Starting phenix.real_space_refine (version: dev) on Mon Dec 19 11:57:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpk_4977/12_2022/6rpk_4977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpk_4977/12_2022/6rpk_4977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpk_4977/12_2022/6rpk_4977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpk_4977/12_2022/6rpk_4977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpk_4977/12_2022/6rpk_4977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpk_4977/12_2022/6rpk_4977.pdb" } resolution = 2.84 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= 0.071 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 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "u PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 50": "NH1" <-> "NH2" Residue "u PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 75": "OD1" <-> "OD2" Residue "u PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 95": "NH1" <-> "NH2" Residue "u GLU 102": "OE1" <-> "OE2" Residue "u ARG 114": "NH1" <-> "NH2" Residue "u GLU 134": "OE1" <-> "OE2" Residue "u ARG 148": "NH1" <-> "NH2" Residue "u ARG 160": "NH1" <-> "NH2" Residue "u PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 215": "NH1" <-> "NH2" Residue "u TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 223": "NH1" <-> "NH2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 160": "NH1" <-> "NH2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ARG 114": "NH1" <-> "NH2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 215": "NH1" <-> "NH2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 75": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H ARG 160": "NH1" <-> "NH2" Residue "H PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "I PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I GLU 102": "OE1" <-> "OE2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I ARG 160": "NH1" <-> "NH2" Residue "I PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 215": "NH1" <-> "NH2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 223": "NH1" <-> "NH2" Residue "J PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J ARG 160": "NH1" <-> "NH2" Residue "J PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 215": "NH1" <-> "NH2" Residue "J TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 223": "NH1" <-> "NH2" Residue "K PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 95": "NH1" <-> "NH2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K ARG 160": "NH1" <-> "NH2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 215": "NH1" <-> "NH2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 223": "NH1" <-> "NH2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L ARG 160": "NH1" <-> "NH2" Residue "L PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 215": "NH1" <-> "NH2" Residue "L TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 223": "NH1" <-> "NH2" Residue "M PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M ARG 148": "NH1" <-> "NH2" Residue "M ARG 160": "NH1" <-> "NH2" Residue "M PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 223": "NH1" <-> "NH2" Residue "N PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 75": "OD1" <-> "OD2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 95": "NH1" <-> "NH2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "N ARG 160": "NH1" <-> "NH2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 215": "NH1" <-> "NH2" Residue "N TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 223": "NH1" <-> "NH2" Residue "O PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 95": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O GLU 134": "OE1" <-> "OE2" Residue "O ARG 148": "NH1" <-> "NH2" Residue "O ARG 160": "NH1" <-> "NH2" Residue "O PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 215": "NH1" <-> "NH2" Residue "O TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 223": "NH1" <-> "NH2" Residue "P PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 75": "OD1" <-> "OD2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "P ARG 148": "NH1" <-> "NH2" Residue "P ARG 160": "NH1" <-> "NH2" Residue "P PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 215": "NH1" <-> "NH2" Residue "P TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 223": "NH1" <-> "NH2" Residue "Q PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 75": "OD1" <-> "OD2" Residue "Q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q GLU 102": "OE1" <-> "OE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "Q ARG 148": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 215": "NH1" <-> "NH2" Residue "Q TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 223": "NH1" <-> "NH2" Residue "R PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R GLU 134": "OE1" <-> "OE2" Residue "R ARG 148": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 215": "NH1" <-> "NH2" Residue "R TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 223": "NH1" <-> "NH2" Residue "S PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "S PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 75": "OD1" <-> "OD2" Residue "S PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S GLU 102": "OE1" <-> "OE2" Residue "S ARG 114": "NH1" <-> "NH2" Residue "S GLU 134": "OE1" <-> "OE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 215": "NH1" <-> "NH2" Residue "S TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 223": "NH1" <-> "NH2" Residue "T PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 50": "NH1" <-> "NH2" Residue "T PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 75": "OD1" <-> "OD2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T GLU 102": "OE1" <-> "OE2" Residue "T ARG 114": "NH1" <-> "NH2" Residue "T GLU 134": "OE1" <-> "OE2" Residue "T ARG 148": "NH1" <-> "NH2" Residue "T ARG 160": "NH1" <-> "NH2" Residue "T PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 215": "NH1" <-> "NH2" Residue "T TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 223": "NH1" <-> "NH2" Residue "U PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 50": "NH1" <-> "NH2" Residue "U PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 75": "OD1" <-> "OD2" Residue "U PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "U ARG 114": "NH1" <-> "NH2" Residue "U GLU 134": "OE1" <-> "OE2" Residue "U ARG 148": "NH1" <-> "NH2" Residue "U ARG 160": "NH1" <-> "NH2" Residue "U PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 215": "NH1" <-> "NH2" Residue "U TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 223": "NH1" <-> "NH2" Residue "V PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 50": "NH1" <-> "NH2" Residue "V PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 75": "OD1" <-> "OD2" Residue "V PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 95": "NH1" <-> "NH2" Residue "V GLU 102": "OE1" <-> "OE2" Residue "V ARG 114": "NH1" <-> "NH2" Residue "V GLU 134": "OE1" <-> "OE2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "V PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 215": "NH1" <-> "NH2" Residue "V TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 223": "NH1" <-> "NH2" Residue "W PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 75": "OD1" <-> "OD2" Residue "W PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W GLU 102": "OE1" <-> "OE2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "W GLU 134": "OE1" <-> "OE2" Residue "W ARG 148": "NH1" <-> "NH2" Residue "W ARG 160": "NH1" <-> "NH2" Residue "W PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 215": "NH1" <-> "NH2" Residue "W TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 223": "NH1" <-> "NH2" Residue "X PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 75": "OD1" <-> "OD2" Residue "X PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X GLU 102": "OE1" <-> "OE2" Residue "X ARG 114": "NH1" <-> "NH2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X ARG 148": "NH1" <-> "NH2" Residue "X ARG 160": "NH1" <-> "NH2" Residue "X PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 215": "NH1" <-> "NH2" Residue "X TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 223": "NH1" <-> "NH2" Residue "Y PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 75": "OD1" <-> "OD2" Residue "Y PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 95": "NH1" <-> "NH2" Residue "Y GLU 102": "OE1" <-> "OE2" Residue "Y ARG 114": "NH1" <-> "NH2" Residue "Y GLU 134": "OE1" <-> "OE2" Residue "Y ARG 148": "NH1" <-> "NH2" Residue "Y ARG 160": "NH1" <-> "NH2" Residue "Y PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 215": "NH1" <-> "NH2" Residue "Y TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 223": "NH1" <-> "NH2" Residue "Z PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 50": "NH1" <-> "NH2" Residue "Z PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 75": "OD1" <-> "OD2" Residue "Z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 95": "NH1" <-> "NH2" Residue "Z GLU 102": "OE1" <-> "OE2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z GLU 134": "OE1" <-> "OE2" Residue "Z ARG 148": "NH1" <-> "NH2" Residue "Z ARG 160": "NH1" <-> "NH2" Residue "Z PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 215": "NH1" <-> "NH2" Residue "Z TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "0 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 75": "OD1" <-> "OD2" Residue "0 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 95": "NH1" <-> "NH2" Residue "0 GLU 102": "OE1" <-> "OE2" Residue "0 ARG 114": "NH1" <-> "NH2" Residue "0 GLU 134": "OE1" <-> "OE2" Residue "0 ARG 148": "NH1" <-> "NH2" Residue "0 ARG 160": "NH1" <-> "NH2" Residue "0 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 215": "NH1" <-> "NH2" Residue "0 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 223": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 50": "NH1" <-> "NH2" Residue "1 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 75": "OD1" <-> "OD2" Residue "1 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 95": "NH1" <-> "NH2" Residue "1 GLU 102": "OE1" <-> "OE2" Residue "1 ARG 114": "NH1" <-> "NH2" Residue "1 GLU 134": "OE1" <-> "OE2" Residue "1 ARG 148": "NH1" <-> "NH2" Residue "1 ARG 160": "NH1" <-> "NH2" Residue "1 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 215": "NH1" <-> "NH2" Residue "1 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 223": "NH1" <-> "NH2" Residue "2 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 50": "NH1" <-> "NH2" Residue "2 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 75": "OD1" <-> "OD2" Residue "2 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 95": "NH1" <-> "NH2" Residue "2 GLU 102": "OE1" <-> "OE2" Residue "2 ARG 114": "NH1" <-> "NH2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 ARG 148": "NH1" <-> "NH2" Residue "2 ARG 160": "NH1" <-> "NH2" Residue "2 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 215": "NH1" <-> "NH2" Residue "2 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 223": "NH1" <-> "NH2" Residue "3 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 50": "NH1" <-> "NH2" Residue "3 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 75": "OD1" <-> "OD2" Residue "3 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 95": "NH1" <-> "NH2" Residue "3 GLU 102": "OE1" <-> "OE2" Residue "3 ARG 114": "NH1" <-> "NH2" Residue "3 GLU 134": "OE1" <-> "OE2" Residue "3 ARG 148": "NH1" <-> "NH2" Residue "3 ARG 160": "NH1" <-> "NH2" Residue "3 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 215": "NH1" <-> "NH2" Residue "3 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 223": "NH1" <-> "NH2" Residue "4 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 50": "NH1" <-> "NH2" Residue "4 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 75": "OD1" <-> "OD2" Residue "4 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 95": "NH1" <-> "NH2" Residue "4 GLU 102": "OE1" <-> "OE2" Residue "4 ARG 114": "NH1" <-> "NH2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 ARG 148": "NH1" <-> "NH2" Residue "4 ARG 160": "NH1" <-> "NH2" Residue "4 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 215": "NH1" <-> "NH2" Residue "4 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 223": "NH1" <-> "NH2" Residue "5 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 75": "OD1" <-> "OD2" Residue "5 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 95": "NH1" <-> "NH2" Residue "5 GLU 102": "OE1" <-> "OE2" Residue "5 ARG 114": "NH1" <-> "NH2" Residue "5 GLU 134": "OE1" <-> "OE2" Residue "5 ARG 148": "NH1" <-> "NH2" Residue "5 ARG 160": "NH1" <-> "NH2" Residue "5 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 215": "NH1" <-> "NH2" Residue "5 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "6 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 50": "NH1" <-> "NH2" Residue "6 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 75": "OD1" <-> "OD2" Residue "6 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 GLU 102": "OE1" <-> "OE2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 GLU 134": "OE1" <-> "OE2" Residue "6 ARG 148": "NH1" <-> "NH2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 215": "NH1" <-> "NH2" Residue "6 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "7 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 50": "NH1" <-> "NH2" Residue "7 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 