Starting phenix.real_space_refine (version: dev) on Sat Apr 9 18:16:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osl_13054/04_2022/7osl_13054_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osl_13054/04_2022/7osl_13054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osl_13054/04_2022/7osl_13054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osl_13054/04_2022/7osl_13054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osl_13054/04_2022/7osl_13054_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7osl_13054/04_2022/7osl_13054_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 365": "OD1" <-> "OD2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 548": "OE1" <-> "OE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 417": "OD1" <-> "OD2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ASP 460": "OD1" <-> "OD2" Residue "C PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 548": "OE1" <-> "OE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 587": "OE1" <-> "OE2" Residue "C TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 663": "OE1" <-> "OE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "D TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D ASP 460": "OD1" <-> "OD2" Residue "D PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 495": "OD1" <-> "OD2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 548": "OE1" <-> "OE2" Residue "D TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 587": "OE1" <-> "OE2" Residue "D TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 365": "OD1" <-> "OD2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "E TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 431": "OE1" <-> "OE2" Residue "E ASP 460": "OD1" <-> "OD2" Residue "E PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 495": "OD1" <-> "OD2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 548": "OE1" <-> "OE2" Residue "E TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 587": "OE1" <-> "OE2" Residue "E TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 663": "OE1" <-> "OE2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 365": "OD1" <-> "OD2" Residue "F GLU 371": "OE1" <-> "OE2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "F GLU 401": "OE1" <-> "OE2" Residue "F TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 407": "OE1" <-> "OE2" Residue "F TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 417": "OD1" <-> "OD2" Residue "F TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "F ASP 460": "OD1" <-> "OD2" Residue "F PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 495": "OD1" <-> "OD2" Residue "F GLU 527": "OE1" <-> "OE2" Residue "F PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 548": "OE1" <-> "OE2" Residue "F TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 663": "OE1" <-> "OE2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 365": "OD1" <-> "OD2" Residue "G GLU 371": "OE1" <-> "OE2" Residue "G GLU 379": "OE1" <-> "OE2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "G GLU 401": "OE1" <-> "OE2" Residue "G TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "G TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 417": "OD1" <-> "OD2" Residue "G TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 431": "OE1" <-> "OE2" Residue "G ASP 460": "OD1" <-> "OD2" Residue "G PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 495": "OD1" <-> "OD2" Residue "G GLU 527": "OE1" <-> "OE2" Residue "G PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 548": "OE1" <-> "OE2" Residue "G TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 587": "OE1" <-> "OE2" Residue "G TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 663": "OE1" <-> "OE2" Residue "H TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 365": "OD1" <-> "OD2" Residue "H GLU 371": "OE1" <-> "OE2" Residue "H GLU 379": "OE1" <-> "OE2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "H GLU 401": "OE1" <-> "OE2" Residue "H TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 407": "OE1" <-> "OE2" Residue "H TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 417": "OD1" <-> "OD2" Residue "H TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 431": "OE1" <-> "OE2" Residue "H ASP 460": "OD1" <-> "OD2" Residue "H PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 495": "OD1" <-> "OD2" Residue "H GLU 527": "OE1" <-> "OE2" Residue "H PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 548": "OE1" <-> "OE2" Residue "H TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 587": "OE1" <-> "OE2" Residue "H TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 663": "OE1" <-> "OE2" Residue "I TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 365": "OD1" <-> "OD2" Residue "I GLU 371": "OE1" <-> "OE2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "I GLU 380": "OE1" <-> "OE2" Residue "I GLU 401": "OE1" <-> "OE2" Residue "I TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 407": "OE1" <-> "OE2" Residue "I TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 417": "OD1" <-> "OD2" Residue "I TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 431": "OE1" <-> "OE2" Residue "I ASP 460": "OD1" <-> "OD2" Residue "I PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 495": "OD1" <-> "OD2" Residue "I GLU 527": "OE1" <-> "OE2" Residue "I PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 