Starting phenix.real_space_refine on Tue Mar 19 00:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzh_8185/03_2024/5jzh_8185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzh_8185/03_2024/5jzh_8185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzh_8185/03_2024/5jzh_8185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzh_8185/03_2024/5jzh_8185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzh_8185/03_2024/5jzh_8185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jzh_8185/03_2024/5jzh_8185.pdb" } resolution = 3.9 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= 0.003 sd= 0.038 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 29400 2.51 5 N 8036 2.21 5 O 9002 1.98 5 H 44226 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 95": "OD1" <-> "OD2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F ASP 97": "OD1" <-> "OD2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 95": "OD1" <-> "OD2" Residue "G ASP 97": "OD1" <-> "OD2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H ASP 97": "OD1" <-> "OD2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 95": "OD1" <-> "OD2" Residue "I ASP 97": "OD1" <-> "OD2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J ASP 97": "OD1" <-> "OD2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K ASP 97": "OD1" <-> "OD2" Residue "K TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 95": "OD1" <-> "OD2" Residue "L ASP 97": "OD1" <-> "OD2" Residue "L TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 95": "OD1" <-> "OD2" Residue "M ASP 97": "OD1" <-> "OD2" Residue "M TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 95": "OD1" <-> "OD2" Residue "N ASP 97": "OD1" <-> "OD2" Residue "N TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90790 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "B" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "C" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "D" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "E" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "F" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "G" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "H" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "I" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "J" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "K" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "L" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "M" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Chain: "N" Number of atoms: 6485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6485 Classifications: {'peptide': 424} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 396} Time building chain proxies: 32.13, per 1000 atoms: 0.35 Number of scatterers: 90790 At special positions: 0 Unit cell: (179.56, 180.9, 188.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 9002 8.00 N 8036 7.00 C 29400 6.00 H 44226 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 164 " distance=2.04 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 75 " distance=2.03 Simple disulfide: pdb=" SG CYS I 159 " - pdb=" SG CYS I 164 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 75 " distance=2.03 Simple disulfide: pdb=" SG CYS J 159 " - pdb=" SG CYS J 164 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 75 " distance=2.03 Simple disulfide: pdb=" SG CYS K 159 " - pdb=" SG CYS K 164 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 164 " distance=2.04 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 75 " distance=2.03 Simple disulfide: pdb=" SG CYS M 159 " - pdb=" SG CYS M 164 " distance=2.04 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 75 " distance=2.03 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 164 " distance=2.04 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: 56.83 Conformation dependent library (CDL) restraints added in 8.1 seconds 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10696 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 0 sheets defined 22.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 27 through 33 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 59 through 62 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 27 through 33 Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 27 through 33 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'F' and resid 59 through 62 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 59 through 62 Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 234 through 237 Processing helix chain 'G' and resid 264 through 268 Processing helix chain 'G' and resid 354 through 361 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 372 through 381 Processing helix chain 'G' and resid 381 through 393 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 27 through 33 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 59 through 62 Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 234 through 237 Processing helix chain 'H' and resid 264 through 268 Processing helix chain 'H' and resid 354 through 361 Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 372 through 381 Processing helix chain 'H' and resid 381 through 393 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 27 through 33 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 59 through 62 Processing helix chain 'I' and resid 97 through 107 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 234 through 237 Processing helix chain 'I' and resid 264 through 268 Processing helix chain 'I' and resid 354 through 361 Processing helix chain 'I' and resid 364 through 368 Processing helix chain 'I' and resid 372 through 381 Processing helix chain 'I' and resid 381 through 393 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 59 through 62 Processing helix chain 'J' and resid 97 through 107 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 264 through 268 Processing helix chain 'J' and resid 354 through 361 Processing helix chain 'J' and resid 364 through 368 Processing helix chain 'J' and resid 372 through 381 Processing helix chain 'J' and resid 381 through 393 Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 27 through 33 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 59 through 62 Processing helix chain 'K' and resid 97 through 107 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 264 through 268 Processing helix chain 'K' and resid 354 through 361 Processing helix chain 'K' and resid 364 through 368 Processing helix chain 'K' and resid 372 through 381 Processing helix chain 'K' and resid 381 through 393 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 27 through 33 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 59 through 62 Processing helix chain 'L' and resid 97 through 107 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 234 through 237 Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 354 through 361 Processing helix chain 'L' and resid 364 through 368 Processing helix chain 'L' and resid 372 through 381 Processing helix chain 'L' and resid 381 through 393 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 27 through 33 Processing helix chain 'M' and resid 34 through 39 Processing