75": "OD1" <-> "OD2" Residue "7 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 95": "NH1" <-> "NH2" Residue "7 GLU 102": "OE1" <-> "OE2" Residue "7 ARG 114": "NH1" <-> "NH2" Residue "7 GLU 134": "OE1" <-> "OE2" Residue "7 ARG 148": "NH1" <-> "NH2" Residue "7 ARG 160": "NH1" <-> "NH2" Residue "7 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 215": "NH1" <-> "NH2" Residue "7 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 223": "NH1" <-> "NH2" Residue "8 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 50": "NH1" <-> "NH2" Residue "8 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 75": "OD1" <-> "OD2" Residue "8 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 95": "NH1" <-> "NH2" Residue "8 GLU 102": "OE1" <-> "OE2" Residue "8 ARG 114": "NH1" <-> "NH2" Residue "8 GLU 134": "OE1" <-> "OE2" Residue "8 ARG 148": "NH1" <-> "NH2" Residue "8 ARG 160": "NH1" <-> "NH2" Residue "8 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 215": "NH1" <-> "NH2" Residue "8 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 223": "NH1" <-> "NH2" Residue "9 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 50": "NH1" <-> "NH2" Residue "9 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 75": "OD1" <-> "OD2" Residue "9 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 95": "NH1" <-> "NH2" Residue "9 GLU 102": "OE1" <-> "OE2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 GLU 134": "OE1" <-> "OE2" Residue "9 ARG 148": "NH1" <-> "NH2" Residue "9 ARG 160": "NH1" <-> "NH2" Residue "9 PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 215": "NH1" <-> "NH2" Residue "9 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 223": "NH1" <-> "NH2" Residue "a PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 75": "OD1" <-> "OD2" Residue "a PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 95": "NH1" <-> "NH2" Residue "a GLU 102": "OE1" <-> "OE2" Residue "a ARG 114": "NH1" <-> "NH2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a ARG 148": "NH1" <-> "NH2" Residue "a ARG 160": "NH1" <-> "NH2" Residue "a PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 215": "NH1" <-> "NH2" Residue "a TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 223": "NH1" <-> "NH2" Residue "b PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 50": "NH1" <-> "NH2" Residue "b PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 75": "OD1" <-> "OD2" Residue "b PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b GLU 102": "OE1" <-> "OE2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b GLU 134": "OE1" <-> "OE2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b ARG 160": "NH1" <-> "NH2" Residue "b PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 215": "NH1" <-> "NH2" Residue "b TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 223": "NH1" <-> "NH2" Residue "c PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 50": "NH1" <-> "NH2" Residue "c PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 75": "OD1" <-> "OD2" Residue "c PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 95": "NH1" <-> "NH2" Residue "c GLU 102": "OE1" <-> "OE2" Residue "c ARG 114": "NH1" <-> "NH2" Residue "c GLU 134": "OE1" <-> "OE2" Residue "c ARG 148": "NH1" <-> "NH2" Residue "c ARG 160": "NH1" <-> "NH2" Residue "c PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 215": "NH1" <-> "NH2" Residue "c TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 223": "NH1" <-> "NH2" Residue "d PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 50": "NH1" <-> "NH2" Residue "d PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 75": "OD1" <-> "OD2" Residue "d PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 95": "NH1" <-> "NH2" Residue "d GLU 102": "OE1" <-> "OE2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d GLU 134": "OE1" <-> "OE2" Residue "d ARG 148": "NH1" <-> "NH2" Residue "d ARG 160": "NH1" <-> "NH2" Residue "d PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 215": "NH1" <-> "NH2" Residue "d TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 223": "NH1" <-> "NH2" Residue "e PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 75": "OD1" <-> "OD2" Residue "e PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 95": "NH1" <-> "NH2" Residue "e GLU 102": "OE1" <-> "OE2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e GLU 134": "OE1" <-> "OE2" Residue "e ARG 148": "NH1" <-> "NH2" Residue "e ARG 160": "NH1" <-> "NH2" Residue "e PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 215": "NH1" <-> "NH2" Residue "e TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 223": "NH1" <-> "NH2" Residue "f PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 50": "NH1" <-> "NH2" Residue "f PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 75": "OD1" <-> "OD2" Residue "f PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 95": "NH1" <-> "NH2" Residue "f GLU 102": "OE1" <-> "OE2" Residue "f ARG 114": "NH1" <-> "NH2" Residue "f GLU 134": "OE1" <-> "OE2" Residue "f ARG 148": "NH1" <-> "NH2" Residue "f ARG 160": "NH1" <-> "NH2" Residue "f PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 215": "NH1" <-> "NH2" Residue "f TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 223": "NH1" <-> "NH2" Residue "g PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 50": "NH1" <-> "NH2" Residue "g PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 75": "OD1" <-> "OD2" Residue "g PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g GLU 102": "OE1" <-> "OE2" Residue "g ARG 114": "NH1" <-> "NH2" Residue "g GLU 134": "OE1" <-> "OE2" Residue "g ARG 148": "NH1" <-> "NH2" Residue "g ARG 160": "NH1" <-> "NH2" Residue "g PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 215": "NH1" <-> "NH2" Residue "g TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 223": "NH1" <-> "NH2" Residue "h PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 50": "NH1" <-> "NH2" Residue "h PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 75": "OD1" <-> "OD2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 95": "NH1" <-> "NH2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 114": "NH1" <-> "NH2" Residue "h GLU 134": "OE1" <-> "OE2" Residue "h ARG 148": "NH1" <-> "NH2" Residue "h ARG 160": "NH1" <-> "NH2" Residue "h PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 215": "NH1" <-> "NH2" Residue "h TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 223": "NH1" <-> "NH2" Residue "i PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 50": "NH1" <-> "NH2" Residue "i PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 75": "OD1" <-> "OD2" Residue "i PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 