Starting phenix.real_space_refine on Wed Apr 10 09:12:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf6_22844/04_2024/7kf6_22844_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf6_22844/04_2024/7kf6_22844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf6_22844/04_2024/7kf6_22844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf6_22844/04_2024/7kf6_22844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf6_22844/04_2024/7kf6_22844_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kf6_22844/04_2024/7kf6_22844_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 23109 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Cu 3 5.60 5 S 108 5.16 5 C 15141 2.51 5 N 3915 2.21 5 O 4242 1.98 5 H 24189 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 41": "OD1" <-> "OD2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 617": "OD1" <-> "OD2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 830": "OD1" <-> "OD2" Residue "A ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 892": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 332": "OD1" <-> "OD2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 569": "OD1" <-> "OD2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "B ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 617": "OD1" <-> "OD2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 892": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 260": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ARG 292": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 298": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 332": "OD1" <-> "OD2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 417": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 519": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 523": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 569": "OD1" <-> "OD2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 617": "OD1" <-> "OD2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C ARG 654": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 730": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 771": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 777": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 784": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C ARG 819": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C ARG 831": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 892": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 893": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 949": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 982": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1011": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 47598 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 15865 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 Chain: "B" Number of atoms: 15864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 15864 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 Chain: "C" Number of atoms: 15866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 15866 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 52, 'TRANS': 962} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'CU1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'CU1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'CU1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.00, per 1000 atoms: 0.32 Number of scatterers: 47598 At special positions: 0 Unit cell: (125.28, 124.2, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 3 28.99 S 108 16.00 O 4242 8.00 N 3915 7.00 C 15141 6.00 H 24189 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.09 Conformation dependent library (CDL) restraints added in 3.6 seconds 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 21 sheets defined 52.9% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.207A pdb=" N ASN A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 66 through 75 removed outlier: 4.735A pdb=" N SER A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 113 removed outlier: 4.098A pdb=" N TYR A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 153 through 162 Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.644A pdb=" N LYS A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 170' Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 328 through 357 Processing helix chain 'A' and resid 361 through 384 removed outlier: 5.112A pdb=" N LEU A 370 " --> pdb=" O ILE A 367 " (cutoff:3.500A) Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 390 through 423 removed outlier: 3.626A pdb=" N ILE A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 466 removed outlier: 4.324A pdb=" N VAL A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 4.837A pdb=" N PHE A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 470 through 494 Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 518 through 556 Proline residue: A 527 - end of helix