: chain B residue 2143 SER Chi-restraints excluded: chain B residue 2145 THR Chi-restraints excluded: chain B residue 2234 GLU Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2360 LEU Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2499 ILE Chi-restraints excluded: chain B residue 2503 GLN Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1222 TYR Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1301 THR Chi-restraints excluded: chain C residue 1684 MET Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1768 VAL Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1885 SER Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2142 THR Chi-restraints excluded: chain C residue 2145 THR Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2503 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1053 SER Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1222 TYR Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1277 ASP Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1622 ILE Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1919 ASN Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2143 SER Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2181 ILE Chi-restraints excluded: chain D residue 2221 GLN Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2503 GLN Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 532 GLN Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1045 MET Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1092 ASN Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1256 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1718 ILE Chi-restraints excluded: chain E residue 1729 TYR Chi-restraints excluded: chain E residue 1768 VAL Chi-restraints excluded: chain E residue 1803 LEU Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1934 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2243 LEU Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2366 ILE Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2492 LEU Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 1021 optimal weight: 1.9990 chunk 1075 optimal weight: 10.0000 chunk 981 optimal weight: 7.9990 chunk 1046 optimal weight: 10.0000 chunk 629 optimal weight: 0.4980 chunk 455 optimal weight: 2.9990 chunk 821 optimal weight: 0.9980 chunk 321 optimal weight: 2.9990 chunk 945 optimal weight: 9.9990 chunk 989 optimal weight: 0.9990 chunk 1042 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2221 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2503 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1575 HIS C1995 GLN C2239 GLN C2503 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1050 GLN D2221 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2503 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 311 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 95500 Z= 0.181 Angle : 0.551 12.990 129690 Z= 0.281 Chirality : 0.040 0.175 14565 Planarity : 0.003 0.048 16710 Dihedral : 5.685 61.028 12861 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.29 % Allowed : 19.22 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: 0.39 (0.08), residues: 11655 helix: 2.16 (0.07), residues: 5470 sheet: -1.03 (0.13), residues: 1700 loop : -1.68 (0.10), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C1846 HIS 0.006 0.001 HIS E1522 PHE 0.009 0.001 PHE D 733 TYR 0.024 0.001 TYR C1984 ARG 0.005 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 511 time to evaluate : 8.274 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: A 28 MET cc_start: 0.8614 (ptp) cc_final: 0.8376 (ptp) REVERT: A 230 MET cc_start: 0.7946 (mtt) cc_final: 0.7713 (mtt) REVERT: A 263 MET cc_start: 0.9602 (tpp) cc_final: 0.8848 (tpp) REVERT: A 659 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8795 (ttm) REVERT: A 694 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8943 (mt) REVERT: A 809 MET cc_start: 0.8766 (mmm) cc_final: 0.8138 (mmm) REVERT: A 899 MET cc_start: 0.8930 (mmm) cc_final: 0.8523 (mmp) REVERT: A 1249 MET cc_start: 0.7417 (ttm) cc_final: 0.7158 (ttp) REVERT: A 1250 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8119 (t) REVERT: A 1293 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9256 (mt) REVERT: A 1630 MET cc_start: 0.8581 (tpp) cc_final: 0.8199 (tpp) REVERT: A 1684 MET cc_start: 0.9016 (ttm) cc_final: 0.8748 (tpp) REVERT: A 1749 MET cc_start: 0.9275 (tpt) cc_final: 0.9059 (tpp) REVERT: A 1845 SER cc_start: 0.8726 (m) cc_final: 