helix chain 'M' and resid 40 through 42 No H-bonds generated for 'chain 'M' and resid 40 through 42' Processing helix chain 'M' and resid 59 through 62 Processing helix chain 'M' and resid 97 through 107 Processing helix chain 'M' and resid 112 through 124 Processing helix chain 'M' and resid 234 through 237 Processing helix chain 'M' and resid 264 through 268 Processing helix chain 'M' and resid 354 through 361 Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'M' and resid 372 through 381 Processing helix chain 'M' and resid 381 through 393 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 27 through 33 Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 40 through 42 No H-bonds generated for 'chain 'N' and resid 40 through 42' Processing helix chain 'N' and resid 59 through 62 Processing helix chain 'N' and resid 97 through 107 Processing helix chain 'N' and resid 112 through 124 Processing helix chain 'N' and resid 234 through 237 Processing helix chain 'N' and resid 264 through 268 Processing helix chain 'N' and resid 354 through 361 Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 372 through 381 Processing helix chain 'N' and resid 381 through 393 672 hydrogen bonds defined for protein. 1680 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: 26.08 Time building geometry restraints manager: 59.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 44254 1.13 - 1.30: 7840 1.30 - 1.47: 19713 1.47 - 1.64: 20117 1.64 - 1.81: 196 Bond restraints: 92120 Sorted by residual: bond pdb=" C ALA A 424 " pdb=" OXT ALA A 424 " ideal model delta sigma weight residual 1.231 0.999 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C ALA C 424 " pdb=" O ALA C 424 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C ALA K 424 " pdb=" O ALA K 424 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C ALA E 424 " pdb=" O ALA E 424 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C ALA H 424 " pdb=" OXT ALA H 424 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 92115 not shown) Histogram of bond angle deviations from ideal: 50.52 - 68.83: 448 68.83 - 87.13: 0 87.13 - 105.44: 3088 105.44 - 123.74: 154450 123.74 - 142.05: 7732 Bond angle restraints: 165718 Sorted by residual: angle pdb=" O TYR D 76 " pdb=" C TYR D 76 " pdb=" N PRO D 77 " ideal model delta sigma weight residual 121.80 59.36 62.44 8.60e-01 1.35e+00 5.27e+03 angle pdb=" O TYR F 76 " pdb=" C TYR F 76 " pdb=" N PRO F 77 " ideal model delta sigma weight residual 121.80 59.40 62.40 8.60e-01 1.35e+00 5.26e+03 angle pdb=" O TYR H 76 " pdb=" C TYR H 76 " pdb=" N PRO H 77 " ideal model delta sigma weight residual 121.80 59.42 62.38 8.60e-01 1.35e+00 5.26e+03 angle pdb=" O TYR J 76 " pdb=" C TYR J 76 " pdb=" N PRO J 77 " ideal model delta sigma weight residual 121.80 59.42 62.38 8.60e-01 1.35e+00 5.26e+03 angle pdb=" O TYR B 76 " pdb=" C TYR B 76 " pdb=" N PRO B 77 " ideal model delta sigma weight residual 121.80 59.43 62.37 8.60e-01 1.35e+00 5.26e+03 ... (remaining 165713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.74: 42385 26.74 - 53.49: 1181 53.49 - 80.23: 310 80.23 - 106.98: 0 106.98 - 133.72: 14 Dihedral angle restraints: 43890 sinusoidal: 23408 harmonic: 20482 Sorted by residual: dihedral pdb=" CA ASP G 222 " pdb=" C ASP G 222 " pdb=" N THR G 223 " pdb=" CA THR G 223 " ideal model delta harmonic sigma weight residual -180.00 -46.28 -133.72 0 5.00e+00 4.00e-02 7.15e+02 dihedral pdb=" CA ASP J 222 " pdb=" C ASP J 222 " pdb=" N THR J 223 " pdb=" CA THR J 223 " ideal model delta harmonic sigma weight residual -180.00 -46.29 -133.71 0 5.00e+00 4.00e-02 7.15e+02 dihedral pdb=" CA ASP M 222 " pdb=" C ASP M 222 " pdb=" N THR M 223 " pdb=" CA THR M 223 " ideal model delta harmonic sigma weight residual -180.00 -46.31 -133.69 0 5.00e+00 4.00e-02 7.15e+02 ... (remaining 43887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3604 0.059 - 0.118: 2136 0.118 - 0.178: 903 0.178 - 0.237: 139 0.237 - 0.296: 50 Chirality restraints: 6832 Sorted by residual: chirality pdb=" CA TRP B 339 " pdb=" N TRP B 339 " pdb=" C TRP B 339 " pdb=" CB TRP B 339 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA TRP E 339 " pdb=" N TRP E 339 " pdb=" C TRP E 339 " pdb=" CB TRP E 339 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA TRP L 339 " pdb=" N TRP L 339 " pdb=" C TRP L 339 " pdb=" CB TRP L 339 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 6829 not shown) Planarity restraints: 14140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY N 320 " -0.062 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" C GLY N 320 " 0.223 2.00e-02 2.50e+03 pdb=" O GLY N 320 " -0.085 2.00e-02 2.50e+03 pdb=" N PHE N 321 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 320 " 0.062 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" C GLY C 320 " -0.223 2.00e-02 2.50e+03 pdb=" O GLY C 320 " 0.085 2.00e-02 2.50e+03 pdb=" N PHE C 321 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 320 " -0.063 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" C GLY M 320 " 0.223 2.00e-02 2.50e+03 pdb=" O GLY M 320 " -0.085 2.00e-02 2.50e+03 pdb=" N PHE M 321 " -0.075 2.00e-02 2.50e+03 ... (remaining 14137 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.89: 1794 1.89 - 2.56: 89323 2.56 - 3.24: 271863 3.24 - 3.92: 362581 3.92 - 4.60: 558562 Nonbonded interactions: 1284123 Sorted by model distance: nonbonded pdb=" HB3 PRO L 211 " pdb=" HG3 PRO L 211 " model vdw 1.208 1.952 nonbonded pdb=" HB3 PRO B 211 " pdb=" HG3 PRO B 211 " model vdw 1.208 1.952 nonbonded pdb=" HB3 PRO K 211 " pdb=" HG3 PRO K 211 " model vdw 1.208 1.952 nonbonded pdb=" HB3 PRO C 211 " pdb=" HG3 PRO C 211 " model vdw 1.208 1.952 nonbonded pdb=" HB3 PRO I 211 " pdb=" HG3 PRO I 211 " model vdw 1.208 1.952 ... (remaining 1284118 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.85 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.040 Extract box with map and model: 5.870 Check model and map are aligned: 1.010 Set scattering table: 0.640 Process input model: 217.500 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 234.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.015 0.232 47894 Z= 0.979 Angle : 2.151 62.436 65394 Z= 1.730 Chirality : 0.083 0.296 6832 Planarity : 0.016 0.147 8554 Dihedral : 10.545 133.719 17024 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 2.73 % Allowed : 9.36 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.00 % 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: -1.57 (0.10), residues: 5908 helix: -1.63 (0.13), residues: 1050 sheet: -0.02 (0.11), residues: 1974 loop : -1.51 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.007 TRP B 227 HIS 0.006 0.001 HIS H 107 PHE 0.019 0.005 PHE C 245 TYR 0.062 0.008 TYR G 314 ARG 0.003 0.001 ARG G 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1231 time to evaluate : 5.