95": "NH1" <-> "NH2" Residue "i GLU 102": "OE1" <-> "OE2" Residue "i ARG 114": "NH1" <-> "NH2" Residue "i GLU 134": "OE1" <-> "OE2" Residue "i ARG 148": "NH1" <-> "NH2" Residue "i ARG 160": "NH1" <-> "NH2" Residue "i PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 215": "NH1" <-> "NH2" Residue "i TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 223": "NH1" <-> "NH2" Residue "j PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "j PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 95": "NH1" <-> "NH2" Residue "j GLU 102": "OE1" <-> "OE2" Residue "j ARG 114": "NH1" <-> "NH2" Residue "j GLU 134": "OE1" <-> "OE2" Residue "j ARG 148": "NH1" <-> "NH2" Residue "j ARG 160": "NH1" <-> "NH2" Residue "j PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 215": "NH1" <-> "NH2" Residue "j TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 223": "NH1" <-> "NH2" Residue "k PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 50": "NH1" <-> "NH2" Residue "k PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 75": "OD1" <-> "OD2" Residue "k PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k GLU 102": "OE1" <-> "OE2" Residue "k ARG 114": "NH1" <-> "NH2" Residue "k GLU 134": "OE1" <-> "OE2" Residue "k ARG 148": "NH1" <-> "NH2" Residue "k ARG 160": "NH1" <-> "NH2" Residue "k PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 215": "NH1" <-> "NH2" Residue "k TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 223": "NH1" <-> "NH2" Residue "l PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 75": "OD1" <-> "OD2" Residue "l PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 95": "NH1" <-> "NH2" Residue "l GLU 102": "OE1" <-> "OE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "l GLU 134": "OE1" <-> "OE2" Residue "l ARG 148": "NH1" <-> "NH2" Residue "l ARG 160": "NH1" <-> "NH2" Residue "l PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 215": "NH1" <-> "NH2" Residue "l TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 223": "NH1" <-> "NH2" Residue "m PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 75": "OD1" <-> "OD2" Residue "m PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 95": "NH1" <-> "NH2" Residue "m GLU 102": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m GLU 134": "OE1" <-> "OE2" Residue "m ARG 148": "NH1" <-> "NH2" Residue "m ARG 160": "NH1" <-> "NH2" Residue "m PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 215": "NH1" <-> "NH2" Residue "m TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 223": "NH1" <-> "NH2" Residue "n PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 50": "NH1" <-> "NH2" Residue "n PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 75": "OD1" <-> "OD2" Residue "n PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 95": "NH1" <-> "NH2" Residue "n GLU 102": "OE1" <-> "OE2" Residue "n ARG 114": "NH1" <-> "NH2" Residue "n GLU 134": "OE1" <-> "OE2" Residue "n ARG 148": "NH1" <-> "NH2" Residue "n ARG 160": "NH1" <-> "NH2" Residue "n PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 215": "NH1" <-> "NH2" Residue "n TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 223": "NH1" <-> "NH2" Residue "o PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 75": "OD1" <-> "OD2" Residue "o PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 95": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 114": "NH1" <-> "NH2" Residue "o GLU 134": "OE1" <-> "OE2" Residue "o ARG 148": "NH1" <-> "NH2" Residue "o ARG 160": "NH1" <-> "NH2" Residue "o PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 215": "NH1" <-> "NH2" Residue "o TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 223": "NH1" <-> "NH2" Residue "p PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 50": "NH1" <-> "NH2" Residue "p PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 75": "OD1" <-> "OD2" Residue "p PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 95": "NH1" <-> "NH2" Residue "p GLU 102": "OE1" <-> "OE2" Residue "p ARG 114": "NH1" <-> "NH2" Residue "p GLU 134": "OE1" <-> "OE2" Residue "p ARG 148": "NH1" <-> "NH2" Residue "p ARG 160": "NH1" <-> "NH2" Residue "p PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 215": "NH1" <-> "NH2" Residue "p TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 223": "NH1" <-> "NH2" Residue "q PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 75": "OD1" <-> "OD2" Residue "q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 95": "NH1" <-> "NH2" Residue "q GLU 102": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q GLU 134": "OE1" <-> "OE2" Residue "q ARG 148": "NH1" <-> "NH2" Residue "q ARG 160": "NH1" <-> "NH2" Residue "q PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 215": "NH1" <-> "NH2" Residue "q TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 223": "NH1" <-> "NH2" Residue "r PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 50": "NH1" <-> "NH2" Residue "r PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 75": "OD1" <-> "OD2" Residue "r PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r GLU 102": "OE1" <-> "OE2" Residue "r ARG 114": "NH1" <-> "NH2" Residue "r GLU 134": "OE1" <-> "OE2" Residue "r ARG 148": "NH1" <-> "NH2" Residue "r ARG 160": "NH1" <-> "NH2" Residue "r PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 215": "NH1" <-> "NH2" Residue "r TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 223": "NH1" <-> "NH2" Residue "s PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 50": "NH1" <-> "NH2" Residue "s PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 75": "OD1" <-> "OD2" Residue "s PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s GLU 102": "OE1" <-> "OE2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s GLU 134": "OE1" <-> "OE2" Residue "s ARG 148": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 215": "NH1" <-> "NH2" Residue "s TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "t PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 50": "NH1" <-> "NH2" Residue "t PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 75": "OD1" <-> "OD2" Residue "t PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 95": "NH1" <-> "NH2" Residue "t GLU 102": "OE1" <-> "OE2" Residue "t ARG 114": "NH1" <-> "NH2" Residue "t GLU 134": "OE1" <-> "OE2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t ARG 160": "NH1" <-> "NH2" Residue "t PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 215": "NH1" <-> "NH2" Residue "t TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 223": "NH1" <-> "NH2" Residue "v PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 50": "NH1" <-> "NH2" Residue "v PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 75": "OD1" <-> "OD2" Residue "v PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 95": "NH1" <-> "NH2" Residue "v GLU 102": "OE1" <-> "OE2" Residue "v ARG 114": "NH1" <-> "NH2" Residue "v GLU 134": "OE1" <-> "OE2" Residue "v ARG 148": "NH1" <-> "NH2" Residue "v ARG 160": "NH1" <-> "NH2" Residue "v PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 215": "NH1" <-> "NH2" Residue "v TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 223": "NH1" <-> "NH2" Residue "w PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 75": "OD1" <-> "OD2" Residue "w PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 95": "NH1" <-> "NH2" Residue "w GLU 102": "OE1" <-> "OE2" Residue "w ARG 114": "NH1" <-> "NH2" Residue "w GLU 134": "OE1" <-> "OE2" Residue "w ARG 148": "NH1" <-> "NH2" Residue "w ARG 160": "NH1" <-> "NH2" Residue "w PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 215": "NH1" <-> "NH2" Residue "w TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 223": "NH1" <-> "NH2" Residue "x PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 50": "NH1" <-> "NH2" Residue "x PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 75": "OD1" <-> "OD2" Residue "x PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 95": "NH1" <-> "NH2" Residue "x GLU 102": "OE1" <-> "OE2" Residue "x ARG 114": "NH1" <-> "NH2" Residue "x GLU 134": "OE1" <-> "OE2" Residue "x ARG 148": "NH1" <-> "NH2" Residue "x ARG 160": "NH1" <-> "NH2" Residue "x PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 215": "NH1" <-> "NH2" Residue "x TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 223": "NH1" <-> "NH2" Residue "y PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 50": "NH1" <-> "NH2" Residue "y PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 75": "OD1" <-> "OD2" Residue "y PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 95": "NH1" <-> "NH2" Residue "y GLU 102": "OE1" <-> "OE2" Residue "y ARG 114": "NH1" <-> "NH2" Residue "y GLU 134": "OE1" <-> "OE2" Residue "y ARG 148": "NH1" <-> "NH2" Residue "y ARG 160": "NH1" <-> "NH2" Residue "y PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 215": "NH1" <-> "NH2" Residue "y TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 223": "NH1" <-> "NH2" Time to flip residues: 0.32s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 103090 Number of models: 1 Model: "" Number of chains: 61 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "u" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "E" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "H" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "I" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "J" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "K" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "L" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "M" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "N" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "O" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "P" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "Q" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "R" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "S" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "T" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "U" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "V" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "W" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "X" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "Y" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "Z" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "0" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "1" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "2" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "3" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "4" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "5" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "6" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "7" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "8" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "9" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "a" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "b" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "d" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "e" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "f" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "g" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "h" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "i" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "j" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "k" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "l" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "m" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "n" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "o" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "p" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "q" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "r" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "s" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "t" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "v" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "w" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "x" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Chain: "y" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1690 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 16, 'TRANS': 184} Time building chain proxies: 41.17, per 1000 atoms: 0.40 Number of scatterers: 103090 At special positions: 0 Unit cell: (212.35, 212.35, 212.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 17568 8.00 N 18361 7.00 C 67100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.48 Conformation dependent library (CDL) restraints added in 10.4 seconds 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22936 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 0 sheets defined 6.