548": "OE1" <-> "OE2" Residue "I TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 587": "OE1" <-> "OE2" Residue "I TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 663": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 47885 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "B" Number of atoms: 5333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5333 Classifications: {'peptide': 327} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 317} Chain: "C" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "D" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "E" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "F" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "G" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "H" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "I" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Time building chain proxies: 21.27, per 1000 atoms: 0.44 Number of scatterers: 47885 At special positions: 0 Unit cell: (182.6, 180.4, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 4511 8.00 N 3935 7.00 C 15151 6.00 H 24225 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: 39.93 Conformation dependent library (CDL) restraints added in 4.1 seconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5582 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 36 sheets defined 49.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 365 through 382 removed outlier: 3.928A pdb=" N TRP A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.858A pdb=" N ILE A 485 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 496 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.674A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.601A pdb=" N ILE A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 4.266A pdb=" N GLU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 606 through 621 Processing helix chain 'A' and resid 632 through 644 removed outlier: 4.846A pdb=" N ARG A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 removed outlier: 3.898A pdb=" N TRP B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.874A pdb=" N ILE B 485 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 496 Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.688A pdb=" N ASP B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.588A pdb=" N ILE B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.247A pdb=" N GLU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 583 through 593 Processing helix chain 'B' and resid 606 through 621 Processing helix chain 'B' and resid 632 through 644 removed outlier: 4.854A pdb=" N ARG B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 382 removed outlier: 3.863A pdb=" N TRP C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.572A pdb=" N ALA C 454 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.879A pdb=" N ILE C 485 " --> pdb=" O LYS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 496 Processing helix chain 'C' and resid 501 through 512 Processing helix chain 'C' and resid 513 through 526 removed outlier: 3.662A pdb=" N ASP C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.601A pdb=" N ILE C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.505A pdb=" N CYS C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 571 Processing helix chain 'C' and resid 583 through 593 Processing helix chain 'C' and resid 606 through 621 Processing helix chain 'C' and resid 632 through 644 removed outlier: 4.844A pdb=" N ARG C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 382 removed outlier: 3.868A pdb=" N TRP D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 Processing helix chain 'D' and resid 464 through 480 Processing helix chain 'D' and resid 481 through 485 removed outlier: 3.861A pdb=" N ILE D 485 " --> pdb=" O LYS D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 496 Processing helix chain 'D' and resid 501 through 512 Processing helix chain 'D' and resid 513 through 526 removed outlier: 3.690A pdb=" N ASP D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.615A pdb=" N ILE D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 4.277A pdb=" N GLU D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 557 " --> pdb=" O ILE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 606 through 621 Processing helix chain 'D' and resid 632 through 644 removed outlier: 4.838A pdb=" N ARG D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR D 638 " --> pdb=" O ASP D 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 382 removed outlier: 3.882A pdb=" N TRP E 375 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 458 Processing helix chain 'E' and resid 464 through 480 Processing helix chain 'E' and resid 481 through 485 removed outlier: 3.872A pdb=" N ILE E 485 " --> pdb=" O LYS E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 496 Processing helix chain 'E' and resid 501 through 512 Processing helix chain 'E' and resid 513 through 526 removed outlier: 3.698A pdb=" N ASP E 519 " --> pdb=" O SER E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.605A pdb=" N ILE E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 562 removed outlier: 4.233A pdb=" N GLU E 556 " --> pdb=" O VAL E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 571 Processing helix chain 'E' and resid 583 through 593 Processing helix chain 'E' and resid 606 through 621 Processing helix chain 'E' and resid 