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 7 ASP cc_start: 0.7994 (p0) cc_final: 0.7696 (p0) REVERT: A 26 VAL cc_start: 0.7912 (t) cc_final: 0.7546 (t) REVERT: A 30 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 228 SER cc_start: 0.8882 (t) cc_final: 0.8605 (p) REVERT: A 335 ASN cc_start: 0.8193 (p0) cc_final: 0.7286 (t0) REVERT: A 350 ASP cc_start: 0.7483 (p0) cc_final: 0.7052 (p0) REVERT: A 385 MET cc_start: 0.9368 (mmm) cc_final: 0.9099 (mmm) REVERT: B 7 ASP cc_start: 0.7983 (p0) cc_final: 0.7615 (p0) REVERT: B 57 MET cc_start: 0.8275 (mtm) cc_final: 0.7874 (mtp) REVERT: B 106 VAL cc_start: 0.9234 (m) cc_final: 0.8977 (t) REVERT: B 228 SER cc_start: 0.8866 (t) cc_final: 0.8600 (p) REVERT: C 26 VAL cc_start: 0.8126 (t) cc_final: 0.7925 (t) REVERT: C 41 MET cc_start: 0.7166 (mmm) cc_final: 0.6961 (mtt) REVERT: C 106 VAL cc_start: 0.9125 (m) cc_final: 0.8908 (t) REVERT: C 183 SER cc_start: 0.9081 (p) cc_final: 0.8785 (p) REVERT: C 228 SER cc_start: 0.8957 (t) cc_final: 0.8627 (p) REVERT: C 265 TRP cc_start: 0.8993 (t-100) cc_final: 0.8772 (t-100) REVERT: C 350 ASP cc_start: 0.7571 (p0) cc_final: 0.7104 (p0) REVERT: D 183 SER cc_start: 0.9097 (p) cc_final: 0.8718 (p) REVERT: D 228 SER cc_start: 0.8940 (t) cc_final: 0.8669 (p) REVERT: D 267 SER cc_start: 0.8819 (p) cc_final: 0.8589 (t) REVERT: E 106 VAL cc_start: 0.9102 (m) cc_final: 0.8851 (t) REVERT: E 228 SER cc_start: 0.8903 (t) cc_final: 0.8498 (p) REVERT: E 335 ASN cc_start: 0.8256 (p0) cc_final: 0.7335 (t0) REVERT: F 183 SER cc_start: 0.8859 (p) cc_final: 0.8543 (p) REVERT: F 228 SER cc_start: 0.8803 (t) cc_final: 0.8501 (p) REVERT: G 41 MET cc_start: 0.7188 (mmm) cc_final: 0.6972 (mtt) REVERT: G 183 SER cc_start: 0.8933 (p) cc_final: 0.8642 (p) REVERT: G 228 SER cc_start: 0.8885 (t) cc_final: 0.8634 (p) REVERT: G 335 ASN cc_start: 0.8222 (p0) cc_final: 0.7662 (t0) REVERT: G 350 ASP cc_start: 0.7557 (p0) cc_final: 0.6894 (p0) REVERT: H 30 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7163 (mt-10) REVERT: H 57 MET cc_start: 0.8343 (mtm) cc_final: 0.8127 (mtm) REVERT: H 128 VAL cc_start: 0.9194 (t) cc_final: 0.8892 (p) REVERT: H 142 VAL cc_start: 0.9475 (t) cc_final: 0.9149 (t) REVERT: H 228 SER cc_start: 0.9048 (t) cc_final: 0.8673 (p) REVERT: H 335 ASN cc_start: 0.8271 (p0) cc_final: 0.7814 (t0) REVERT: H 350 ASP cc_start: 0.7595 (p0) cc_final: 0.6999 (p0) REVERT: H 385 MET cc_start: 0.9531 (mmm) cc_final: 0.9227 (tpp) REVERT: I 41 MET cc_start: 0.7414 (mmm) cc_final: 0.6857 (mtt) REVERT: I 183 SER cc_start: 0.9077 (p) cc_final: 0.8793 (p) REVERT: I 223 THR cc_start: 0.6045 (m) cc_final: 0.5811 (m) REVERT: I 228 SER cc_start: 0.8857 (t) cc_final: 0.8498 (p) REVERT: J 183 SER cc_start: 0.8952 (p) cc_final: 0.8588 (p) REVERT: J 223 THR cc_start: 0.6784 (m) cc_final: 0.6508 (m) REVERT: J 228 SER cc_start: 0.8684 (t) cc_final: 0.8291 (p) REVERT: J 350 ASP cc_start: 0.7375 (p0) cc_final: 0.6873 (p0) REVERT: K 30 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7260 (mt-10) REVERT: K 61 TYR cc_start: 0.7035 (m-80) cc_final: 0.6796 (m-80) REVERT: K 183 SER cc_start: 0.8679 (p) cc_final: 0.8451 (p) REVERT: K 228 SER cc_start: 0.8658 (t) cc_final: 0.8252 (p) REVERT: K 335 ASN cc_start: 0.7876 (p0) cc_final: 0.7450 (t0) REVERT: L 140 MET cc_start: 0.8464 (mmm) cc_final: 0.8141 (mtp) REVERT: L 142 VAL cc_start: 0.9362 (t) cc_final: 0.9157 (t) REVERT: L 183 SER cc_start: 0.8919 (p) cc_final: 0.8517 (p) REVERT: L 228 SER cc_start: 0.8803 (t) cc_final: 0.8305 (p) REVERT: L 335 ASN cc_start: 0.8217 (p0) cc_final: 0.7590 (t0) REVERT: M 136 VAL cc_start: 0.8586 (t) cc_final: 0.8321 (t) REVERT: M 183 SER cc_start: 0.9082 (p) cc_final: 0.8758 (p) REVERT: M 228 SER cc_start: 0.8771 (t) cc_final: 0.8227 (p) REVERT: M 335 ASN cc_start: 0.8198 (p0) cc_final: 0.7491 (t0) REVERT: M 345 ILE cc_start: 0.8973 (mm) cc_final: 0.8681 (mm) REVERT: N 57 MET cc_start: 0.8226 (mtm) cc_final: 0.7849 (mtp) REVERT: N 106 VAL cc_start: 0.9203 (m) cc_final: 0.8944 (t) outliers start: 0 outliers final: 0 residues processed: 1231 average time/residue: 1.2264 time to fit residues: 2426.3427 Evaluate side-chains 728 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 728 time to evaluate : 5.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 0.9980 chunk 445 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 460 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 533 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 195 GLN F 195 GLN H 195 GLN J 195 GLN J 335 ASN M 409 GLN N 195 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 47894 Z= 0.241 Angle : 0.679 6.359 65394 Z= 0.365 Chirality : 0.049 0.152 6832 Planarity : 0.007 0.085 8554 Dihedral : 6.538 58.815 6468 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.18 % Favored : 91.91 % Rotamer: Outliers : 1.37 % Allowed : 6.66 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.75 % Twisted Proline : 2.68 % Twisted General : 0.25 % 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: -0.99 (0.10), residues: 5908 helix: -0.04 (0.16), residues: 966 sheet: -0.71 (0.11), residues: 2044 loop : -0.71 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 339 HIS 0.002 0.001 HIS L 121 PHE 0.015 0.001 PHE H 12 TYR 0.021 0.002 TYR C 314 ARG 0.005 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 847 time to evaluate : 5.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 VAL cc_start: 0.7983 (t) cc_final: 0.7726 (t) REVERT: A 30 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6837 (mt-10) REVERT: A 140 MET cc_start: 0.8564 (mmm) cc_final: 0.8353 (mtp) REVERT: A 350 ASP cc_start: 0.7202 (p0) cc_final: 0.6824 (p0) REVERT: B 57 MET cc_start: 0.7906 (mtm) cc_final: 0.7690 (mtp) REVERT: B 228 SER cc_start: 0.8955 (t) cc_final: 0.8627 (m) REVERT: C 350 ASP cc_start: 0.7502 (p0) cc_final: 0.7006 (p0) REVERT: D 25 PRO cc_start: 0.7344 (Cg_exo) cc_final: 0.7072 (Cg_endo) REVERT: D 140 MET cc_start: 0.8511 (mmm) cc_final: 0.7921 (mtp) REVERT: D 267 SER cc_start: 0.8895 (p) cc_final: 0.8602 (t) REVERT: E 25 PRO cc_start: 0.6950 (Cg_exo) cc_final: 0.6657 (Cg_endo) REVERT: E 50 LEU cc_start: 0.8209 (tp) cc_final: 0.7970 (tp) REVERT: E 228 SER cc_start: 0.8935 (t) cc_final: 0.8673 (m) REVERT: F 25 PRO cc_start: 0.7176 (Cg_exo) cc_final: 0.6850 (Cg_endo) REVERT: F 100 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: F 291 ILE cc_start: 0.9293 (mt) cc_final: 0.8986 (tt) REVERT: G 100 ASP cc_start: 0.7749 (t70) cc_final: 0.7380 (m-30) REVERT: G 228 SER cc_start: 0.8787 (t) cc_final: 0.8566 (m) REVERT: G 335 ASN cc_start: 0.8169 (p0) cc_final: 0.7633 (t0) REVERT: G 350 ASP cc_start: 0.7285 (p0) cc_final: 0.6682 (p0) REVERT: H 25 PRO cc_start: 0.7402 (Cg_exo) cc_final: 0.7143 (Cg_endo) REVERT: H 41 MET cc_start: 0.6870 (mmm) cc_final: 0.6477 (mtt) REVERT: H 128 VAL cc_start: 0.9156 (t) cc_final: 0.8892 (p) REVERT: H 140 MET cc_start: 0.8511 (mmm) cc_final: 0.8163 (mtp) REVERT: H 335 ASN cc_start: 0.8299 (p0) cc_final: 0.7712 (t0) REVERT: H 350 ASP cc_start: 0.7336 (p0) cc_final: 0.6766 (p0) REVERT: H 385 MET cc_start: 0.9475 (mmm) cc_final: 0.9272 (mmm) REVERT: I 25 PRO cc_start: 0.6887 (Cg_exo) cc_final: 0.6634 (Cg_endo) REVERT: I 41 MET cc_start: 0.7321 (mmm) cc_final: 0.6751 (mtt) REVERT: I 140 MET cc_start: 0.8636 (mmm) cc_final: 0.8317 (mtp) REVERT: I 350 ASP cc_start: 0.7716 (p0) cc_final: 0.7038 (p0) REVERT: J 140 MET cc_start: 0.8758 (mmm) cc_final: 0.8046 (mtp) REVERT: J 350 ASP cc_start: 0.7238 (p0) cc_final: 0.6714 (p0) REVERT: J 362 ARG cc_start: 0.7922 (mtp-110) cc_final: 0.7717 (mtp180) REVERT: K 25 PRO cc_start: 0.6788 (Cg_exo) cc_final: 0.6498 (Cg_endo) REVERT: K 50 LEU cc_start: 0.7849 (tp) cc_final: 0.7643 (tp) REVERT: K 100 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: K 183 SER cc_start: 0.8839 (p) cc_final: 0.8571 (p) REVERT: K 228 SER cc_start: 0.8602 (t) cc_final: 0.8229 (m) REVERT: K 254 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7113 (tp30) REVERT: K 335 ASN cc_start: 0.7970 (p0) cc_final: 0.7419 (t0) REVERT: L 140 MET cc_start: 0.8344 (mmm) cc_final: 0.8094 (mtp) REVERT: M 7 ASP cc_start: 0.7763 (p0) cc_final: 0.7531 (p0) REVERT: N 25 PRO cc_start: 0.7533 (Cg_exo) cc_final: 0.7293 (Cg_endo) REVERT: N 228 SER cc_start: 0.8953 (t) cc_final: 0.8521 (m) REVERT: N 315 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7904 (t0) outliers start: 68 outliers final: 51 residues processed: 885 average time/residue: 1.1163 time to fit residues: 1633.3014 Evaluate side-chains 712 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 657 time to evaluate : 5.