removed outlier: 4.024A pdb=" N HIS A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TRP A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Proline residue: A 536 - end of helix removed outlier: 3.528A pdb=" N THR A 539 " --> pdb=" O TRP A 535 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU A 551 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Proline residue: A 553 - end of helix removed outlier: 3.632A pdb=" N LYS A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 597 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 690 through 706 removed outlier: 4.098A pdb=" N GLU A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 740 through 752 removed outlier: 4.150A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 783 No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 836 through 847 Processing helix chain 'A' and resid 861 through 887 removed outlier: 4.842A pdb=" N ASN A 869 " --> pdb=" O GLU A 866 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL A 876 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Proline residue: A 877 - end of helix removed outlier: 4.073A pdb=" N VAL A 885 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 918 Proline residue: A 905 - end of helix removed outlier: 4.467A pdb=" N LEU A 914 " --> pdb=" O GLY A 910 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP A 916 " --> pdb=" O ILE A 912 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP A 917 " --> pdb=" O TRP A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 952 Processing helix chain 'A' and resid 955 through 960 removed outlier: 4.622A pdb=" N ASN A 960 " --> pdb=" O SER A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 977 Processing helix chain 'A' and resid 981 through 999 Proline residue: A 997 - end of helix Processing helix chain 'A' and resid 1006 through 1019 Proline residue: A1015 - end of helix Processing helix chain 'A' and resid 1023 through 1036 removed outlier: 3.653A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1032 - end of helix Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.208A pdb=" N ASN B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 14 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 66 through 75 removed outlier: 4.734A pdb=" N SER B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 4.097A pdb=" N TYR B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.644A pdb=" N LYS B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N THR B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 328 through 357 Processing helix chain 'B' and resid 361 through 384 removed outlier: 5.111A pdb=" N LEU B 370 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 390 through 423 removed outlier: 3.625A pdb=" N ILE B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 466 removed outlier: 4.323A pdb=" N VAL B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 448 - end of helix removed outlier: 4.836A pdb=" N PHE B 461 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Proline residue: B 463 - end of helix Processing helix chain 'B' and resid 470 through 494 Proline residue: B 477 - end of helix Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 518 through 556 Proline residue: B 527 - end of helix removed outlier: 4.024A pdb=" N HIS B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Proline residue: B 536 - end of helix removed outlier: 3.528A pdb=" N THR B 539 " --> pdb=" O TRP B 535 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Proline residue: B 553 - end of helix removed outlier: 3.630A pdb=" N LYS B 556 " --> pdb=" O TRP B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 642 through 652 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 690 through 706 removed outlier: 4.098A pdb=" N GLU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 736 Processing helix chain 'B' and resid 740 through 752 removed outlier: 4.150A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 783 No H-bonds generated for 'chain 'B' and resid 780 through 783' Processing helix chain 'B' and resid 836 through 847 Processing helix chain 'B' and resid 861 through 887 removed outlier: 4.843A pdb=" N ASN B 869 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL B 876 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Proline residue: B 877 - end of helix removed outlier: 4.072A pdb=" N VAL B 885 " --> pdb=" O ILE B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 918 Proline residue: B 905 - end of helix removed outlier: 4.466A pdb=" N LEU B 914 " --> pdb=" O GLY B 910 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 915 " --> pdb=" O GLY B 911 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP B 916 " --> pdb=" O ILE B 912 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N TRP B 917 " --> pdb=" O TRP B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 952 Processing helix chain 'B' and resid 955 through 960 removed outlier: 4.621A