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'u' and resid 32 through 40 Processing helix chain 'u' and resid 74 through 76 No H-bonds generated for 'chain 'u' and resid 74 through 76' Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'F' and resid 32 through 40 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'G' and resid 32 through 40 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'H' and resid 32 through 40 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'K' and resid 32 through 40 Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'L' and resid 32 through 40 Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'M' and resid 32 through 40 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'N' and resid 32 through 40 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'O' and resid 32 through 40 Processing helix chain 'O' and resid 74 through 76 No H-bonds generated for 'chain 'O' and resid 74 through 76' Processing helix chain 'P' and resid 32 through 40 Processing helix chain 'P' and resid 74 through 76 No H-bonds generated for 'chain 'P' and resid 74 through 76' Processing helix chain 'Q' and resid 32 through 40 Processing helix chain 'Q' and resid 74 through 76 No H-bonds generated for 'chain 'Q' and resid 74 through 76' Processing helix chain 'R' and resid 32 through 40 Processing helix chain 'R' and resid 74 through 76 No H-bonds generated for 'chain 'R' and resid 74 through 76' Processing helix chain 'S' and resid 32 through 40 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'T' and resid 32 through 40 Processing helix chain 'T' and resid 74 through 76 No H-bonds generated for 'chain 'T' and resid 74 through 76' Processing helix chain 'U' and resid 32 through 40 Processing helix chain 'U' and resid 74 through 76 No H-bonds generated for 'chain 'U' and resid 74 through 76' Processing helix chain 'V' and resid 32 through 40 Processing helix chain 'V' and resid 74 through 76 No H-bonds generated for 'chain 'V' and resid 74 through 76' Processing helix chain 'W' and resid 32 through 40 Processing helix chain 'W' and resid 74 through 76 No H-bonds generated for 'chain 'W' and resid 74 through 76' Processing helix chain 'X' and resid 32 through 40 Processing helix chain 'X' and resid 74 through 76 No H-bonds generated for 'chain 'X' and resid 74 through 76' Processing helix chain 'Y' and resid 32 through 40 Processing helix chain 'Y' and resid 74 through 76 No H-bonds generated for 'chain 'Y' and resid 74 through 76' Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 74 through 76 No H-bonds generated for 'chain 'Z' and resid 74 through 76' Processing helix chain '0' and resid 32 through 40 Processing helix chain '0' and resid 74 through 76 No H-bonds generated for 'chain '0' and resid 74 through 76' Processing helix chain '1' and resid 32 through 40 Processing helix chain '1' and resid 74 through 76 No H-bonds generated for 'chain '1' and resid 74 through 76' Processing helix chain '2' and resid 32 through 40 Processing helix chain '2' and resid 74 through 76 No H-bonds generated for 'chain '2' and resid 74 through 76' Processing helix chain '3' and resid 32 through 40 Processing helix chain '3' and resid 74 through 76 No H-bonds generated for 'chain '3' and resid 74 through 76' Processing helix chain '4' and resid 32 through 40 Processing helix chain '4' and resid 74 through 76 No H-bonds generated for 'chain '4' and resid 74 through 76' Processing helix chain '5' and resid 32 through 40 Processing helix chain '5' and resid 74 through 76 No H-bonds generated for 'chain '5' and resid 74 through 76' Processing helix chain '6' and resid 32 through 40 Processing helix chain '6' and resid 74 through 76 No H-bonds generated for 'chain '6' and resid 74 through 76' Processing helix chain '7' and resid 32 through 40 Processing helix chain '7' and resid 74 through 76 No H-bonds generated for 'chain '7' and resid 74 through 76' Processing helix chain '8' and resid 32 through 40 Processing helix chain '8' and resid 74 through 76 No H-bonds generated for 'chain '8' and resid 74 through 76' Processing helix chain '9' and resid 32 through 40 Processing helix chain '9' and resid 74 through 76 No H-bonds generated for 'chain '9' and resid 74 through 76' Processing helix chain 'a' and resid 32 through 40 Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'b' and resid 32 through 40 Processing helix chain 'b' and resid 74 through 76 No H-bonds generated for 'chain 'b' and resid 74 through 76' Processing helix chain 'c' and resid 32 through 40 Processing helix chain 'c' and resid 74 through 76 No H-bonds generated for 'chain 'c' and resid 74 through 76' Processing helix chain 'd' and resid 32 through 40 Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'e' and resid 32 through 40 Processing helix chain 'e' and resid 74 through 76 No H-bonds generated for 'chain 'e' and resid 74 through 76' Processing helix chain 'f' and resid 32 through 40 Processing helix chain 'f' and resid 74 through 76 No H-bonds generated for 'chain 'f' and resid 74 through 76' Processing helix chain 'g' and resid 32 through 40 Processing helix chain 'g' and resid 74 through 76 No H-bonds generated for 'chain 'g' and resid 74 through 76' Processing helix chain 'h' and resid 32 through 40 Processing helix chain 'h' and resid 74 through 76 No H-bonds generated for 'chain 'h' and resid 74 through 76' Processing helix chain 'i' and resid 32 through 40 Processing helix chain 'i' and resid 74 through 76 No H-bonds generated for 'chain 'i' and resid 74 through 76' Processing helix chain 'j' and resid 32 through 40 Processing helix chain 'j' and resid 74 through 76 No H-bonds generated for 'chain 'j' and resid 74 through 76' Processing helix chain 'k' and resid 32 through 40 Processing helix chain 'k' and resid 74 through 76 No H-bonds generated for 'chain 'k' and resid 74 through 76' Processing helix chain 'l' and resid 32 through 40 Processing helix chain 'l' and resid 74 through 76 No H-bonds generated for 'chain 'l' and resid 74 through 76' Processing helix chain 'm' and resid 32 through 40 Processing helix chain 'm' and resid 74 through 76 No H-bonds generated for 'chain 'm' and resid 74 through 76' Processing helix chain 'n' and resid 32 through 40 Processing helix chain 'n' and resid 74 through 76 No H-bonds generated for 'chain 'n' and resid 74 through 76' Processing helix chain 'o' and resid 32 through 40 Processing helix chain 'o' and resid 74 through 76 No H-bonds generated for 'chain 'o' and resid 74 through 76' Processing helix chain 'p' and resid 32 through 40 Processing helix chain 'p' and resid 74 through 76 No H-bonds generated for 'chain 'p' and resid 74 through 76' Processing helix chain 'q' and resid 32 through 40 Processing helix chain 'q' and resid 74 through 76 No H-bonds generated for 'chain 'q' and resid 74 through 76' Processing helix chain 'r' and resid 32 through 40 Processing helix chain 'r' and resid 74 through 76 No H-bonds generated for 'chain 'r' and resid 74 through 76' Processing helix chain 's' and resid 32 through 40 Processing helix chain 's' and resid 74 through 76 No H-bonds generated for 'chain 's' and resid 74 through 76' Processing helix chain 't' and resid 32 through 40 Processing helix chain 't' and resid 74 through 76 No H-bonds generated for 'chain 't' and resid 74 through 76' Processing helix chain 'v' and resid 32 through 40 Processing helix chain 'v' and resid 74 through 76 No H-bonds generated for 'chain 'v' and resid 74 through 76' Processing helix chain 'w' and resid 32 through 40 Processing helix chain 'w' and resid 74 through 76 No H-bonds generated for 'chain 'w' and resid 74 through 76' Processing helix chain 'x' and resid 32 through 40 Processing helix chain 'x' and resid 74 through 76 No H-bonds generated for 'chain 'x' and resid 74 through 76' Processing helix chain 'y' and resid 32 through 40 Processing helix chain 'y' and resid 74 through 76 No H-bonds generated for 'chain 'y' and resid 74 through 76' 305 hydrogen bonds defined for protein. 