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 36 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 250 VAL Chi-restraints excluded: chain N residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 444 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 577 optimal weight: 4.9990 chunk 476 optimal weight: 3.9990 chunk 530 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 429 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 409 GLN C 388 ASN C 409 GLN E 409 GLN G 409 GLN I 409 GLN L 195 GLN L 409 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 47894 Z= 0.223 Angle : 0.595 6.895 65394 Z= 0.315 Chirality : 0.046 0.152 6832 Planarity : 0.005 0.071 8554 Dihedral : 5.728 30.941 6468 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.64 % Favored : 93.13 % Rotamer: Outliers : 1.91 % Allowed : 7.71 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.75 % Twisted Proline : 1.79 % 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: -0.92 (0.11), residues: 5908 helix: 0.50 (0.17), residues: 966 sheet: -0.87 (0.11), residues: 2044 loop : -0.67 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 339 HIS 0.003 0.001 HIS K 107 PHE 0.019 0.002 PHE H 12 TYR 0.021 0.002 TYR C 314 ARG 0.005 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 722 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 PRO cc_start: 0.7516 (Cg_exo) cc_final: 0.7253 (Cg_endo) REVERT: A 140 MET cc_start: 0.8773 (mmm) cc_final: 0.8097 (mtp) REVERT: A 227 TRP cc_start: 0.7170 (t60) cc_final: 0.6832 (t60) REVERT: A 350 ASP cc_start: 0.7407 (p0) cc_final: 0.7118 (p0) REVERT: A 385 MET cc_start: 0.9225 (mmm) cc_final: 0.8897 (tpp) REVERT: B 228 SER cc_start: 0.8784 (t) cc_final: 0.8440 (m) REVERT: B 389 LEU cc_start: 0.9367 (mt) cc_final: 0.9156 (mm) REVERT: C 350 ASP cc_start: 0.7555 (p0) cc_final: 0.7217 (p0) REVERT: D 25 PRO cc_start: 0.7317 (Cg_exo) cc_final: 0.7007 (Cg_endo) REVERT: D 198 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8508 (ptpt) REVERT: E 25 PRO cc_start: 0.6786 (Cg_exo) cc_final: 0.6445 (Cg_endo) REVERT: E 228 SER cc_start: 0.8900 (t) cc_final: 0.8658 (m) REVERT: F 25 PRO cc_start: 0.7225 (Cg_exo) cc_final: 0.6876 (Cg_endo) REVERT: F 95 ASP cc_start: 0.6659 (p0) cc_final: 0.6356 (p0) REVERT: F 291 ILE cc_start: 0.9224 (mt) cc_final: 0.8958 (tt) REVERT: G 25 PRO cc_start: 0.7109 (Cg_exo) cc_final: 0.6893 (Cg_endo) REVERT: H 41 MET cc_start: 0.6961 (mmm) cc_final: 0.6438 (mtt) REVERT: H 128 VAL cc_start: 0.9212 (t) cc_final: 0.8941 (p) REVERT: H 350 ASP cc_start: 0.7591 (p0) cc_final: 0.7223 (p0) REVERT: H 385 MET cc_start: 0.9451 (mmm) cc_final: 0.9181 (tpp) REVERT: I 25 PRO cc_start: 0.6824 (Cg_exo) cc_final: 0.6547 (Cg_endo) REVERT: I 41 MET cc_start: 0.7311 (mmm) cc_final: 0.6918 (mtt) REVERT: I 315 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8213 (t0) REVERT: J 140 MET cc_start: 0.8890 (mmm) cc_final: 0.8427 (mtp) REVERT: J 350 ASP cc_start: 0.7442 (p0) cc_final: 0.6897 (p0) REVERT: K 25 PRO cc_start: 0.6868 (Cg_exo) cc_final: 0.6548 (Cg_endo) REVERT: K 50 LEU cc_start: 0.8046 (tp) cc_final: 0.7808 (tp) REVERT: K 183 SER cc_start: 0.8880 (p) cc_final: 0.8590 (p) REVERT: K 228 SER cc_start: 0.8738 (t) cc_final: 0.8324 (m) REVERT: M 7 ASP cc_start: 0.7630 (p0) cc_final: 0.7385 (p0) REVERT: M 25 PRO cc_start: 0.7140 (Cg_exo) cc_final: 0.6888 (Cg_endo) REVERT: N 25 PRO cc_start: 0.7414 (Cg_exo) cc_final: 0.7083 (Cg_endo) REVERT: N 57 MET cc_start: 0.7239 (mtp) cc_final: 0.6972 (mtp) REVERT: N 227 TRP cc_start: 0.7631 (t60) cc_final: 0.7367 (t60) REVERT: N 228 SER cc_start: 0.8933 (t) cc_final: 0.8559 (m) REVERT: N 256 SER cc_start: 0.8016 (m) cc_final: 0.7760 (m) outliers start: 95 outliers final: 84 residues processed: 776 average time/residue: 1.0539 time to fit residues: 1359.0985 Evaluate side-chains 716 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 630 time to evaluate : 5.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 198 LYS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 301 ASP Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 196 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 315 ASP Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain M residue 100 ASP Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 267 SER Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 291 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 6.9990 chunk 402 optimal weight: 6.9990 chunk 277 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 536 optimal weight: 4.9990 chunk 568 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 508 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN F 226 ASN F 378 GLN F 388 ASN G 388 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 GLN I 195 GLN J 388 ASN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 388 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 47894 Z= 0.308 Angle : 0.612 5.796 65394 Z= 0.325 Chirality : 0.047 0.186 6832 Planarity : 0.005 0.076 8554 Dihedral : 5.645 31.027 6468 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.68 % Favored : 92.10 % Rotamer: Outliers : 2.66 % Allowed : 8.03 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.75 % Twisted Proline : 0.60 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5908 helix: 0.35 (0.17), residues: 966 sheet: -1.06 (0.11), residues: 1890 loop : -0.82 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 227 HIS 0.003 0.001 HIS F 332 PHE 0.012 0.002 PHE H 12 TYR 0.020 0.002 TYR G 314 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 664 time to evaluate : 5.