0.8423 (p) REVERT: A 1934 MET cc_start: 0.9109 (tmm) cc_final: 0.8791 (tmm) REVERT: A 1936 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8373 (t70) REVERT: A 1984 TYR cc_start: 0.8545 (t80) cc_final: 0.8046 (t80) REVERT: A 2030 MET cc_start: 0.9073 (tpp) cc_final: 0.8800 (ttm) REVERT: A 2032 MET cc_start: 0.8567 (tpp) cc_final: 0.7661 (tpp) REVERT: A 2086 MET cc_start: 0.8497 (mmm) cc_final: 0.8154 (mmm) REVERT: A 2106 HIS cc_start: 0.7873 (m170) cc_final: 0.7356 (m90) REVERT: A 2390 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8760 (t0) REVERT: B 263 MET cc_start: 0.9569 (tpp) cc_final: 0.9197 (tpp) REVERT: B 613 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 669 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8839 (p) REVERT: B 809 MET cc_start: 0.8972 (mmm) cc_final: 0.8690 (mmm) REVERT: B 968 GLN cc_start: 0.8606 (mp10) cc_final: 0.8331 (mp10) REVERT: B 1225 ASP cc_start: 0.6954 (p0) cc_final: 0.6588 (p0) REVERT: B 1250 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8023 (t) REVERT: B 1534 MET cc_start: 0.8122 (mmm) cc_final: 0.7739 (mmm) REVERT: B 1749 MET cc_start: 0.9383 (tpp) cc_final: 0.9099 (tpp) REVERT: B 1845 SER cc_start: 0.8712 (m) cc_final: 0.8362 (p) REVERT: B 2032 MET cc_start: 0.8380 (tpp) cc_final: 0.8073 (tpp) REVERT: B 2149 MET cc_start: 0.8569 (mmm) cc_final: 0.8299 (mmm) REVERT: B 2182 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 2289 CYS cc_start: 0.8932 (m) cc_final: 0.8583 (t) REVERT: B 2291 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8621 (mtm) REVERT: B 2308 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 2360 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8785 (tt) REVERT: B 2390 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8452 (t0) REVERT: B 2503 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8481 (mt0) REVERT: C 65 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8732 (mt) REVERT: C 490 MET cc_start: 0.8198 (tpp) cc_final: 0.7889 (tpp) REVERT: C 522 MET cc_start: 0.9134 (tmm) cc_final: 0.8777 (tmm) REVERT: C 613 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9038 (tt) REVERT: C 707 MET cc_start: 0.8073 (mpp) cc_final: 0.7823 (mpp) REVERT: C 734 MET cc_start: 0.8666 (mmm) cc_final: 0.8340 (mmm) REVERT: C 809 MET cc_start: 0.8864 (mmm) cc_final: 0.8649 (mmm) REVERT: C 899 MET cc_start: 0.8961 (mmm) cc_final: 0.8615 (mmp) REVERT: C 976 GLU cc_start: 0.8492 (tp30) cc_final: 0.8221 (tp30) REVERT: C 1225 ASP cc_start: 0.6868 (p0) cc_final: 0.6245 (p0) REVERT: C 1334 MET cc_start: 0.7913 (mmm) cc_final: 0.7664 (mmm) REVERT: C 1612 PHE cc_start: 0.9331 (t80) cc_final: 0.8965 (t80) REVERT: C 1684 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7881 (ttm) REVERT: C 1712 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9190 (p) REVERT: C 1749 MET cc_start: 0.9457 (tpp) cc_final: 0.9254 (tpp) REVERT: C 1936 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (t70) REVERT: C 2270 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9175 (mp) REVERT: C 2316 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8689 (t) REVERT: C 2486 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8922 (t) REVERT: C 2503 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: D 28 MET cc_start: 0.8534 (ptp) cc_final: 0.8274 (ptp) REVERT: D 65 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 148 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9171 (tt) REVERT: D 263 MET cc_start: 0.9517 (tpp) cc_final: 0.9003 (tpp) REVERT: D 669 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8923 (p) REVERT: D 775 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8665 (m) REVERT: D 899 MET cc_start: 0.8901 (mmm) cc_final: 0.8616 (mmp) REVERT: D 968 GLN cc_start: 0.8704 (mp10) cc_final: 0.8392 (mp10) REVERT: D 1045 MET cc_start: 0.8729 (mmm) cc_final: 0.8389 (mmm) REVERT: D 1534 MET cc_start: 0.7974 (mmm) cc_final: 0.7677 (mmm) REVERT: D 1845 SER cc_start: 0.8357 (m) cc_final: 0.8105 (p) REVERT: D 1865 MET cc_start: 0.8649 (tmm) cc_final: 0.8190 (tmm) REVERT: D 2030 MET cc_start: 0.8865 (tpp) cc_final: 0.8649 (tpp) REVERT: D 2032 MET cc_start: 0.7988 (mmm) cc_final: 0.7755 (tpp) REVERT: D 2308 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8428 (mt) REVERT: D 2374 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8539 (mt) REVERT: D 2390 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8318 (t0) REVERT: D 2503 