pdb=" N ASN B 960 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 977 Processing helix chain 'B' and resid 981 through 999 Proline residue: B 997 - end of helix Processing helix chain 'B' and resid 1006 through 1019 Proline residue: B1015 - end of helix Processing helix chain 'B' and resid 1023 through 1036 removed outlier: 3.652A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1032 - end of helix Processing helix chain 'C' and resid 7 through 32 removed outlier: 4.207A pdb=" N ASN C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 66 through 75 removed outlier: 4.733A pdb=" N SER C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 removed outlier: 4.098A pdb=" N TYR C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.646A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR C 170 " --> pdb=" O TYR C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 170' Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 328 through 357 Processing helix chain 'C' and resid 361 through 384 removed outlier: 5.111A pdb=" N LEU C 370 " --> pdb=" O ILE C 367 " (cutoff:3.500A) Proline residue: C 371 - end of helix Processing helix chain 'C' and resid 390 through 423 removed outlier: 3.625A pdb=" N ILE C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ALA C 406 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 466 removed outlier: 4.325A pdb=" N VAL C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Proline residue: C 448 - end of helix removed outlier: 4.835A pdb=" N PHE C 461 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) Proline residue: C 463 - end of helix Processing helix chain 'C' and resid 470 through 494 Proline residue: C 477 - end of helix Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'C' and resid 518 through 556 Proline residue: C 527 - end of helix removed outlier: 4.025A pdb=" N HIS C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TRP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Proline residue: C 536 - end of helix removed outlier: 3.528A pdb=" N THR C 539 " --> pdb=" O TRP C 535 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C 551 " --> pdb=" O VAL C 547 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Proline residue: C 553 - end of helix removed outlier: 3.632A pdb=" N LYS C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 597 Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 642 through 652 Processing helix chain 'C' and resid 665 through 673 Processing helix chain 'C' and resid 690 through 706 removed outlier: 4.099A pdb=" N GLU C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 736 Processing helix chain 'C' and resid 740 through 752 removed outlier: 4.150A pdb=" N PHE C 746 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL C 751 " --> pdb=" O VAL C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 783 No H-bonds generated for 'chain 'C' and resid 780 through 783' Processing helix chain 'C' and resid 836 through 847 Processing helix chain 'C' and resid 861 through 887 removed outlier: 4.843A pdb=" N ASN C 869 " --> pdb=" O GLU C 866 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N VAL C 876 " --> pdb=" O LYS C 873 " (cutoff:3.500A) Proline residue: C 877 - end of helix removed outlier: 4.073A pdb=" N VAL C 885 " --> pdb=" O ILE C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 918 Proline residue: C 905 - end of helix removed outlier: 4.466A pdb=" N LEU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU C 915 " --> pdb=" O GLY C 911 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP C 916 " --> pdb=" O ILE C 912 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP C 917 " --> pdb=" O TRP C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 952 Processing helix chain 'C' and resid 955 through 960 removed outlier: 4.622A pdb=" N ASN C 960 " --> pdb=" O SER C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 977 Processing helix chain 'C' and resid 981 through 999 Proline residue: C 997 - end of helix Processing helix chain 'C' and resid 1006 through 1019 Proline residue: C1015 - end of helix Processing helix chain 'C' and resid 1023 through 1036 removed outlier: 3.653A pdb=" N ILE C1031 " --> pdb=" O SER C1027 " (cutoff:3.500A) Proline residue: C1032 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 46 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 177 through 180 removed outlier: 4.065A pdb=" N ALA A 285 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 140 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 325 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA A 143 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N THR A 323 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 145 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE A 321 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 263 through 269 Processing sheet with id= D, first strand: chain 'A' and resid 274 through 277 removed