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 140 MET cc_start: 0.8917 (mmm) cc_final: 0.8131 (mtp) REVERT: A 350 ASP cc_start: 0.7588 (p0) cc_final: 0.7307 (p0) REVERT: A 385 MET cc_start: 0.9223 (mmm) cc_final: 0.8520 (mmm) REVERT: B 228 SER cc_start: 0.9008 (t) cc_final: 0.8637 (m) REVERT: C 135 TYR cc_start: 0.7955 (m-80) cc_final: 0.7588 (m-10) REVERT: D 25 PRO cc_start: 0.7408 (Cg_exo) cc_final: 0.7122 (Cg_endo) REVERT: E 25 PRO cc_start: 0.7059 (Cg_exo) cc_final: 0.6647 (Cg_endo) REVERT: E 228 SER cc_start: 0.8990 (t) cc_final: 0.8704 (m) REVERT: E 304 TYR cc_start: 0.8417 (m-10) cc_final: 0.8139 (m-10) REVERT: E 314 TYR cc_start: 0.7615 (m-80) cc_final: 0.7232 (m-80) REVERT: F 95 ASP cc_start: 0.6971 (p0) cc_final: 0.6767 (p0) REVERT: F 291 ILE cc_start: 0.9255 (mt) cc_final: 0.9046 (tt) REVERT: F 314 TYR cc_start: 0.7762 (m-80) cc_final: 0.7210 (m-80) REVERT: G 314 TYR cc_start: 0.7569 (m-80) cc_final: 0.7358 (m-80) REVERT: G 350 ASP cc_start: 0.7543 (p0) cc_final: 0.7032 (p0) REVERT: H 41 MET cc_start: 0.7044 (mmm) cc_final: 0.6586 (mtt) REVERT: H 128 VAL cc_start: 0.9274 (t) cc_final: 0.9001 (p) REVERT: H 140 MET cc_start: 0.8656 (mmm) cc_final: 0.8192 (mtp) REVERT: H 385 MET cc_start: 0.9328 (mmm) cc_final: 0.8659 (mmm) REVERT: I 25 PRO cc_start: 0.6965 (Cg_exo) cc_final: 0.6594 (Cg_endo) REVERT: I 41 MET cc_start: 0.7316 (mmm) cc_final: 0.7045 (mtt) REVERT: I 314 TYR cc_start: 0.7604 (m-80) cc_final: 0.7357 (m-80) REVERT: I 350 ASP cc_start: 0.7753 (p0) cc_final: 0.7210 (p0) REVERT: J 140 MET cc_start: 0.8992 (mmm) cc_final: 0.8077 (mtp) REVERT: K 25 PRO cc_start: 0.6984 (Cg_exo) cc_final: 0.6607 (Cg_endo) REVERT: K 228 SER cc_start: 0.8971 (t) cc_final: 0.8570 (m) REVERT: M 7 ASP cc_start: 0.7424 (p0) cc_final: 0.7170 (p0) REVERT: M 135 TYR cc_start: 0.7744 (m-80) cc_final: 0.7411 (m-10) REVERT: M 304 TYR cc_start: 0.8173 (m-10) cc_final: 0.7968 (m-10) REVERT: N 25 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7287 (Cg_endo) REVERT: N 57 MET cc_start: 0.7460 (mtp) cc_final: 0.7151 (mtp) outliers start: 132 outliers final: 108 residues processed: 747 average time/residue: 1.0327 time to fit residues: 1292.9823 Evaluate side-chains 694 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 586 time to evaluate : 5.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 422 LEU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 291 ILE Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 267 SER Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 291 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 423 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 485 optimal weight: 4.9990 chunk 392 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 510 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN F 226 ASN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 GLN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 47894 Z= 0.360 Angle : 0.619 5.570 65394 Z= 0.329 Chirality : 0.047 0.151 6832 Planarity : 0.005 0.076 8554 Dihedral : 5.672 32.849 6468 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.90 % Allowed : 8.67 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % 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: -1.31 (0.11), residues: 5908 helix: 0.17 (0.17), residues: 966 sheet: -1.15 (0.11), residues: 1890 loop : -0.92 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 339 HIS 0.004 0.001 HIS F 332 PHE 0.011 0.002 PHE B 245 TYR 0.021 0.002 TYR A 215 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 618 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.9230 (mmm) cc_final: 0.8812 (mmm) REVERT: B 228 SER cc_start: 0.8976 (t) cc_final: 0.8583 (m) REVERT: B 304 TYR cc_start: 0.8120 (m-10) cc_final: 0.7811 (m-10) REVERT: C 135 TYR cc_start: 0.7864 (m-80) cc_final: 0.7522 (m-10) REVERT: D 25 PRO cc_start: 0.7544 (Cg_exo) cc_final: 0.7246 (Cg_endo) REVERT: E 25 PRO cc_start: 0.7167 (Cg_exo) cc_final: 0.6702 (Cg_endo) REVERT: E 180 ASP cc_start: 0.8269 (t0) cc_final: 0.8067 (t0) REVERT: E 304 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8300 (m-10) REVERT: E 314 TYR cc_start: 0.7505 (m-80) cc_final: 0.6978 (m-80) REVERT: F 291 ILE cc_start: 0.9310 (mt) cc_final: 0.9090 (tt) REVERT: F 314 TYR cc_start: 0.7754 (m-80) cc_final: 0.7295 (m-80) REVERT: G 314 TYR cc_start: 0.7541 (m-80) cc_final: 0.7071 (m-80) REVERT: H 128 VAL cc_start: 0.9306 (t) cc_final: 0.9027 (p) REVERT: H 140 MET cc_start: 0.8812 (mmm) cc_final: 0.8264 (mtp) REVERT: H 227 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7141 (t60) REVERT: I 25 PRO cc_start: 0.6944 (Cg_exo) cc_final: 0.6573 (Cg_endo) REVERT: I 314 TYR cc_start: 0.7597 (m-80) cc_final: 0.7049 (m-80) REVERT: I 350 ASP cc_start: 0.7721 (p0) cc_final: 0.7338 (p0) REVERT: J 140 MET cc_start: 0.9014 (mmm) cc_final: 0.7952 (mtp) REVERT: J 314 TYR cc_start: 0.7757 (m-80) cc_final: 0.7188 (m-80) REVERT: K 228 SER cc_start: 0.9042 (t) cc_final: 0.8590 (m) REVERT: K 304 TYR cc_start: 0.8284 (m-10) cc_final: 0.8024 (m-10) REVERT: K 314 TYR cc_start: 0.7344 (m-80) cc_final: 0.6973 (m-80) REVERT: M 135 TYR cc_start: 0.7887 (m-80) cc_final: 0.7567 (m-10) REVERT: M 314 TYR cc_start: 0.7462 (m-80) cc_final: 0.6903 (m-80) REVERT: N 25 PRO cc_start: 0.7650 (Cg_exo) cc_final: 0.7341 (Cg_endo) REVERT: N 57 MET cc_start: 0.7419 (mtp) cc_final: 0.7115 (mtp) REVERT: N 291 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8855 (tt) REVERT: N 304 TYR cc_start: 0.8155 (m-10) cc_final: 0.7939 (m-10) outliers start: 144 outliers final: 122 residues processed: 704 average time/residue: 1.0992 time to fit residues: 1296.8148 Evaluate side-chains 691 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 566 time to evaluate : 5.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 227 TRP Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 403 ASP Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 227 TRP Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 227 TRP Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 291 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 215 TYR Chi-restraints excluded: chain L residue 227 TRP Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 227 TRP Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 228 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 267 SER Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 4.9990 chunk 511 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 568 optimal weight: 3.9990 chunk 472 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 413 ASN E 388 ASN F 409 GLN H 378 GLN I 335 ASN I 388 ASN J 409 GLN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 388 ASN K 409 GLN ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 388 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 47894 Z= 0.327 Angle : 0.596 5.346 65394 Z= 0.315 Chirality : 0.047 0.151 6832 Planarity : 0.005 0.071 8554 Dihedral : 5.662 37.230 6468 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.98 % Allowed : 9.66 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % 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: -1.40 (0.11), residues: 5908 helix: 0.21 (0.17), residues: 966 sheet: -1.28 (0.12), residues: 1876 loop : -0.98 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 227 HIS 0.004 0.001 HIS F 332 PHE 0.010 0.002 PHE C 343 TYR 0.021 0.002 TYR C 304 ARG 0.004 0.000 ARG E 391 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 590 time to evaluate : 5.