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8406 (mt0) REVERT: E 28 MET cc_start: 0.8719 (ptp) cc_final: 0.8386 (ptp) REVERT: E 65 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8687 (mt) REVERT: E 263 MET cc_start: 0.9521 (tpp) cc_final: 0.8908 (tpp) REVERT: E 433 MET cc_start: 0.8478 (tpt) cc_final: 0.8047 (tpt) REVERT: E 518 SER cc_start: 0.9479 (OUTLIER) cc_final: 0.9238 (t) REVERT: E 584 MET cc_start: 0.8301 (mmm) cc_final: 0.7924 (mmm) REVERT: E 694 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8910 (mt) REVERT: E 899 MET cc_start: 0.8961 (mmm) cc_final: 0.8533 (mmp) REVERT: E 968 GLN cc_start: 0.8752 (mp10) cc_final: 0.8511 (mp10) REVERT: E 1225 ASP cc_start: 0.6706 (p0) cc_final: 0.6324 (p0) REVERT: E 1250 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7921 (t) REVERT: E 1749 MET cc_start: 0.9131 (tpt) cc_final: 0.8914 (tpp) REVERT: E 1838 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8360 (ptm-80) REVERT: E 1845 SER cc_start: 0.8858 (m) cc_final: 0.8510 (p) REVERT: E 1936 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8528 (t70) REVERT: E 2032 MET cc_start: 0.8415 (tpp) cc_final: 0.7982 (tpp) REVERT: E 2109 GLN cc_start: 0.8275 (tp40) cc_final: 0.7456 (tp-100) REVERT: E 2182 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7784 (tm-30) REVERT: E 2291 MET cc_start: 0.8855 (mtm) cc_final: 0.8562 (mtp) REVERT: E 2390 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8299 (t0) REVERT: E 2492 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8840 (mt) outliers start: 337 outliers final: 268 residues processed: 804 average time/residue: 0.8174 time to fit residues: 1175.2989 Evaluate side-chains 802 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 495 time to evaluate : 8.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1222 TYR Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2143 SER Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2366 ILE Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1630 MET Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1718 ILE Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1768 VAL Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1934 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2143 SER Chi-restraints excluded: chain B residue 2145 THR Chi-restraints excluded: chain B residue 2234 GLU Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2360 LEU Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2503 GLN Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1002 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1222 TYR Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1272 THR Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1301 THR Chi-restraints excluded: chain C residue 1613 SER Chi-restraints excluded: chain C residue 1684 MET Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1768 VAL Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1885 SER Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2142 THR Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain C residue 2503 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1053 SER Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1222 TYR Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1919 ASN Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2143 SER Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2181 ILE Chi-restraints excluded: chain D residue 2221 GLN Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2503 GLN Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 446 ASN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 532 GLN Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1045 MET Chi-restraints excluded: chain E residue 1052 LEU Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1092 ASN Chi-restraints excluded: chain E residue 1104 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1181 LEU Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1256 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1718 ILE Chi-restraints excluded: chain E residue 1729 TYR Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1934 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2143 SER Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2243 LEU Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2366 ILE Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2492 LEU Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 687 optimal weight: 0.8980 chunk 1106 optimal weight: 0.0010 chunk 675 optimal weight: 0.7980 chunk 524 optimal weight: 7.9990 chunk 769 optimal weight: 0.9990 chunk 1160 optimal weight: 10.0000 chunk 1068 optimal weight: 7.9990 chunk 924 optimal weight: 2.9990 chunk 95 optimal weight: 0.0060 chunk 713 optimal weight: 0.9990 chunk 566 optimal weight: 1.