outlier: 6.828A pdb=" N GLN A 629 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 605 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 627 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY A 607 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 625 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 820 through 826 Processing sheet with id= F, first strand: chain 'A' and resid 758 through 760 Processing sheet with id= G, first strand: chain 'A' and resid 719 through 728 removed outlier: 5.649A pdb=" N GLY A 809 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG A 722 " --> pdb=" O SER A 807 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER A 807 " --> pdb=" O ARG A 722 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE A 724 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS A 805 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 726 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP A 803 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 Processing sheet with id= I, first strand: chain 'B' and resid 177 through 180 removed outlier: 4.067A pdb=" N ALA B 285 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 140 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 325 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 143 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR B 323 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 145 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE B 321 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 263 through 269 Processing sheet with id= K, first strand: chain 'B' and resid 274 through 277 removed outlier: 6.831A pdb=" N GLN B 629 " --> pdb=" O ALA B 603 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 605 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR B 627 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLY B 607 " --> pdb=" O GLU B 625 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU B 625 " --> pdb=" O GLY B 607 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 820 through 826 Processing sheet with id= M, first strand: chain 'B' and resid 758 through 760 Processing sheet with id= N, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.649A pdb=" N GLY B 809 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG B 722 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER B 807 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 724 " --> pdb=" O LYS B 805 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS B 805 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 726 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 803 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 46 through 52 Processing sheet with id= P, first strand: chain 'C' and resid 177 through 180 removed outlier: 4.067A pdb=" N ALA C 285 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR C 140 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 325 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA C 143 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR C 323 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 145 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE C 321 " --> pdb=" O VAL C 145 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 263 through 269 Processing sheet with id= R, first strand: chain 'C' and resid 274 through 277 removed outlier: 6.831A pdb=" N GLN C 629 " --> pdb=" O ALA C 603 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL C 605 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 627 " --> pdb=" O VAL C 605 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY C 607 " --> pdb=" O GLU C 625 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU C 625 " --> pdb=" O GLY C 607 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 820 through 826 Processing sheet with id= T, first strand: chain 'C' and resid 758 through 760 Processing sheet with id= U, first strand: chain 'C' and resid 719 through 728 removed outlier: 5.648A pdb=" N GLY C 809 " --> pdb=" O GLY C 720 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ARG C 722 " --> pdb=" O SER C 807 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER C 807 " --> pdb=" O ARG C 722 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE C 724 " --> pdb=" O LYS C 805 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C 805 " --> pdb=" O ILE C 724 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL C 726 " --> pdb=" O ASP C 803 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP C 803 " --> pdb=" O VAL C 726 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 3051 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: 15.68 Time building geometry restraints manager: 29.