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8874 (mmm) cc_final: 0.8217 (mtp) REVERT: A 215 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8421 (p90) REVERT: A 385 MET cc_start: 0.9188 (mmm) cc_final: 0.8844 (mmm) REVERT: B 41 MET cc_start: 0.6646 (mtt) cc_final: 0.6434 (mtt) REVERT: C 135 TYR cc_start: 0.7763 (m-80) cc_final: 0.7429 (m-10) REVERT: C 183 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 350 ASP cc_start: 0.7951 (p0) cc_final: 0.7457 (p0) REVERT: D 25 PRO cc_start: 0.7694 (Cg_exo) cc_final: 0.7396 (Cg_endo) REVERT: D 315 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7957 (t0) REVERT: E 25 PRO cc_start: 0.7335 (Cg_exo) cc_final: 0.6893 (Cg_endo) REVERT: F 291 ILE cc_start: 0.9278 (mt) cc_final: 0.9035 (tt) REVERT: F 314 TYR cc_start: 0.7930 (m-80) cc_final: 0.7488 (m-80) REVERT: F 315 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8111 (t0) REVERT: G 314 TYR cc_start: 0.7702 (m-80) cc_final: 0.7286 (m-80) REVERT: G 315 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8017 (t70) REVERT: H 128 VAL cc_start: 0.9302 (t) cc_final: 0.9021 (p) REVERT: H 140 MET cc_start: 0.8907 (mmm) cc_final: 0.8353 (mtp) REVERT: H 215 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8414 (p90) REVERT: H 385 MET cc_start: 0.9261 (mmm) cc_final: 0.8901 (mmm) REVERT: I 25 PRO cc_start: 0.7003 (Cg_exo) cc_final: 0.6617 (Cg_endo) REVERT: I 140 MET cc_start: 0.8858 (mmm) cc_final: 0.8641 (mtp) REVERT: I 314 TYR cc_start: 0.7800 (m-80) cc_final: 0.7256 (m-80) REVERT: J 140 MET cc_start: 0.9003 (mmm) cc_final: 0.8230 (mtp) REVERT: J 168 THR cc_start: 0.8911 (m) cc_final: 0.8559 (t) REVERT: J 215 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8693 (p90) REVERT: J 314 TYR cc_start: 0.7904 (m-80) cc_final: 0.7184 (m-80) REVERT: K 180 ASP cc_start: 0.8378 (t0) cc_final: 0.8127 (t0) REVERT: K 314 TYR cc_start: 0.7443 (m-80) cc_final: 0.6979 (m-80) REVERT: L 315 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8075 (t0) REVERT: M 135 TYR cc_start: 0.7833 (m-80) cc_final: 0.7506 (m-10) REVERT: N 25 PRO cc_start: 0.7489 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: N 291 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8847 (tt) REVERT: N 314 TYR cc_start: 0.7775 (m-80) cc_final: 0.7561 (m-80) REVERT: N 315 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7827 (t0) outliers start: 148 outliers final: 118 residues processed: 691 average time/residue: 1.0535 time to fit residues: 1207.0222 Evaluate side-chains 669 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 541 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 323 ARG Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 274 THR Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 168 THR Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 168 THR Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 215 TYR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain L residue 215 TYR Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 272 SER Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 215 TYR Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 227 TRP Chi-restraints excluded: chain N residue 228 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 267 SER Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 291 ILE Chi-restraints excluded: chain N residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 324 optimal weight: 0.9990 chunk 415 optimal weight: 2.9990 chunk 321 optimal weight: 2.9990 chunk 478 optimal weight: 0.0020 chunk 317 optimal weight: 4.9990 chunk 566 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 345 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN D 388 ASN D 413 ASN H 388 ASN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 47894 Z= 0.155 Angle : 0.518 5.235 65394 Z= 0.269 Chirality : 0.045 0.148 6832 Planarity : 0.005 0.067 8554 Dihedral : 5.200 32.611 6468 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.81 % Allowed : 11.13 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % 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: -1.12 (0.11), residues: 5908 helix: 0.53 (0.17), residues: 966 sheet: -1.14 (0.12), residues: 1904 loop : -0.79 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 45 HIS 0.003 0.001 HIS A 107 PHE 0.008 0.001 PHE H 12 TYR 0.020 0.001 TYR I 215 ARG 0.004 0.000 ARG K 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 595 time to evaluate : 6.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8229 (mm) cc_final: 0.7853 (tp) REVERT: A 128 VAL cc_start: 0.9218 (t) cc_final: 0.8909 (p) REVERT: A 140 MET cc_start: 0.8793 (mmm) cc_final: 0.8237 (mtp) REVERT: A 215 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8390 (p90) REVERT: A 314 TYR cc_start: 0.8161 (m-80) cc_final: 0.7702 (m-80) REVERT: A 385 MET cc_start: 0.9194 (mmm) cc_final: 0.8875 (mmm) REVERT: B 41 MET cc_start: 0.6607 (mtt) cc_final: 0.6404 (mtt) REVERT: B 215 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8370 (p90) REVERT: B 304 TYR cc_start: 0.8076 (m-10) cc_final: 0.7854 (m-10) REVERT: C 128 VAL cc_start: 0.9262 (t) cc_final: 0.9010 (p) REVERT: C 135 TYR cc_start: 0.7688 (m-80) cc_final: 0.7384 (m-10) REVERT: D 25 PRO cc_start: 0.7530 (Cg_exo) cc_final: 0.7234 (Cg_endo) REVERT: E 25 PRO cc_start: 0.7178 (Cg_exo) cc_final: 0.6717 (Cg_endo) REVERT: E 180 ASP cc_start: 0.8329 (t0) cc_final: 0.8112 (t0) REVERT: F 125 TYR cc_start: 0.9100 (m-80) cc_final: 0.8884 (m-80) REVERT: F 314 TYR cc_start: 0.7796 (m-80) cc_final: 0.7316 (m-80) REVERT: F 388 ASN cc_start: 0.9241 (t0) cc_final: 0.8973 (t0) REVERT: G 314 TYR cc_start: 0.7629 (m-80) cc_final: 0.7093 (m-80) REVERT: H 128 VAL cc_start: 0.9252 (t) cc_final: 0.8945 (p) REVERT: H 215 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8398 (p90) REVERT: H 314 TYR cc_start: 0.8173 (m-80) cc_final: 0.7611 (m-80) REVERT: H 385 MET cc_start: 0.9246 (mmm) cc_final: 0.8929 (mmm) REVERT: I 25 PRO cc_start: 0.6811 (Cg_exo) cc_final: 0.6433 (Cg_endo) REVERT: J 140 MET cc_start: 0.8927 (mmm) cc_final: 0.8288 (mtp) REVERT: J 168 THR cc_start: 0.8915 (m) cc_final: 0.8531 (t) REVERT: J 215 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8376 (p90) REVERT: J 314 TYR cc_start: 0.8229 (m-80) cc_final: 0.7862 (m-80) REVERT: K 180 ASP cc_start: 0.8404 (t0) cc_final: 0.8132 (t0) REVERT: K 314 TYR cc_start: 0.7465 (m-80) cc_final: 0.7007 (m-80) REVERT: L 168 THR cc_start: 0.8633 (m) cc_final: 0.8353 (t) REVERT: M 135 TYR cc_start: 0.7771 (m-80) cc_final: 0.7466 (m-10) REVERT: N 25 PRO cc_start: 0.7334 (Cg_exo) cc_final: 0.7038 (Cg_endo) REVERT: N 215 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8259 (p90) outliers start: 90 outliers final: 78 residues processed: 650 average time/residue: 1.0543 time to fit residues: 1139.4630 Evaluate side-chains 638 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 555 time to evaluate : 5.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 215 TYR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 315 ASP Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 297 LEU Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 215 TYR Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 272 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 215 TYR Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 228 SER Chi-restraints excluded: chain N residue 233 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 360 optimal weight: 2.9990 chunk 386 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 445 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 47894 Z= 0.282 Angle : 0.560 5.405 65394 Z= 0.293 Chirality : 0.046 0.147 6832 Planarity : 0.005 0.070 8554 Dihedral : 5.341 35.991 6468 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.31 % Allowed : 11.03 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5908 helix: 0.35 (0.17), residues: 966 sheet: -1.22 (0.12), residues: 1904 loop : -0.86 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 45 HIS 0.004 0.001 HIS F 332 PHE 0.009 0.001 PHE E 343 TYR 0.022 0.002 TYR G 215 ARG 0.004 0.000 ARG N 391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 556 time to evaluate : 5.