632 through 644 removed outlier: 4.844A pdb=" N ARG E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR E 638 " --> pdb=" O ASP E 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 382 removed outlier: 3.886A pdb=" N TRP F 375 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 458 Processing helix chain 'F' and resid 464 through 480 Processing helix chain 'F' and resid 481 through 485 removed outlier: 3.885A pdb=" N ILE F 485 " --> pdb=" O LYS F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 496 Processing helix chain 'F' and resid 501 through 512 Processing helix chain 'F' and resid 513 through 526 removed outlier: 3.719A pdb=" N ASP F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 removed outlier: 3.590A pdb=" N ILE F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 removed outlier: 4.269A pdb=" N GLU F 556 " --> pdb=" O VAL F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 571 Processing helix chain 'F' and resid 583 through 593 Processing helix chain 'F' and resid 606 through 621 Processing helix chain 'F' and resid 632 through 644 removed outlier: 4.845A pdb=" N ARG F 637 " --> pdb=" O LEU F 633 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR F 638 " --> pdb=" O ASP F 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 382 removed outlier: 3.902A pdb=" N TRP G 375 " --> pdb=" O GLU G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 464 through 480 Processing helix chain 'G' and resid 481 through 485 removed outlier: 3.873A pdb=" N ILE G 485 " --> pdb=" O LYS G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 496 Processing helix chain 'G' and resid 501 through 512 Processing helix chain 'G' and resid 513 through 526 removed outlier: 3.652A pdb=" N ASP G 519 " --> pdb=" O SER G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 545 removed outlier: 3.611A pdb=" N ILE G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 562 removed outlier: 4.217A pdb=" N GLU G 556 " --> pdb=" O VAL G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 571 Processing helix chain 'G' and resid 583 through 593 Processing helix chain 'G' and resid 606 through 621 Processing helix chain 'G' and resid 632 through 644 removed outlier: 4.858A pdb=" N ARG G 637 " --> pdb=" O LEU G 633 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR G 638 " --> pdb=" O ASP G 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 382 removed outlier: 3.888A pdb=" N TRP H 375 " --> pdb=" O GLU H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 458 Processing helix chain 'H' and resid 464 through 480 Processing helix chain 'H' and resid 481 through 485 removed outlier: 3.877A pdb=" N ILE H 485 " --> pdb=" O LYS H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 496 Processing helix chain 'H' and resid 501 through 512 Processing helix chain 'H' and resid 513 through 526 removed outlier: 3.701A pdb=" N ASP H 519 " --> pdb=" O SER H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 545 removed outlier: 3.618A pdb=" N ILE H 537 " --> pdb=" O ASP H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 562 removed outlier: 4.238A pdb=" N GLU H 556 " --> pdb=" O VAL H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 571 Processing helix chain 'H' and resid 583 through 593 Processing helix chain 'H' and resid 606 through 621 Processing helix chain 'H' and resid 632 through 644 removed outlier: 4.836A pdb=" N ARG H 637 " --> pdb=" O LEU H 633 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR H 638 " --> pdb=" O ASP H 634 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 382 removed outlier: 3.894A pdb=" N TRP I 375 " --> pdb=" O GLU I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 458 Processing helix chain 'I' and resid 464 through 480 Processing helix chain 'I' and resid 481 through 485 removed outlier: 3.885A pdb=" N ILE I 485 " --> pdb=" O LYS I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 496 Processing helix chain 'I' and resid 501 through 512 Processing helix chain 'I' and resid 513 through 526 removed outlier: 3.690A pdb=" N ASP I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 545 removed outlier: 3.619A pdb=" N ILE I 537 " --> pdb=" O ASP I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 562 removed outlier: 4.252A pdb=" N GLU I 556 " --> pdb=" O VAL I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 571 Processing helix chain 'I' and resid 583 through 593 Processing helix chain 'I' and resid 606 through 621 Processing helix chain 'I' and resid 632 through 644 removed outlier: 4.881A pdb=" N ARG I 637 " --> pdb=" O LEU I 633 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR I 638 " --> pdb=" O ASP I 634 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.837A pdb=" N LEU A 353 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 391 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 355 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 393 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 357 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA A 399 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 410 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 404 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 433 through 438 removed outlier: 6.316A pdb=" N SER A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR A 444 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.346A pdb=" N ILE A 629 