915 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: 17.33 Time building geometry restraints manager: 33.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 32441 1.34 - 1.45: 20252 1.45 - 1.57: 53935 1.57 - 1.68: 0 1.68 - 1.80: 122 Bond restraints: 106750 Sorted by residual: bond pdb=" CB VAL R 99 " pdb=" CG2 VAL R 99 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CB VAL a 99 " pdb=" CG2 VAL a 99 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CB VAL L 99 " pdb=" CG2 VAL L 99 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CB VAL E 99 " pdb=" CG2 VAL E 99 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 bond pdb=" CB VAL F 99 " pdb=" CG2 VAL F 99 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.51e+00 ... (remaining 106745 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.18: 5063 107.18 - 113.90: 53363 113.90 - 120.62: 43065 120.62 - 127.33: 42066 127.33 - 134.05: 1623 Bond angle restraints: 145180 Sorted by residual: angle pdb=" N THR 1 153 " pdb=" CA THR 1 153 " pdb=" C THR 1 153 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N THR 4 153 " pdb=" CA THR 4 153 " pdb=" C THR 4 153 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N THR r 153 " pdb=" CA THR r 153 " pdb=" C THR r 153 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N THR I 153 " pdb=" CA THR I 153 " pdb=" C THR I 153 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.52e+01 angle pdb=" N THR w 153 " pdb=" CA THR w 153 " pdb=" C THR w 153 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.52e+01 ... (remaining 145175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 53058 14.04 - 28.07: 6173 28.07 - 42.11: 2562 42.11 - 56.15: 122 56.15 - 70.19: 61 Dihedral angle restraints: 61976 sinusoidal: 26108 harmonic: 35868 Sorted by residual: dihedral pdb=" CA THR v 153 " pdb=" C THR v 153 " pdb=" N PRO v 154 " pdb=" CA PRO v 154 " ideal model delta harmonic sigma weight residual 180.00 142.73 37.27 0 5.00e+00 4.00e-02 5.56e+01 dihedral pdb=" CA THR H 153 " pdb=" C THR H 153 " pdb=" N PRO H 154 " pdb=" CA PRO H 154 " ideal model delta harmonic sigma weight residual 180.00 142.73 37.27 0 5.00e+00 4.00e-02 5.56e+01 dihedral pdb=" CA THR q 153 " pdb=" C THR q 153 " pdb=" N PRO q 154 " pdb=" CA PRO q 154 " ideal model delta harmonic sigma weight residual 180.00 142.73 37.27 0 5.00e+00 4.00e-02 5.56e+01 ... (remaining 61973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 8333 0.035 - 0.071: 3819 0.071 - 0.106: 1341 0.106 - 0.141: 598 0.141 - 0.176: 122 Chirality restraints: 14213 Sorted by residual: chirality pdb=" CB VAL K 52 " pdb=" CA VAL K 52 " pdb=" CG1 VAL K 52 " pdb=" CG2 VAL K 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB VAL Y 52 " pdb=" CA VAL Y 52 " pdb=" CG1 VAL Y 52 " pdb=" CG2 VAL Y 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB VAL j 52 " pdb=" CA VAL j 52 " pdb=" CG1 VAL j 52 " pdb=" CG2 VAL j 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 14210 not shown) Planarity restraints: 19093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR r 153 " 0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO r 154 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO r 154 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO r 154 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 4 153 " 0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO 4 154 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO 4 154 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO 4 154 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 153 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO C 154 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 154 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 154 " -0.047 5.00e-02 4.00e+02 ... (remaining 19090 not shown) Histogram of nonbonded interaction distances: 0.15 - 1.10: 447 1.10 - 2.05: 2116 2.05 - 3.00: 56342 3.00 - 3.95: 286598 3.95 - 4.90: 574889 Warning: very small nonbonded interaction distances. Nonbonded interactions: 920392 Sorted by model distance: nonbonded pdb=" CG ASP A 140 " pdb=" N ILE t 78 " model vdw 0.152 3.350 nonbonded pdb=" CG GLN A 195 " pdb=" O PHE t 201 " model vdw 0.274 3.440 nonbonded pdb=" CA GLY A 115 " pdb=" C LYS t 189 " model vdw 0.322 3.670 nonbonded pdb=" CD PRO A 154 " pdb=" CD LYS t 189 " model vdw 0.322 3.840 nonbonded pdb=" CB ASP A 169 " pdb=" N THR t 153 " model vdw 0.333 3.520 ... (remaining 920387 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 67100 2.51 5 N 18361 2.21 5 O 17568 1.98 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.070 Extract box with map and model: 12.210 Check model and map are aligned: 1.580 Convert atoms to be neutral: 0.910 Process input model: 174.850 Find NCS groups from input model: 5.270 Set up NCS constraints: 1.280 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 106750 Z= 0.380 Angle : 0.828 8.603 145180 Z= 0.480 Chirality : 0.049 0.176 14213 Planarity : 0.008 0.084 19093 Dihedral : 13.255 70.186 39040 Min Nonbonded Distance : 0.152 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.53 % Favored : 93.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.06), residues: 12139 helix: -4.58 (0.05), residues: 671 sheet: -2.21 (0.07), residues: 4514 loop : -2.43 (0.06), residues: 6954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1646 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1646 time to evaluate : 9.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1646 average time/residue: 1.8201 time to fit residues: 4058.6726 Evaluate side-chains 1188 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1188 time to evaluate : 9.