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 VAL cc_start: 0.9252 (t) cc_final: 0.8966 (p) REVERT: A 140 MET cc_start: 0.8844 (mmm) cc_final: 0.8272 (mtp) REVERT: A 215 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8459 (p90) REVERT: A 385 MET cc_start: 0.9217 (mmm) cc_final: 0.8917 (mmm) REVERT: B 41 MET cc_start: 0.6694 (mtt) cc_final: 0.6460 (mtt) REVERT: B 215 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8413 (p90) REVERT: B 304 TYR cc_start: 0.8252 (m-10) cc_final: 0.8010 (m-10) REVERT: C 128 VAL cc_start: 0.9276 (t) cc_final: 0.9025 (p) REVERT: C 135 TYR cc_start: 0.7796 (m-80) cc_final: 0.7470 (m-10) REVERT: C 183 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8951 (p) REVERT: C 350 ASP cc_start: 0.7901 (p0) cc_final: 0.7460 (p0) REVERT: D 25 PRO cc_start: 0.7543 (Cg_exo) cc_final: 0.7297 (Cg_endo) REVERT: E 180 ASP cc_start: 0.8360 (t0) cc_final: 0.8106 (t0) REVERT: F 215 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8607 (p90) REVERT: F 314 TYR cc_start: 0.7888 (m-80) cc_final: 0.7391 (m-80) REVERT: G 314 TYR cc_start: 0.7725 (m-80) cc_final: 0.7259 (m-80) REVERT: H 128 VAL cc_start: 0.9288 (t) cc_final: 0.8987 (p) REVERT: H 215 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8500 (p90) REVERT: H 385 MET cc_start: 0.9214 (mmm) cc_final: 0.8865 (mmm) REVERT: I 25 PRO cc_start: 0.6919 (Cg_exo) cc_final: 0.6545 (Cg_endo) REVERT: I 180 ASP cc_start: 0.8016 (t0) cc_final: 0.7452 (t70) REVERT: I 314 TYR cc_start: 0.7705 (m-80) cc_final: 0.7111 (m-80) REVERT: J 140 MET cc_start: 0.9046 (mmm) cc_final: 0.8252 (mtp) REVERT: J 168 THR cc_start: 0.8962 (m) cc_final: 0.8597 (t) REVERT: J 215 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8688 (p90) REVERT: J 314 TYR cc_start: 0.8254 (m-80) cc_final: 0.7786 (m-80) REVERT: J 351 LYS cc_start: 0.8565 (mttt) cc_final: 0.8200 (mttp) REVERT: K 180 ASP cc_start: 0.8450 (t0) cc_final: 0.8181 (t0) REVERT: K 215 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7860 (p90) REVERT: K 314 TYR cc_start: 0.7452 (m-80) cc_final: 0.6944 (m-80) REVERT: M 135 TYR cc_start: 0.7772 (m-80) cc_final: 0.7461 (m-10) REVERT: N 25 PRO cc_start: 0.7427 (Cg_exo) cc_final: 0.7127 (Cg_endo) REVERT: N 215 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8443 (p90) outliers start: 115 outliers final: 97 residues processed: 626 average time/residue: 1.0544 time to fit residues: 1097.2599 Evaluate side-chains 647 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 542 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain J residue 215 TYR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 215 TYR Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain L residue 215 TYR Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 272 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 215 TYR Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 249 LEU Chi-restraints excluded: chain M residue 291 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 228 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 267 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 3.9990 chunk 542 optimal weight: 3.9990 chunk 495 optimal weight: 3.9990 chunk 528 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 414 optimal weight: 0.4980 chunk 162 optimal weight: 2.9990 chunk 477 optimal weight: 3.9990 chunk 499 optimal weight: 3.9990 chunk 526 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 47894 Z= 0.202 Angle : 0.526 5.306 65394 Z= 0.273 Chirality : 0.045 0.143 6832 Planarity : 0.005 0.068 8554 Dihedral : 5.170 35.400 6468 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.01 % Allowed : 11.41 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % 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: -1.18 (0.11), residues: 5908 helix: 0.47 (0.17), residues: 966 sheet: -1.21 (0.12), residues: 1904 loop : -0.79 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 45 HIS 0.002 0.001 HIS H 107 PHE 0.008 0.001 PHE C 343 TYR 0.020 0.001 TYR I 215 ARG 0.003 0.000 ARG N 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 576 time to evaluate : 5.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8217 (mm) cc_final: 0.7843 (tp) REVERT: A 128 VAL cc_start: 0.9238 (t) cc_final: 0.8941 (p) REVERT: A 140 MET cc_start: 0.8831 (mmm) cc_final: 0.8286 (mtp) REVERT: A 215 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8471 (p90) REVERT: A 385 MET cc_start: 0.9188 (mmm) cc_final: 0.8893 (mmm) REVERT: B 41 MET cc_start: 0.6677 (mtt) cc_final: 0.6443 (mtt) REVERT: B 215 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8475 (p90) REVERT: C 128 VAL cc_start: 0.9285 (t) cc_final: 0.9032 (p) REVERT: C 135 TYR cc_start: 0.7760 (m-80) cc_final: 0.7451 (m-10) REVERT: C 350 ASP cc_start: 0.7900 (p0) cc_final: 0.7423 (p0) REVERT: D 25 PRO cc_start: 0.7491 (Cg_exo) cc_final: 0.7249 (Cg_endo) REVERT: D 168 THR cc_start: 0.8669 (m) cc_final: 0.8395 (t) REVERT: E 128 VAL cc_start: 0.9121 (t) cc_final: 0.8900 (p) REVERT: E 180 ASP cc_start: 0.8332 (t0) cc_final: 0.8100 (t0) REVERT: E 351 LYS cc_start: 0.8824 (mttt) cc_final: 0.8497 (mttp) REVERT: F 215 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8465 (p90) REVERT: F 314 TYR cc_start: 0.7854 (m-80) cc_final: 0.7220 (m-80) REVERT: G 314 TYR cc_start: 0.7655 (m-80) cc_final: 0.7088 (m-80) REVERT: H 128 VAL cc_start: 0.9262 (t) cc_final: 0.8999 (p) REVERT: H 140 MET cc_start: 0.8853 (mmm) cc_final: 0.8593 (mtp) REVERT: H 215 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8511 (p90) REVERT: H 385 MET cc_start: 0.9222 (mmm) cc_final: 0.8902 (mmm) REVERT: I 25 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6520 (Cg_endo) REVERT: I 180 ASP cc_start: 0.7985 (t0) cc_final: 0.7416 (t70) REVERT: J 140 MET cc_start: 0.9037 (mmm) cc_final: 0.8255 (mtp) REVERT: J 168 THR cc_start: 0.8949 (m) cc_final: 0.8575 (t) REVERT: J 215 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8519 (p90) REVERT: J 314 TYR cc_start: 0.8259 (m-80) cc_final: 0.7781 (m-80) REVERT: J 351 LYS cc_start: 0.8546 (mttt) cc_final: 0.8174 (mttp) REVERT: K 128 VAL cc_start: 0.9188 (t) cc_final: 0.8929 (p) REVERT: K 180 ASP cc_start: 0.8461 (t0) cc_final: 0.8210 (t0) REVERT: K 215 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7699 (p90) REVERT: K 314 TYR cc_start: 0.7499 (m-80) cc_final: 0.6944 (m-80) REVERT: L 168 THR cc_start: 0.8646 (m) cc_final: 0.8348 (t) REVERT: M 128 VAL cc_start: 0.9275 (t) cc_final: 0.8977 (p) REVERT: M 135 TYR cc_start: 0.7745 (m-80) cc_final: 0.7438 (m-10) REVERT: N 25 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.6991 (Cg_endo) REVERT: N 215 