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 24183 1.03 - 1.23: 18 1.23 - 1.42: 9471 1.42 - 1.62: 14187 1.62 - 1.81: 210 Bond restraints: 48069 Sorted by residual: bond pdb=" C MET C 672 " pdb=" N LEU C 673 " ideal model delta sigma weight residual 1.335 1.280 0.055 1.38e-02 5.25e+03 1.60e+01 bond pdb=" C MET B 672 " pdb=" N LEU B 673 " ideal model delta sigma weight residual 1.335 1.286 0.049 1.38e-02 5.25e+03 1.24e+01 bond pdb=" C MET A 672 " pdb=" N LEU A 673 " ideal model delta sigma weight residual 1.335 1.289 0.046 1.38e-02 5.25e+03 1.13e+01 bond pdb=" N GLU B 625 " pdb=" H GLU B 625 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" N MET B 573 " pdb=" H MET B 573 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 48064 not shown) Histogram of bond angle deviations from ideal: 75.92 - 87.55: 6 87.55 - 99.17: 3 99.17 - 110.80: 53378 110.80 - 122.42: 27930 122.42 - 134.05: 6173 Bond angle restraints: 87490 Sorted by residual: angle pdb=" CB LEU C 492 " pdb=" CG LEU C 492 " pdb=" HG LEU C 492 " ideal model delta sigma weight residual 109.00 76.43 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CB LEU B 673 " pdb=" CG LEU B 673 " pdb=" HG LEU B 673 " ideal model delta sigma weight residual 109.00 76.61 32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" CD1 LEU B 673 " pdb=" CG LEU B 673 " pdb=" HG LEU B 673 " ideal model delta sigma weight residual 108.00 75.92 32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" CD2 LEU C 492 " pdb=" CG LEU C 492 " pdb=" HG LEU C 492 " ideal model delta sigma weight residual 108.00 76.07 31.93 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CD2 LEU B 673 " pdb=" CG LEU B 673 " pdb=" HG LEU B 673 " ideal model delta sigma weight residual 108.00 76.24 31.76 3.00e+00 1.11e-01 1.12e+02 ... (remaining 87485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 20353 17.51 - 35.02: 1442 35.02 - 52.52: 454 52.52 - 70.03: 132 70.03 - 87.54: 12 Dihedral angle restraints: 22393 sinusoidal: 12400 harmonic: 9993 Sorted by residual: dihedral pdb=" C MET B 672 " pdb=" N MET B 672 " pdb=" CA MET B 672 " pdb=" CB MET B 672 " ideal model delta harmonic sigma weight residual -122.60 -112.84 -9.76 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" C MET C 672 " pdb=" N MET C 672 " pdb=" CA MET C 672 " pdb=" CB MET C 672 " ideal model delta harmonic sigma weight residual -122.60 -112.97 -9.63 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" CA GLU B 228 " pdb=" C GLU B 228 " pdb=" N TYR B 229 " pdb=" CA TYR B 229 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 22390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3722 0.100 - 0.200: 133 0.200 - 0.300: 0 0.300 - 0.399: 3 0.399 - 0.499: 6 Chirality restraints: 3864 Sorted by residual: chirality pdb=" CG LEU C 492 " pdb=" CB LEU C 492 " pdb=" CD1 LEU C 492 " pdb=" CD2 LEU C 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" CG LEU A 492 " pdb=" CB LEU A 492 " pdb=" CD1 LEU A 492 " pdb=" CD2 LEU A 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CG LEU B 492 " pdb=" CB LEU B 492 " pdb=" CD1 LEU B 492 " pdb=" CD2 LEU B 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.05e+00 ... (remaining 3861 not shown) Planarity restraints: 6969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 967 " 0.161 2.00e-02 2.50e+03 1.77e-01 4.70e+02 pdb=" CD GLN B 967 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 967 " -0.156 2.00e-02 2.50e+03 pdb=" NE2 GLN B 967 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 967 " -0.261 2.00e-02 2.50e+03 pdb="HE22 GLN B 967 " 0.264 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 967 " -0.159 2.00e-02 2.50e+03 1.73e-01 4.51e+02 pdb=" CD GLN C 967 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN C 967 " 0.153 2.00e-02 2.50e+03 pdb=" NE2 GLN C 967 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN C 967 " 0.255 2.00e-02 2.50e+03 pdb="HE22 GLN C 967 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 967 " -0.152 2.00e-02 2.50e+03 1.66e-01 4.11e+02 pdb=" CD GLN A 967 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN A 967 " 0.147 2.00e-02 2.50e+03 pdb=" NE2 GLN A 967 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 967 " 0.243 2.00e-02 2.50e+03 pdb="HE22 GLN A 967 " -0.246 2.00e-02 2.50e+03 ... (remaining 6966 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1761 2.15 - 2.76: 92315 2.76 - 3.37: 134117 3.37 - 3.99: 165693 3.99 - 4.60: 259628 Nonbonded interactions: 653514 Sorted by model distance: nonbonded pdb=" O GLY B 469 " pdb=" H ARG B 473 " model vdw 1.533 1.850 nonbonded pdb=" O GLY C 469 " pdb=" H ARG C 473 " model vdw 1.534 1.850 nonbonded pdb=" O GLY A 469 " pdb=" H ARG A 473 " model vdw 1.535 1.850 nonbonded pdb=" H GLY C 721 " pdb=" O GLY C 809 " model vdw 1.577 1.850 nonbonded pdb=" H GLY B 721 " pdb=" O GLY B 809 " model vdw 1.577 1.850 ... (remaining 653509 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' and (resid 5 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 116 through 1039 or resid 1101)) selection = chain 'B' selection = (chain 'C' and (resid 5 through 114 or (resid 115 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 116 through 