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2221 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2221 GLN ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 311 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1807 ASN ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.216 95500 Z= 0.184 Angle : 0.611 59.175 129690 Z= 0.322 Chirality : 0.040 0.301 14565 Planarity : 0.004 0.116 16710 Dihedral : 5.655 60.972 12850 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.05 % Allowed : 19.54 % Favored : 77.41 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.20 % 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: 0.41 (0.08), residues: 11655 helix: 2.18 (0.07), residues: 5470 sheet: -1.02 (0.13), residues: 1700 loop : -1.68 (0.10), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1819 HIS 0.015 0.001 HIS D2106 PHE 0.074 0.001 PHE E1556 TYR 0.030 0.001 TYR A1975 ARG 0.008 0.000 ARG B2233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 495 time to evaluate : 9.436 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: A 28 MET cc_start: 0.8610 (ptp) cc_final: 0.8372 (ptp) REVERT: A 230 MET cc_start: 0.7942 (mtt) cc_final: 0.7713 (mtt) REVERT: A 263 MET cc_start: 0.9601 (tpp) cc_final: 0.8842 (tpp) REVERT: A 659 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8791 (ttm) REVERT: A 694 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8941 (mt) REVERT: A 809 MET cc_start: 0.8757 (mmm) cc_final: 0.8136 (mmm) REVERT: A 899 MET cc_start: 0.8929 (mmm) cc_final: 0.8520 (mmp) REVERT: A 1249 MET cc_start: 0.7416 (ttm) cc_final: 0.7151 (ttp) REVERT: A 1250 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8116 (t) REVERT: A 1293 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9255 (mt) REVERT: A 1630 MET cc_start: 0.8580 (tpp) cc_final: 0.8190 (tpp) REVERT: A 1684 MET cc_start: 0.9014 (ttm) cc_final: 0.8746 (tpp) REVERT: A 1749 MET cc_start: 0.9275 (tpt) cc_final: 0.9057 (tpp) REVERT: A 1845 SER cc_start: 0.8712 (m) cc_final: 0.8421 (p) REVERT: A 1934 MET cc_start: 0.9109 (tmm) cc_final: 0.8790 (tmm) REVERT: A 1936 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8365 (t70) REVERT: A 1984 TYR cc_start: 0.8543 (t80) cc_final: 0.8041 (t80) REVERT: A 2030 MET cc_start: 0.9064 (tpp) cc_final: 0.8795 (ttm) REVERT: A 2032 MET cc_start: 0.8570 (tpp) cc_final: 0.7659 (tpp) REVERT: A 2086 MET cc_start: 0.8494 (mmm) cc_final: 0.8145 (mmm) REVERT: A 2106 HIS cc_start: 0.7853 (m170) cc_final: 0.7346 (m90) REVERT: A 2390 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8756 (t0) REVERT: B 263 MET cc_start: 0.9567 (tpp) cc_final: 0.9195 (tpp) REVERT: B 613 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9093 (tt) REVERT: B 669 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.8835 (p) REVERT: B 809 MET cc_start: 0.8961 (mmm) cc_final: 0.8703 (mmm) REVERT: B 968 GLN cc_start: 0.8602 (mp10) cc_final: 0.8329 (mp10) REVERT: B 1225 ASP cc_start: 0.6946 (p0) cc_final: 0.6583 (p0) REVERT: B 1250 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8021 (t) REVERT: B 1534 MET cc_start: 0.8123 (mmm) cc_final: 0.7737 (mmm) REVERT: B 1749 MET cc_start: 0.9386 (tpp) cc_final: 0.9099 (tpp) REVERT: B 1845 SER cc_start: 0.8709 (m) cc_final: 0.8357 (p) REVERT: B 2032 MET cc_start: 0.8375 (tpp) cc_final: 0.8049 (tpp) REVERT: B 2149 MET cc_start: 0.8565 (mmm) cc_final: 0.8286 (mmm) REVERT: B 2182 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 2289 CYS cc_start: 0.8924 (m) cc_final: 0.8580 (t) REVERT: B 2291 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8614 (mtm) REVERT: B 2308 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8145 (mp) REVERT: B 2360 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8782 (tt) REVERT: B 2390 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8444 (t0) REVERT: C 490 MET cc_start: 0.8194 (tpp) cc_final: 0.7883 (tpp) REVERT: C 522 MET cc_start: 0.9132 (tmm) cc_final: 0.8774 (tmm) REVERT: C 613 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9037 (tt) REVERT: C 707 MET cc_start: 0.8075 (mpp) cc_final: 0.7841 (mpp) REVERT: C 734 MET cc_start: 0.8662 (mmm) cc_final: 0.8334 (mmm) REVERT: C 899 MET cc_start: 0.8961 (mmm) cc_final: 0.8614 (mmp) REVERT: C 976 GLU cc_start: 0.8485 (tp30) cc_final: 0.8215 (tp30) REVERT: C 1225 ASP cc_start: 0.6842 (p0) cc_final: 0.6345 (p0) REVERT: C 1334 MET cc_start: 0.7950 (mmm) cc_final: 0.7674 (mmm) REVERT: C 1612 PHE cc_start: 0.9349 (t80) cc_final: 0.8987 (t80) REVERT: C 1684 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7878 (ttm) REVERT: C 1712 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9190 (p) REVERT: C 1749 MET cc_start: 0.9457 (tpp) cc_final: 0.9253 (tpp) REVERT: C 1936 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8679 (t70) REVERT: C 2270 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9172 (mp) REVERT: C 2316 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8685 (t) REVERT: C 2486 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8916 (t) REVERT: D 28 MET cc_start: 0.8528 (ptp) cc_final: 0.8272 (ptp) REVERT: D 65 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8807 (mt) REVERT: D 263 MET cc_start: 0.9515 (tpp) cc_final: 0.9002 (tpp) REVERT: D 669 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8921 (p) REVERT: D 775 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8661 (m) REVERT: D 899 MET cc_start: 0.8900 (mmm) cc_final: 0.8614 (mmp) REVERT: D 968 GLN cc_start: 0.8704 (mp10) cc_final: 0.8388 (mp10) REVERT: D 1045 MET cc_start: 0.8755 (mmm) cc_final: 0.8362 (mmm) REVERT: D 1053 SER cc_start: 0.8543 (OUTLIER) cc_final: 0.8190 (p) REVERT: D 1334 MET cc_start: 0.7416 (tpp) cc_final: 0.7036 (tpp) REVERT: D 1534 MET cc_start: 0.7969 (mmm) cc_final: 0.7654 (mmm) REVERT: D 1845 SER cc_start: 0.8367 (m) cc_final: 0.8109 (p) REVERT: D 1865 MET cc_start: 0.8642 (tmm) cc_final: 0.8178 (tmm) REVERT: D 2030 MET cc_start: 0.8860 (tpp) cc_final: 0.8638 (tpp) REVERT: D 2032 MET cc_start: 0.7992 (mmm) cc_final: 0.7754 (tpp) REVERT: D 2308 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (mt) REVERT: D 2390 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8306 (t0) REVERT: E 28 MET cc_start: 0.8715 (ptp) cc_final: 0.8385 (ptp) REVERT: E 65 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8685 (mt) REVERT: E 263 MET cc_start: 0.9519 (tpp) cc_final: 0.8904 (tpp) REVERT: E 433 MET cc_start: 0.8369 (tpt) cc_final: 0.8043 (tpt) REVERT: E 518 SER cc_start: 0.9481 (OUTLIER) cc_final: 0.9236 (t) REVERT: E 584 MET cc_start: 0.8300 (mmm) cc_final: 0.7918 (mmm) REVERT: E 694 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8908 (mt) REVERT: E 899 MET cc_start: 0.8961 (mmm) cc_final: 0.8531 (mmp) REVERT: E 968 GLN cc_start: 0.8749 (mp10) cc_final: 0.8507 (mp10) REVERT: E 1225 ASP cc_start: 0.6700 (p0) cc_final: 0.6318 (p0) REVERT: E 1250 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7920 (t) REVERT: E 1334 MET cc_start: 0.8171 (tpp) cc_final: 0.7253 (mmm) REVERT: E 1749 MET cc_start: 0.9135 (tpt) cc_final: 0.8934 (tpp) REVERT: E 1838 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8356 (ptm-80) REVERT: E 1845 SER cc_start: 0.8853 (m) cc_final: 0.8508 (p) REVERT: E 1936 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8522 (t70) REVERT: E 2032 MET cc_start: 0.8414 (tpp) cc_final: 0.7979 (tpp) REVERT: E 2109 GLN cc_start: 0.8272 (tp40) cc_final: 0.7455 (tp-100) REVERT: E 2182 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 2291 MET cc_start: 0.8854 (mtm) cc_final: 0.8557 (mtp) REVERT: E 2390 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8318 (t0) REVERT: E 2492 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8847 (mt) outliers start: 312 outliers final: 262 residues processed: 761 average time/residue: 0.8658 time to fit residues: 1182.8392 Evaluate side-chains 788 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 492 time to evaluate : 8.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 446 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 532 GLN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 750 MET Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1222 TYR Chi-restraints excluded: chain A residue 1250 THR Chi-restraints excluded: chain A residue 1255 MET Chi-restraints excluded: chain A residue 1256 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1301 THR Chi-restraints excluded: chain A residue 1692 VAL Chi-restraints excluded: chain A residue 1704 ILE Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1818 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1893 ASP Chi-restraints excluded: chain A residue 1900 MET Chi-restraints excluded: chain A residue 1919 ASN Chi-restraints excluded: chain A residue 1936 HIS Chi-restraints excluded: chain A residue 2017 THR Chi-restraints excluded: chain A residue 2081 LEU Chi-restraints excluded: chain A residue 2142 THR Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2147 LEU Chi-restraints excluded: chain A residue 2181 ILE Chi-restraints excluded: chain A residue 2229 LEU Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2348 THR Chi-restraints excluded: chain A residue 2366 ILE Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2523 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 608 ASN Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 892 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1047 ASN Chi-restraints excluded: chain B residue 1053 SER Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1222 TYR Chi-restraints excluded: chain B residue 1250 THR Chi-restraints excluded: chain B residue 1256 THR Chi-restraints excluded: chain B residue 1277 ASP Chi-restraints excluded: chain B residue 1596 THR Chi-restraints excluded: chain B residue 1622 ILE Chi-restraints excluded: chain B residue 1630 MET Chi-restraints excluded: chain B residue 1692 VAL Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1718 ILE Chi-restraints excluded: chain B residue 1729 TYR Chi-restraints excluded: chain B residue 1768 VAL Chi-restraints excluded: chain B residue 1785 ILE Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1900 MET Chi-restraints excluded: chain B residue 1934 MET Chi-restraints excluded: chain B residue 1936 HIS Chi-restraints excluded: chain B residue 2081 LEU Chi-restraints excluded: chain B residue 2143 SER Chi-restraints excluded: chain B residue 2145 THR Chi-restraints excluded: chain B residue 2234 GLU Chi-restraints excluded: chain B residue 2291 MET Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain B residue 2348 THR Chi-restraints excluded: chain B residue 2360 LEU Chi-restraints excluded: chain B residue 2366 ILE Chi-restraints excluded: chain B residue 2390 ASN Chi-restraints excluded: chain B residue 2523 SER Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 608 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 750 MET Chi-restraints excluded: chain C residue 795 LEU Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1058 ASN Chi-restraints excluded: chain C residue 1104 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1222 TYR Chi-restraints excluded: chain C residue 1256 THR Chi-restraints excluded: chain C residue 1272 THR Chi-restraints excluded: chain C residue 1277 ASP Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1684 MET Chi-restraints excluded: chain C residue 1692 VAL Chi-restraints excluded: chain C residue 1704 ILE Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1725 SER Chi-restraints excluded: chain C residue 1729 TYR Chi-restraints excluded: chain C residue 1768 VAL Chi-restraints excluded: chain C residue 1797 MET Chi-restraints excluded: chain C residue 1811 SER Chi-restraints excluded: chain C residue 1832 ASP Chi-restraints excluded: chain C residue 1875 MET Chi-restraints excluded: chain C residue 1900 MET Chi-restraints excluded: chain C residue 1936 HIS Chi-restraints excluded: chain C residue 1965 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 1999 LEU Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2142 THR Chi-restraints excluded: chain C residue 2270 LEU Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain C residue 2348 THR Chi-restraints excluded: chain C residue 2486 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 322 ASN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 446 ASN Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 608 ASN Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain D residue 691 ASP Chi-restraints excluded: chain D residue 707 MET Chi-restraints excluded: chain D residue 771 GLU Chi-restraints excluded: chain D residue 775 THR Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 892 VAL Chi-restraints excluded: chain D residue 901 THR Chi-restraints excluded: chain D residue 972 THR Chi-restraints excluded: chain D residue 1047 ASN Chi-restraints excluded: chain D residue 1053 SER Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1104 THR Chi-restraints excluded: chain D residue 1222 TYR Chi-restraints excluded: chain D residue 1256 THR Chi-restraints