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 577 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 667 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL A 579 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 669 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 581 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 597 Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 393 removed outlier: 6.833A pdb=" N LEU B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 391 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 355 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 393 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 357 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA B 399 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 410 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 404 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 433 through 438 removed outlier: 6.310A pdb=" N SER B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR B 444 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.329A pdb=" N ILE B 629 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 577 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 667 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 579 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 669 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 581 " --> pdb=" O THR B 669 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 594 through 597 Processing sheet with id=AA9, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.861A pdb=" N LEU C 353 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN C 391 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 355 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 393 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C 357 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 399 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 410 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU C 404 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N SER C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 433 through 438 removed outlier: 6.292A pdb=" N SER C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR C 444 " --> pdb=" O PHE C 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 652 through 654 removed outlier: 6.333A pdb=" N ILE C 629 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 577 " --> pdb=" O LYS C 665 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU C 667 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 579 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR C 669 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 581 " --> pdb=" O THR C 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 594 through 597 Processing sheet with id=AB4, first strand: chain 'D' and resid 389 through 393 removed outlier: 6.849A pdb=" N LEU D 353 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN D 391 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU D 355 " --> pdb=" O ASN D 391 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL D 393 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 357 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA D 399 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 410 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU D 404 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 433 through 438 removed outlier: 6.310A pdb=" N SER D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR D 444 " --> pdb=" O PHE D 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 652 through 654 removed outlier: 6.336A pdb=" N ILE D 629 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 577 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU D 667 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 579 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR D 669 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 581 " --> pdb=" O THR D 669 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 594 through 597 Processing sheet with id=AB8, first strand: chain 'E' and resid 389 through 393 removed outlier: 6.852A pdb=" N LEU E 353 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN E 391 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU E 355 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL E 393 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU E 357 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA E 399 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR E 410 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU E 404 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 433 through 438 removed outlier: 6.308A pdb=" N SER E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR E 444 " --> pdb=" O PHE E 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 652 through 654 removed outlier: 6.352A pdb=" N ILE E 629 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL E 628 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN E 578 " --> pdb=" O VAL E 628 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 630 " --> pdb=" O ASN E 578 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP E 580 " --> pdb=" O LEU E 630 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 577 " --> pdb=" O LYS E 665 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU E 667 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL E 579 