1039 or resid 1101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.510 Extract box with map and model: 2.850 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 112.210 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 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 : 0.003 0.055 23880 Z= 0.166 Angle : 0.530 6.127 32502 Z= 0.296 Chirality : 0.045 0.499 3864 Planarity : 0.003 0.035 4086 Dihedral : 12.630 84.998 8715 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.14), residues: 3027 helix: -1.37 (0.12), residues: 1587 sheet: -2.19 (0.21), residues: 441 loop : -3.25 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 421 HIS 0.001 0.000 HIS A 382 PHE 0.005 0.001 PHE A 243 TYR 0.033 0.001 TYR B 947 ARG 0.002 0.000 ARG B 637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 841 time to evaluate : 2.611 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: A 700 ILE cc_start: 0.7198 (mm) cc_final: 0.6973 (mm) REVERT: B 26 TRP cc_start: 0.7034 (t60) cc_final: 0.6821 (t60) REVERT: B 110 VAL cc_start: 0.8607 (p) cc_final: 0.8378 (t) REVERT: C 408 ILE cc_start: 0.7586 (mt) cc_final: 0.7206 (mt) REVERT: C 412 GLU cc_start: 0.6156 (tm-30) cc_final: 0.5689 (tm-30) REVERT: C 1020 MET cc_start: 0.6370 (mmp) cc_final: 0.5782 (mmp) outliers start: 0 outliers final: 0 residues processed: 841 average time/residue: 0.7587 time to fit residues: 948.7081 Evaluate side-chains 554 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 382 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 23880 Z= 0.414 Angle : 0.700 12.039 32502 Z= 0.365 Chirality : 0.058 1.634 3864 Planarity : 0.005 0.054 4086 Dihedral : 4.464 24.098 3261 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.66 % Favored : 92.17 % Rotamer: Outliers : 2.32 % Allowed : 11.18 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.15), residues: 3027 helix: -0.58 (0.13), residues: 1584 sheet: -1.82 (0.21), residues: 468 loop : -2.94 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 636 HIS 0.037 0.002 HIS B 526 PHE 0.022 0.002 PHE B 746 TYR 0.041 0.003 TYR B 229 ARG 0.006 0.001 ARG A 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 623 time to evaluate : 2.624 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 804 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6743 (mt) REVERT: B 947 TYR cc_start: 0.7204 (m-10) cc_final: 0.6997 (m-80) REVERT: C 580 ILE cc_start: 0.8192 (tp) cc_final: 0.7934 (tp) REVERT: C 1020 MET cc_start: 0.6796 (mmp) cc_final: 0.6162 (mmp) outliers start: 58 outliers final: 38 residues processed: 652 average time/residue: 0.7334 time to fit residues: 730.2803 Evaluate side-chains 599 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 560 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 847 LYS Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 923 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 75 optimal weight: 0.0970 chunk 275 optimal weight: 0.4980 chunk 297 optimal weight: 0.2980 chunk 245 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23880 Z= 0.162 Angle : 0.558 10.184 32502 Z= 0.278 Chirality : 0.056 1.704 3864 Planarity : 0.004 0.037 4086 Dihedral : 4.058 21.457 3261 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 1.24 % Allowed : 13.61 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3027 helix: -0.00 (0.13), residues: 1590 sheet: -1.42 (0.23), residues: 423 loop : -2.68 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 358 HIS 0.007 0.001 HIS C 526 PHE 0.016 0.001 PHE C 465 TYR 0.019 0.001 TYR C 229 ARG 0.005 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 583 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 ILE cc_start: 0.6914 (pt) cc_final: 0.6676 (mt) REVERT: C 580 ILE cc_start: 0.8124 (tp) cc_final: 0.7886 (tp) REVERT: C 986 MET cc_start: 0.7142 (mtp) cc_final: 0.6841 (mtm) REVERT: C 1020 MET cc_start: 0.6651 (mmp) cc_final: 0.5957 (mmp) outliers start: 31 outliers final: 26 residues processed: 597 average time/residue: 0.7133 time to fit residues: 644.8427 Evaluate side-chains 571 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 545 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 913 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 276 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 262 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23880 Z= 0.168 Angle : 0.549 10.111 32502 Z= 0.272 Chirality : 0.056 1.709 3864 Planarity : 0.004 0.039 4086 Dihedral : 3.953 20.743 3261 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 1.32 % Allowed : 14.21 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 3027 helix: 0.30 (0.13), residues: 1590 sheet: -1.32 (0.23), residues: 432 loop : -2.38 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS C 415 PHE 0.013 0.001 PHE C 480 TYR 0.020 0.001 TYR A 229 ARG 0.004 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 567 time to evaluate : 2.644 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: B 1012 ILE cc_start: 0.7097 (mt) cc_final: 0.6879 (mm) REVERT: C 580 ILE cc_start: 0.8134 (tp) cc_final: 0.7865 (tp) REVERT: C 1020 MET cc_start: 0.6675 (mmp) cc_final: 0.5967 (mmp) outliers start: 33 outliers final: 26 residues processed: 576 average time/residue: 0.7131 time to fit residues: 618.8906 Evaluate side-chains 569 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 543 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23880 Z= 0.264 Angle : 0.590 10.269 32502 Z= 0.301 Chirality : 0.057 1.702 3864 Planarity : 0.004 0.064 4086 Dihedral : 4.257 24.661 3261 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.20 % Favored : 92.70 % Rotamer: Outliers : 2.08 % Allowed : 14.85 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 3027 helix: 0.28 (0.13), residues: 1605 sheet: -1.35 (0.23), residues: 450 loop : -2.42 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS B 526 PHE 0.018 0.001 PHE C 746 TYR 0.017 0.002 TYR A 974 ARG 0.007 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 567 time to evaluate : 2.659 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: A 132 ASP cc_start: 0.7522 (t0) cc_final: 0.7282 (t0) REVERT: B 18 MET cc_start: 0.7042 (mmp) cc_final: 0.6839 (mmp) REVERT: B 893 ARG cc_start: 0.6476 (mtp85) cc_final: 0.6201 (mtp85) REVERT: B 1012 ILE cc_start: 0.7422 (mt) cc_final: 0.7208 (mm) REVERT: C 18 MET cc_start: 0.7022 (mmp) cc_final: 0.6789 (mmp) REVERT: C 580 ILE cc_start: 0.8218 (tp) cc_final: 0.7956 (tp) outliers start: 52 outliers final: 39 residues processed: 590 average time/residue: 0.7223 time to fit residues: 643.9433 Evaluate side-chains 577 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 538 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 153 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23880 Z= 0.232 Angle : 0.572 10.321 32502 Z= 0.290 Chirality : 0.057 1.722 3864 Planarity : 0.004 0.057 4086 Dihedral : 4.234 24.326 3261 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.24 % Favored : 93.66 % Rotamer: Outliers : 2.20 % Allowed : 15.61 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 3027 helix: 0.44 (0.13), residues: 1617 sheet: -1.16 (0.24), residues: 411 loop : -2.37 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 636 HIS 0.005 0.001 HIS A 526 PHE 0.013 0.001 PHE C 14 TYR 0.018 0.001 TYR A 229 ARG 0.007 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 567 time to evaluate : 2.685 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: A 132 ASP cc_start: 0.7620 (t0) cc_final: 0.7222 (t0) REVERT: C 580 ILE cc_start: 0.8211 (tp) cc_final: 0.7966 (tp) REVERT: C 869 ASN cc_start: 0.7281 (p0) cc_final: 0.7025 (p0) outliers start: 55 outliers final: 46 residues processed: 588 average time/residue: 0.7552 time to fit residues: 674.3913 Evaluate side-chains 595 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 549 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 700 ILE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23880 Z= 0.363 Angle : 0.641 10.305 32502 Z= 0.334 Chirality : 0.058 1.693 3864 Planarity : 0.005 0.051 4086 Dihedral : 4.620 26.190 3261 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.16 % Favored : 91.74 % Rotamer: Outliers : 2.87 % Allowed : 16.13 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 3027 helix: 0.16 (0.13), residues: 1620 sheet: -1.56 (0.23), residues: 441 loop : -2.41 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1000 HIS 0.009 0.001 HIS A 526 PHE 0.020 0.002 PHE C 746 TYR 0.017 0.002 TYR C 104 ARG 0.007 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 576 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7734 (t0) cc_final: 0.7333 (t0) REVERT: A 226 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: B 26 TRP cc_start: 0.7808 (t60) cc_final: 0.7590 (t60) REVERT: B 869 ASN cc_start: 0.6858 (p0) cc_final: 0.6646 (p0) REVERT: C 580 ILE cc_start: 0.8102 (tp) cc_final: 0.7884 (tp) REVERT: C 869 ASN cc_start: 0.7453 (p0) cc_final: 0.7191 (p0) REVERT: C 1016 MET cc_start: 0.6485 (mmt) cc_final: 0.6166 (mmt) REVERT: C 1020 MET cc_start: 0.6953 (mmp) cc_final: 0.6358 (mmp) outliers start: 72 outliers final: 62 residues processed: 612 average time/residue: 0.6991 time to fit residues: 649.9394 Evaluate side-chains 613 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 550 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 821 THR Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 0.2980 chunk 116 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 198 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23880 Z= 0.163 Angle : 0.568 10.518 32502 Z= 0.284 Chirality : 0.057 1.726 3864 Planarity : 0.004 0.049 4086 Dihedral : 4.232 23.483 3261 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 1.76 % Allowed : 18.04 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 3027 helix: 0.66 (0.13), residues: 1617 sheet: -1.13 (0.24), residues: 402 loop : -2.18 