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8490 (p90) REVERT: N 304 TYR cc_start: 0.8188 (m-10) cc_final: 0.7970 (m-10) outliers start: 100 outliers final: 88 residues processed: 641 average time/residue: 1.0895 time to fit residues: 1165.2560 Evaluate side-chains 652 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 557 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain G residue 61 TYR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 215 TYR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 215 TYR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 215 TYR Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 272 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 215 TYR Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 228 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 267 SER Chi-restraints excluded: chain N residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 5.9990 chunk 558 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 585 optimal weight: 0.8980 chunk 539 optimal weight: 5.9990 chunk 466 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 360 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 47894 Z= 0.347 Angle : 0.584 5.366 65394 Z= 0.308 Chirality : 0.047 0.150 6832 Planarity : 0.005 0.072 8554 Dihedral : 5.458 42.022 6468 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.07 % Allowed : 11.61 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % 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: -1.41 (0.11), residues: 5908 helix: 0.25 (0.17), residues: 966 sheet: -1.37 (0.12), residues: 1904 loop : -0.93 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 227 HIS 0.004 0.001 HIS J 332 PHE 0.010 0.002 PHE E 245 TYR 0.026 0.002 TYR G 215 ARG 0.004 0.000 ARG N 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11816 Ramachandran restraints generated. 5908 Oldfield, 0 Emsley, 5908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 541 time to evaluate : 5.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8247 (mm) cc_final: 0.7865 (tp) REVERT: A 128 VAL cc_start: 0.9313 (t) cc_final: 0.9034 (p) REVERT: A 140 MET cc_start: 0.8871 (mmm) cc_final: 0.8300 (mtp) REVERT: A 215 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8554 (p90) REVERT: A 385 MET cc_start: 0.9224 (mmm) cc_final: 0.8945 (mmm) REVERT: B 41 MET cc_start: 0.6786 (mtt) cc_final: 0.6545 (mtt) REVERT: B 215 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8636 (p90) REVERT: C 128 VAL cc_start: 0.9308 (t) cc_final: 0.9050 (p) REVERT: C 135 TYR cc_start: 0.7832 (m-80) cc_final: 0.7529 (m-10) REVERT: C 350 ASP cc_start: 0.7958 (p0) cc_final: 0.7551 (p0) REVERT: E 128 VAL cc_start: 0.9172 (t) cc_final: 0.8962 (p) REVERT: F 215 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.8698 (p90) REVERT: G 314 TYR cc_start: 0.7821 (m-80) cc_final: 0.7269 (m-80) REVERT: H 128 VAL cc_start: 0.9333 (t) cc_final: 0.9040 (p) REVERT: H 215 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8645 (p90) REVERT: H 385 MET cc_start: 0.9203 (mmm) cc_final: 0.8882 (mmm) REVERT: I 25 PRO cc_start: 0.7022 (Cg_exo) cc_final: 0.6673 (Cg_endo) REVERT: J 140 MET cc_start: 0.9064 (mmm) cc_final: 0.8203 (mtp) REVERT: J 168 THR cc_start: 0.8987 (m) cc_final: 0.8602 (t) REVERT: J 215 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8778 (p90) REVERT: J 314 TYR cc_start: 0.8343 (m-80) cc_final: 0.7694 (m-80) REVERT: J 351 LYS cc_start: 0.8633 (mttt) cc_final: 0.8207 (mttp) REVERT: K 128 VAL cc_start: 0.9236 (t) cc_final: 0.8987 (p) REVERT: K 180 ASP cc_start: 0.8488 (t0) cc_final: 0.8171 (t0) REVERT: K 215 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7916 (p90) REVERT: K 304 TYR cc_start: 0.8104 (m-10) cc_final: 0.7853 (m-10) REVERT: K 314 TYR cc_start: 0.7675 (m-80) cc_final: 0.7037 (m-80) REVERT: L 351 LYS cc_start: 0.8669 (mttt) cc_final: 0.8233 (mttp) REVERT: M 128 VAL cc_start: 0.9311 (t) cc_final: 0.9049 (p) REVERT: M 135 TYR cc_start: 0.7772 (m-80) cc_final: 0.7459 (m-10) REVERT: N 25 PRO cc_start: 0.7431 (Cg_exo) cc_final: 0.7118 (Cg_endo) REVERT: N 215 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8600 (p90) outliers start: 103 outliers final: 93 residues processed: 612 average time/residue: 1.0955 time to fit residues: 1118.0718 Evaluate side-chains 633 residues out of total 4970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 533 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 227 TRP Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 233 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 233 TYR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 233 TYR Chi-restraints excluded: chain F residue 403 ASP Chi-restraints excluded: chain G residue 61 TYR Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 233 TYR Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain H residue 57 MET Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 215 TYR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 233 TYR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 215 TYR Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 233 TYR Chi-restraints excluded: chain K residue 173 SER Chi-restraints excluded: chain K residue 215 TYR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 233 TYR Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 215 TYR Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain L residue 233 TYR Chi-restraints excluded: chain L residue 272 SER Chi-restraints excluded: chain L residue 389 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 173 SER Chi-restraints excluded: chain M residue 215 TYR Chi-restraints excluded: chain M residue 233 TYR Chi-restraints excluded: chain M residue 349 LYS Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 TYR Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 215 TYR Chi-restraints excluded: chain N residue 228 SER Chi-restraints excluded: chain N residue 233 TYR Chi-restraints excluded: chain N residue 267 SER Chi-restraints excluded: chain N residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 3.9990 chunk 496 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 467 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 479 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** K 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.092887 restraints weight = 200324.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097001 restraints weight = 96207.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.099683 restraints weight = 60610.839| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 47894 Z= 0.227 Angle : 0.538 5.329 65394 Z= 0.280 Chirality : 0.045 0.145 6832 Planarity : 0.005 0.069 8554 Dihedral : 5.304 41.140 6468 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.11 % Allowed : 11.61 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 5908 helix: 0.38 (0.17), residues: 966 sheet: -1.36 (0.12), residues: 1904 loop : -0.87 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 45 HIS 0.003 0.001 HIS F 107 PHE 0.007 0.001 PHE C 343 TYR 0.023 0.002 TYR G 215 ARG 0.003 0.000 ARG N 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19469.73 seconds wall clock time: 342 minutes 35.22 seconds (20555.22 seconds total)