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR E 669 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU E 581 " --> pdb=" O THR E 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 594 through 597 Processing sheet with id=AC3, first strand: chain 'F' and resid 389 through 393 removed outlier: 6.856A pdb=" N LEU F 353 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN F 391 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 355 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 393 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 357 " --> pdb=" O VAL F 393 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA F 399 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR F 410 " --> pdb=" O PHE F 402 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU F 404 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 433 through 438 removed outlier: 6.308A pdb=" N SER F 441 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR F 444 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 652 through 654 removed outlier: 6.346A pdb=" N ILE F 629 " --> pdb=" O LEU F 653 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N VAL F 628 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN F 578 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU F 630 " --> pdb=" O ASN F 578 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP F 580 " --> pdb=" O LEU F 630 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 577 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU F 667 " --> pdb=" O LEU F 577 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 579 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR F 669 " --> pdb=" O VAL F 579 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU F 581 " --> pdb=" O THR F 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 594 through 597 Processing sheet with id=AC7, first strand: chain 'G' and resid 389 through 393 removed outlier: 6.851A pdb=" N LEU G 353 " --> pdb=" O ILE G 389 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASN G 391 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 355 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL G 393 " --> pdb=" O LEU G 355 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 357 " --> pdb=" O VAL G 393 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA G 399 " --> pdb=" O SER G 358 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR G 410 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU G 404 " --> pdb=" O SER G 408 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER G 408 " --> pdb=" O LEU G 404 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 433 through 438 removed outlier: 6.294A pdb=" N SER G 441 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR G 444 " --> pdb=" O PHE G 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 652 through 654 removed outlier: 6.335A pdb=" N ILE G 629 " --> pdb=" O LEU G 653 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N VAL G 628 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN G 578 " --> pdb=" O VAL G 628 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU G 630 " --> pdb=" O ASN G 578 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP G 580 " --> pdb=" O LEU G 630 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU G 577 " --> pdb=" O LYS G 665 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU G 667 " --> pdb=" O LEU G 577 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL G 579 " --> pdb=" O LEU G 667 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR G 669 " --> pdb=" O VAL G 579 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU G 581 " --> pdb=" O THR G 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 594 through 597 Processing sheet with id=AD2, first strand: chain 'H' and resid 389 through 393 removed outlier: 6.851A pdb=" N LEU H 353 " --> pdb=" O ILE H 389 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN H 391 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU H 355 " --> pdb=" O ASN H 391 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL H 393 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU H 357 " --> pdb=" O VAL H 393 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA H 399 " --> pdb=" O SER H 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR H 410 " --> pdb=" O PHE H 402 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU H 404 " --> pdb=" O SER H 408 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER H 408 " --> pdb=" O LEU H 404 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 433 through 438 removed outlier: 6.302A pdb=" N SER H 441 " --> pdb=" O LEU H 437 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR H 444 " --> pdb=" O PHE H 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 652 through 654 removed outlier: 6.349A pdb=" N ILE H 629 " --> pdb=" O LEU H 653 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU H 577 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU H 667 " --> pdb=" O LEU H 577 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL H 579 " --> pdb=" O LEU H 667 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR H 669 " --> pdb=" O VAL H 579 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU H 581 " --> pdb=" O THR H 669 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 594 through 597 Processing sheet with id=AD6, first strand: chain 'I' and resid 389 through 393 