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 823 HIS 0.006 0.001 HIS A 415 PHE 0.014 0.001 PHE A 480 TYR 0.013 0.001 TYR C 974 ARG 0.010 0.000 ARG C 722 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 571 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7578 (t0) cc_final: 0.7258 (t0) REVERT: B 30 THR cc_start: 0.8098 (t) cc_final: 0.7780 (m) REVERT: B 997 PRO cc_start: 0.6924 (Cg_endo) cc_final: 0.6708 (Cg_exo) REVERT: C 30 THR cc_start: 0.8080 (t) cc_final: 0.7860 (m) REVERT: C 580 ILE cc_start: 0.8200 (tp) cc_final: 0.7953 (tp) REVERT: C 869 ASN cc_start: 0.7471 (p0) cc_final: 0.7206 (p0) outliers start: 44 outliers final: 37 residues processed: 586 average time/residue: 0.7233 time to fit residues: 643.9200 Evaluate side-chains 595 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 558 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 902 SER Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23880 Z= 0.255 Angle : 0.587 10.325 32502 Z= 0.299 Chirality : 0.057 1.696 3864 Planarity : 0.004 0.055 4086 Dihedral : 4.335 25.615 3261 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 1.92 % Allowed : 18.24 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 3027 helix: 0.53 (0.13), residues: 1629 sheet: -1.43 (0.23), residues: 441 loop : -2.24 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1000 HIS 0.007 0.001 HIS A 415 PHE 0.013 0.001 PHE C 746 TYR 0.014 0.001 TYR C 974 ARG 0.006 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 565 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7644 (t0) cc_final: 0.7264 (t0) REVERT: B 30 THR cc_start: 0.8323 (t) cc_final: 0.7988 (m) REVERT: B 997 PRO cc_start: 0.6912 (Cg_endo) cc_final: 0.6695 (Cg_exo) REVERT: C 30 THR cc_start: 0.8165 (t) cc_final: 0.7939 (m) REVERT: C 580 ILE cc_start: 0.8271 (tp) cc_final: 0.8018 (tp) REVERT: C 869 ASN cc_start: 0.7478 (p0) cc_final: 0.7233 (p0) outliers start: 48 outliers final: 43 residues processed: 584 average time/residue: 0.7416 time to fit residues: 663.5625 Evaluate side-chains 598 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 555 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 902 SER Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 277 optimal weight: 8.9990 chunk 240 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23880 Z= 0.305 Angle : 0.622 10.224 32502 Z= 0.321 Chirality : 0.058 1.709 3864 Planarity : 0.005 0.077 4086 Dihedral : 4.563 27.250 3261 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 2.04 % Allowed : 18.40 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3027 helix: 0.34 (0.13), residues: 1629 sheet: -1.32 (0.24), residues: 411 loop : -2.40 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1000 HIS 0.010 0.001 HIS A 415 PHE 0.016 0.002 PHE A 480 TYR 0.016 0.002 TYR C 974 ARG 0.011 0.001 ARG A 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 573 time to evaluate : 2.646 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: A 132 ASP cc_start: 0.7670 (t0) cc_final: 0.7313 (t0) REVERT: A 884 PHE cc_start: 0.7179 (t80) cc_final: 0.6978 (t80) REVERT: B 30 THR cc_start: 0.8388 (t) cc_final: 0.8035 (m) REVERT: B 281 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: C 30 THR cc_start: 0.8217 (t) cc_final: 0.7992 (m) REVERT: C 128 GLU cc_start: 0.6571 (mp0) cc_final: 0.6349 (mp0) REVERT: C 132 ASP cc_start: 0.7564 (t0) cc_final: 0.7276 (t0) REVERT: C 580 ILE cc_start: 0.8145 (tp) cc_final: 0.7939 (tp) REVERT: C 869 ASN cc_start: 0.7486 (p0) cc_final: 0.7236 (p0) outliers start: 51 outliers final: 45 residues processed: 596 average time/residue: 0.7166 time to fit residues: 650.0425 Evaluate side-chains 611 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 565 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 229 TYR Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 581 SER Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 923 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 923 SER Chi-restraints excluded: chain C residue 992 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123086 restraints weight = 122611.565| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.22 r_work: 0.3364 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23880 Z= 0.206 Angle : 0.589 10.429 32502 Z= 0.299 Chirality : 0.057 1.709 3864 Planarity : 0.004 0.061 4086 Dihedral : 4.409 27.181 3261 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.90 % Rotamer: Outliers : 2.12 % Allowed : 18.68 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3027 helix: 0.53 (0.13), residues: 1626 sheet: -1.28 (0.24), residues: 411 loop : -2.28 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 358 HIS 0.008 0.001 HIS A 415 PHE 0.015 0.001 PHE A 480 TYR 0.015 0.001 TYR C 974 ARG 0.010 0.000 ARG C 722 =============================================================================== Job complete usr+sys time: 11171.32 seconds wall clock time: 192 minutes 53.79 seconds (11573.79 seconds total)