excluded: chain D residue 1290 THR Chi-restraints excluded: chain D residue 1596 THR Chi-restraints excluded: chain D residue 1692 VAL Chi-restraints excluded: chain D residue 1704 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1729 TYR Chi-restraints excluded: chain D residue 1818 ILE Chi-restraints excluded: chain D residue 1900 MET Chi-restraints excluded: chain D residue 1919 ASN Chi-restraints excluded: chain D residue 1936 HIS Chi-restraints excluded: chain D residue 2029 VAL Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2142 THR Chi-restraints excluded: chain D residue 2143 SER Chi-restraints excluded: chain D residue 2145 THR Chi-restraints excluded: chain D residue 2181 ILE Chi-restraints excluded: chain D residue 2289 CYS Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2348 THR Chi-restraints excluded: chain D residue 2390 ASN Chi-restraints excluded: chain D residue 2510 LEU Chi-restraints excluded: chain D residue 2523 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 532 GLN Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 608 ASN Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 691 ASP Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 750 MET Chi-restraints excluded: chain E residue 824 LEU Chi-restraints excluded: chain E residue 892 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 972 THR Chi-restraints excluded: chain E residue 1045 MET Chi-restraints excluded: chain E residue 1053 SER Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1076 VAL Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1181 LEU Chi-restraints excluded: chain E residue 1222 TYR Chi-restraints excluded: chain E residue 1250 THR Chi-restraints excluded: chain E residue 1256 THR Chi-restraints excluded: chain E residue 1277 ASP Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1596 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1690 THR Chi-restraints excluded: chain E residue 1692 VAL Chi-restraints excluded: chain E residue 1704 ILE Chi-restraints excluded: chain E residue 1718 ILE Chi-restraints excluded: chain E residue 1729 TYR Chi-restraints excluded: chain E residue 1838 ARG Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1893 ASP Chi-restraints excluded: chain E residue 1934 MET Chi-restraints excluded: chain E residue 1936 HIS Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2143 SER Chi-restraints excluded: chain E residue 2147 LEU Chi-restraints excluded: chain E residue 2243 LEU Chi-restraints excluded: chain E residue 2289 CYS Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2348 THR Chi-restraints excluded: chain E residue 2366 ILE Chi-restraints excluded: chain E residue 2390 ASN Chi-restraints excluded: chain E residue 2492 LEU Chi-restraints excluded: chain E residue 2499 ILE Chi-restraints excluded: chain E residue 2510 LEU Chi-restraints excluded: chain E residue 2523 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 734 optimal weight: 10.0000 chunk 984 optimal weight: 0.4980 chunk 283 optimal weight: 0.8980 chunk 852 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 256 optimal weight: 0.0980 chunk 925 optimal weight: 4.9990 chunk 387 optimal weight: 10.0000 chunk 950 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2221 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** B2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047341 restraints weight = 430708.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048675 restraints weight = 230455.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.049443 restraints weight = 149777.519| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.324 95500 Z= 0.185 Angle : 0.609 47.121 129690 Z= 0.336 Chirality : 0.040 0.218 14565 Planarity : 0.004 0.116 16710 Dihedral : 5.645 60.972 12848 Min Nonbonded Distance : 0.951 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.89 % Allowed : 19.65 % Favored : 77.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.20 % 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: 0.41 (0.08), residues: 11655 helix: 2.18 (0.07), residues: 5470 sheet: -1.02 (0.13), residues: 1700 loop : -1.68 (0.10), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1819 HIS 0.015 0.001 HIS D2106 PHE 0.074 0.001 PHE E1556 TYR 0.030 0.001 TYR A1975 ARG 0.008 0.000 ARG B2233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20542.31 seconds wall clock time: 365 minutes 13.54 seconds (21913.54 seconds total)