removed outlier: 6.847A pdb=" N LEU I 353 " --> pdb=" O ILE I 389 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASN I 391 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU I 355 " --> pdb=" O ASN I 391 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL I 393 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU I 357 " --> pdb=" O VAL I 393 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA I 399 " --> pdb=" O SER I 358 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR I 410 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU I 404 " --> pdb=" O SER I 408 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER I 408 " --> pdb=" O LEU I 404 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 433 through 438 removed outlier: 6.301A pdb=" N SER I 441 " --> pdb=" O LEU I 437 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR I 444 " --> pdb=" O PHE I 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 652 through 654 removed outlier: 6.319A pdb=" N ILE I 629 " --> pdb=" O LEU I 653 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU I 577 " --> pdb=" O LYS I 665 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU I 667 " --> pdb=" O LEU I 577 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL I 579 " --> pdb=" O LEU I 667 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR I 669 " --> pdb=" O VAL I 579 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU I 581 " --> pdb=" O THR I 669 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 594 through 597 1166 hydrogen bonds defined for protein. 3372 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: 18.94 Time building geometry restraints manager: 41.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 24216 1.02 - 1.22: 9 1.22 - 1.41: 9636 1.41 - 1.61: 14285 1.61 - 1.81: 117 Bond restraints: 48263 Sorted by residual: bond pdb=" N ASN G 345 " pdb=" H1 ASN G 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN B 345 " pdb=" H1 ASN B 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN E 345 " pdb=" H1 ASN E 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN D 345 " pdb=" H1 ASN D 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN C 345 " pdb=" H1 ASN C 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 48258 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.98: 538 105.98 - 113.03: 57908 113.03 - 120.08: 14247 120.08 - 127.14: 14631 127.14 - 134.19: 198 Bond angle restraints: 87522 Sorted by residual: angle pdb=" C ARG E 499 " pdb=" N LYS E 500 " pdb=" CA LYS E 500 " ideal model delta sigma weight residual 121.85 132.23 -10.38 1.77e+00 3.19e-01 3.44e+01 angle pdb=" C ARG B 499 " pdb=" N LYS B 500 " pdb=" CA LYS B 500 " ideal model delta sigma weight residual 121.85 132.15 -10.30 1.77e+00 3.19e-01 3.39e+01 angle pdb=" C ARG H 499 " pdb=" N LYS H 500 " pdb=" CA LYS H 500 " ideal model delta sigma weight residual 121.85 132.12 -10.27 1.77e+00 3.19e-01 3.37e+01 angle pdb=" C ARG G 499 " pdb=" N LYS G 500 " pdb=" CA LYS G 500 " ideal model delta sigma weight residual 121.85 132.12 -10.27 1.77e+00 3.19e-01 3.36e+01 angle pdb=" C ARG D 499 " pdb=" N LYS D 500 " pdb=" CA LYS D 500 " ideal model delta sigma weight residual 121.85 132.10 -10.25 1.77e+00 3.19e-01 3.35e+01 ... (remaining 87517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17803 17.99 - 35.99: 995 35.99 - 53.98: 172 53.98 - 71.98: 330 71.98 - 89.97: 11 Dihedral angle restraints: 19311 sinusoidal: 9417 harmonic: 9894 Sorted by residual: dihedral pdb=" CD ARG C 510 " pdb=" NE ARG C 510 " pdb=" CZ ARG C 510 " pdb=" NH1 ARG C 510 " ideal model delta sinusoidal sigma weight residual 0.00 -32.44 32.44 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CD ARG F 510 " pdb=" NE ARG F 510 " pdb=" CZ ARG F 510 " pdb=" NH1 ARG F 510 " ideal model delta sinusoidal sigma weight residual 0.00 -32.18 32.18 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CD ARG B 510 " pdb=" NE ARG B 510 " pdb=" CZ ARG B 510 " pdb=" NH1 ARG B 510 " ideal model delta sinusoidal sigma weight residual 0.00 -32.15 32.15 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 19308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2540 0.061 - 0.121: 994 0.121 - 0.182: 222 0.182 - 0.242: 53 0.242 - 0.303: 35 Chirality restraints: 3844 Sorted by residual: chirality pdb=" CA ILE I 496 " pdb=" N ILE I 496 " pdb=" C ILE I 496 " pdb=" CB ILE I 496 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE G 496 " pdb=" N ILE G 496 " pdb=" C ILE G 496 " pdb=" CB ILE G 496 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE H 496 " pdb=" N ILE H 496 " pdb=" C ILE H 496 " pdb=" CB ILE H 496 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3841 not shown) Planarity restraints: 6960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 535 " -0.095 9.50e-02 1.11e+02 6.57e-02 7.54e+01 pdb=" NE ARG B 535 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 535 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG B 535 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 535 " 0.115 2.00e-02 2.50e+03 pdb="HH11 ARG B 535 " -0.014 2.00e-02 2.50e+03 pdb="HH12 ARG B 535 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG B 535 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG B 535 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 535 " -0.096 9.50e-02 1.11e+02 6.54e-02 7.42e+01 pdb=" NE ARG C 535 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG C 535 " -0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG C 535 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 535 " 0.115 2.00e-02 2.50e+03 pdb="HH11 ARG C 535 " -0.015 2.00e-02 2.50e+03 pdb="HH12 ARG C 535 " 0.049 2.00e-02 2.50e+03 pdb="HH21 ARG C 535 " 0.010 2.00e-02 2.50e+03 pdb="HH22 ARG C 535 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 535 " 0.097 9.50e-02 1.11e+02 6.55e-02 7.41e+01 pdb=" NE ARG G 535 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 535 " 0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG G 535 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 535 " -0.115 2.00e-02 2.50e+03 pdb="HH11 ARG G 535 " 0.014 2.00e-02 2.50e+03 pdb="HH12 ARG G 535 " -0.049 2.00e-02 2.50e+03 pdb="HH21 ARG G 535 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG G 535 " 0.100 2.00e-02 2.50e+03 ... (remaining 6957 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2504 2.21 - 2.81: 98298 2.81 - 3.40: 120593 3.40 - 4.00: 156727 4.00 - 4.60: 246052 Nonbonded interactions: 624174 Sorted by model distance: nonbonded pdb=" O PRO E 648 " pdb=" HG SER E 649 " model vdw 1.610 1.850 nonbonded pdb=" O PRO A 648 " pdb=" HG SER A 649 " model vdw 1.613 1.850 nonbonded pdb=" O PRO H 648 " pdb=" HG SER H 649 " model vdw 1.618 1.850 nonbonded pdb=" O PRO C 648 " pdb=" HG SER C 649 " model vdw 1.618 1.850 nonbonded pdb=" O PRO D 648 " pdb=" HG SER D 649 " model vdw 1.618 1.850 ... (remaining 624169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 345 through 670) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 15151 2.51 5 N 3935 2.21 5 O 4511 1.98 5 H 24225 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.720 Extract box with map and model: 7.600 Check model and map are aligned: 0.750 Convert atoms to be neutral: 0.400 Process input model: 139.250 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 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 : 0.010 0.063 24038 Z= 0.609 Angle : 1.263 10.417 32537 Z= 0.790 Chirality : 0.071 0.303 3844 Planarity : 0.008 0.116 4115 Dihedral : 12.138 83.575 9084 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 0.00 % 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: -2.09 (0.13), residues: 2917 helix: -1.89 (0.11), residues: 1386 sheet: -0.16 (0.20), residues: 560 loop : -0.98 (0.17), residues: 971 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.8348 time to fit residues: 572.3650 Evaluate side-chains 217 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 4.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9980 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 225 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24038 Z= 0.232 Angle : 0.641 6.516 32537 Z= 0.367 Chirality : 0.046 0.182 3844 Planarity : 0.004 0.045 4115 Dihedral : 4.716 23.379 3178 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 0.63 % 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: -0.33 (0.15), residues: 2917 helix: 0.21 (0.13), residues: 1386 sheet: -0.06 (0.20), residues: 576 loop : -0.72 (0.19), residues: 955 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 213 average time/residue: 0.9014 time to fit residues: 295.1761 Evaluate side-chains 183 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 5.344 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5780 time to fit residues: 21.8337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 0.0000 chunk 210 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 24038 Z= 0.180 Angle : 0.527 6.157 32537 Z= 0.298 Chirality : 0.044 0.183 3844 Planarity : 0.003 0.024 4115 Dihedral : 4.539 24.518 3178 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 0.37 % 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: 0.23 (0.15), residues: 2917 helix: 0.93 (0.14), residues: 1386 sheet: -0.16 (0.20), residues: 576 loop : -0.64 (0.19), residues: 955 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 188 average time/residue: 0.8769 time to fit residues: 249.9760 Evaluate side-chains 157 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 4.132 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5088 time to fit residues: 10.8377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 0.1980 chunk 278 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 24038 Z= 0.152 Angle : 0.486 5.644 32537 Z= 0.273 Chirality : 0.043 0.170 3844 Planarity : 0.003 0.022 4115 Dihedral : 4.411 24.166 3178 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.30 % 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: 0.57 (0.16), residues: 2917 helix: 1.26 (0.14), residues: 1386 sheet: -0.19 (0.20), residues: 576 loop : -0.42 (0.21), residues: 955 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 4.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 171 average time/residue: 0.8011 time to fit residues: 221.8314 Evaluate side-chains 156 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 4.208 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5200 time to fit residues: 11.2258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 360 ASN G 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 24038 Z= 0.240 Angle : 0.529 6.304 32537 Z= 0.296 Chirality : 0.044 0.181 3844 Planarity : 0.003 0.031 4115 Dihedral : 4.407 23.884 3178 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.48 % 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: 0.43 (0.15), residues: 2917 helix: 1.19 (0.14), residues: 1386 sheet: -0.29 (0.19), residues: 575 loop : -0.54 (0.21), residues: 956 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 4.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 167 average time/residue: 0.7725 time to fit residues: 206.9952 Evaluate side-chains 158 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 4.494 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4949 time to fit residues: 13.3047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 24038 Z= 0.279 Angle : 0.553 6.617 32537 Z= 0.309 Chirality : 0.045 0.187 3844 Planarity : 0.003 0.030 4115 Dihedral : 4.504 24.312 3178 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.63 % 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: 0.30 (0.15), residues: 2917 helix: 1.10 (0.14), residues: 1386 sheet: -0.33 (0.19), residues: 575 loop : -0.64 (0.20), residues: 956 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 4.103 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.7784 time to fit residues: 212.8225 Evaluate side-chains 157 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 4.319 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4976 time to fit residues: 16.4198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 0.4980 chunk 203 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 24038 Z= 0.171 Angle : 0.493 5.998 32537 Z= 0.274 Chirality : 0.043 0.172 3844 Planarity : 0.003 0.025 4115 Dihedral : 4.355 24.498 3178 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 0.11 % 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: 0.59 (0.16), residues: 2917 helix: 1.36 (0.14), residues: 1386 sheet: -0.27 (0.19), residues: 575 loop : -0.49 (0.21), residues: 956 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 152 average time/residue: 0.7979 time to fit residues: 194.2618 Evaluate side-chains 145 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 4.170 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4723 time to fit residues: 6.1139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 218 optimal weight: 7.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 24038 Z= 0.139 Angle : 0.467 6.012 32537 Z= 0.258 Chirality : 0.043 0.164 3844 Planarity : 0.002 0.021 4115 Dihedral : 4.186 23.732 3178 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.04 % 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: 0.83 (0.16), residues: 2917 helix: 1.56 (0.14), residues: 1386 sheet: -0.17 (0.20), residues: 575 loop : -0.38 (0.21), residues: 956 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.7827 time to fit residues: 192.6089 Evaluate side-chains 148 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 4.053 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5016 time to fit residues: 6.1080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 257 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24038 Z= 0.175 Angle : 0.481 6.022 32537 Z= 0.264 Chirality : 0.043 0.173 3844 Planarity : 0.003 0.027 4115 Dihedral : 4.152 23.076 3178 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.04 % 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: 0.84 (0.16), residues: 2917 helix: 1.56 (0.14), residues: 1386 sheet: -0.14 (0.20), residues: 575 loop : -0.36 (0.21), residues: 956 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.7822 time to fit residues: 195.1455 Evaluate side-chains 152 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 166 optimal weight: 0.0670 chunk 129 optimal weight: 0.1980 chunk 190 optimal weight: 0.6980 chunk 286 optimal weight: 0.0040 chunk 264 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 24038 Z= 0.113 Angle : 0.450 7.164 32537 Z= 0.245 Chirality : 0.042 0.158 3844 Planarity : 0.002 0.018 4115 Dihedral : 3.999 22.730 3178 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.00 % 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: 1.11 (0.16), residues: 2917 helix: 1.80 (0.14), residues: 1386 sheet: -0.06 (0.20), residues: 575 loop : -0.22 (0.21), residues: 956 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.7868 time to fit residues: 198.2931 Evaluate side-chains 150 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 4.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 0.0050 chunk 228 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 0.0870 chunk 42 optimal weight: 8.9990 overall best weight: 0.7374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 GLN H 612 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.185012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127185 restraints weight = 81804.691| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.32 r_work: 0.3406 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work: 0.3303 rms_B_bonded: 3.09 restraints_weight: 0.1250 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 24038 Z= 0.120 Angle : 0.441 7.225 32537 Z= 0.240 Chirality : 0.042 0.163 3844 Planarity : 0.002 0.019 4115 Dihedral : 3.898 22.615 3178 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.07 % 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: 1.19 (0.16), residues: 2917 helix: 1.87 (0.14), residues: 1386 sheet: -0.05 (0.20), residues: 575 loop : -0.16 (0.21), residues: 956 =============================================================================== Job complete usr+sys time: 6773.43 seconds wall clock time: 122 minutes 19.00 seconds (7339.00 seconds total)