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.5037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 1030 optimal weight: 0.3980 chunk 924 optimal weight: 7.9990 chunk 513 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 494 optimal weight: 2.9990 chunk 956 optimal weight: 10.0000 chunk 370 optimal weight: 0.3980 chunk 581 optimal weight: 10.0000 chunk 711 optimal weight: 10.0000 chunk 1107 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 211 ASN u 176 GLN u 179 ASN u 181 GLN u 211 ASN ** u 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 45 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 176 GLN B 179 ASN B 211 ASN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN C 176 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 213 GLN D 45 ASN D 171 ASN D 176 GLN D 179 ASN D 181 GLN D 211 ASN E 45 ASN E 51 GLN E 176 GLN E 181 GLN E 190 GLN E 211 ASN E 213 GLN F 45 ASN F 51 GLN F 176 GLN F 181 GLN F 190 GLN F 211 ASN F 213 GLN G 176 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 HIS ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 176 GLN ** I 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 ASN I 213 GLN J 45 ASN J 171 ASN J 176 GLN J 179 ASN J 181 GLN J 211 ASN K 45 ASN K 171 ASN K 176 GLN K 179 ASN K 181 GLN K 211 ASN L 45 ASN L 51 GLN L 176 GLN L 181 GLN L 190 GLN L 211 ASN L 213 GLN M 176 GLN M 179 ASN M 181 GLN M 211 ASN ** M 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 ASN N 45 ASN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS N 176 GLN N 179 ASN N 211 ASN ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 ASN O 176 GLN ** O 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 ASN O 213 GLN P 45 ASN P 176 GLN ** P 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 211 ASN P 213 GLN Q 45 ASN Q 171 ASN Q 176 GLN Q 179 ASN Q 181 GLN Q 211 ASN R 45 ASN R 51 GLN R 176 GLN R 181 GLN R 190 GLN R 211 ASN R 213 GLN S 176 GLN S 179 ASN S 181 GLN S 211 ASN ** S 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 ASN T 45 ASN ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 HIS T 176 GLN T 179 ASN T 211 ASN ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 ASN U 51 GLN U 176 GLN U 181 GLN U 190 GLN U 211 ASN U 213 GLN V 176 GLN V 179 ASN V 181 GLN V 211 ASN ** V 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN W 45 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 HIS W 176 GLN W 179 ASN W 211 ASN ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 ASN X 176 GLN ** X 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 211 ASN X 213 GLN Y 45 ASN Y 171 ASN Y 176 GLN Y 179 ASN Y 181 GLN Y 211 ASN Z 176 GLN Z 179 ASN Z 181 GLN Z 211 ASN ** Z 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 ASN 0 45 ASN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 69 HIS 0 176 GLN 0 179 ASN 0 211 ASN ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 ASN 1 176 GLN ** 1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 211 ASN 1 213 GLN 2 45 ASN 2 171 ASN 2 176 GLN 2 179 ASN 2 181 GLN 2 211 ASN 3 45 ASN 3 51 GLN 3 176 GLN 3 181 GLN 3 190 GLN 3 211 ASN 3 213 GLN 4 45 ASN 4 176 GLN ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 211 ASN 4 213 GLN 5 45 ASN 5 171 ASN 5 176 GLN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 211 ASN 6 45 ASN 6 51 GLN 6 176 GLN 6 181 GLN 6 190 GLN 6 211 ASN 6 213 GLN 7 176 GLN 7 179 ASN 7 181 GLN 7 211 ASN ** 7 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 41 ASN 8 45 ASN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 69 HIS 8 176 GLN 8 179 ASN 8 211 ASN ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 45 ASN 9 171 ASN 9 176 GLN 9 179 ASN 9 181 GLN 9 211 ASN a 45 ASN a 51 GLN a 176 GLN a 181 GLN a 190 GLN a 211 ASN a 213 GLN b 176 GLN b 179 ASN b 181 GLN b 211 ASN ** b 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 ASN c 45 ASN ** c 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 HIS c 176 GLN c 179 ASN c 211 ASN ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN d 176 GLN ** d 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 211 ASN d 213 GLN e 45 ASN e 176 GLN ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 211 ASN e 213 GLN f 45 ASN f 171 ASN f 176 GLN f 179 ASN f 181 GLN f 211 ASN g 45 ASN g 51 GLN g 176 GLN g 181 GLN g 190 GLN g 211 ASN g 213 GLN h 176 GLN h 179 ASN h 181 GLN h 211 ASN ** h 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 41 ASN i 45 ASN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 69 HIS i 176 GLN i 179 ASN i 211 ASN ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 45 ASN j 171 ASN j 176 GLN j 179 ASN j 181 GLN j 211 ASN k 51 GLN k 176 GLN k 181 GLN k 190 GLN k 211 ASN k 213 GLN l 176 GLN l 179 ASN l 181 GLN l 211 ASN ** l 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 41 ASN m 45 ASN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 69 HIS m 176 GLN m 179 ASN m 211 ASN ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 45 ASN n 176 GLN ** n 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 211 ASN n 213 GLN o 51 GLN ** o 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 176 GLN o 181 GLN o 190 GLN o 211 ASN o 213 GLN p 176 GLN p 179 ASN p 181 GLN p 211 ASN ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 ASN q 45 ASN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 69 HIS q 176 GLN q 179 ASN q 211 ASN ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 45 ASN r 176 GLN ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 211 ASN r 213 GLN s 45 ASN ** s 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 176 GLN ** s 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 211 ASN ** t 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 104 GLN ** t 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 41 ASN v 69 HIS v 176 GLN ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 211 ASN ** v 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 ASN w 176 GLN ** w 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 211 ASN w 213 GLN x 45 ASN x 171 ASN x 176 GLN x 179 ASN x 181 GLN x 211 ASN y 45 ASN y 51 GLN y 176 GLN y 181 GLN y 190 GLN y 211 ASN y 213 GLN Total number of N/Q/H flips: 308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.032 106750 Z= 0.740 Angle : 0.893 36.896 145180 Z= 0.477 Chirality : 0.053 1.139 14213 Planarity : 0.008 0.238 19093 Dihedral : 6.428 86.194 13969 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.14 % Favored : 95.18 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.35 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.06), residues: 12139 helix: -3.61 (0.09), residues: 667 sheet: -2.09 (0.06), residues: 4843 loop : -2.28 (0.07), residues: 6629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1987 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 420 poor density : 1567 time to evaluate : 9.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 420 outliers final: 95 residues processed: 1818 average time/residue: 1.7291 time to fit residues: 4370.8240 Evaluate side-chains 1486 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1391 time to evaluate : 11.154 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 47 residues processed: 48 average time/residue: 1.3964 time to fit residues: 114.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 615 optimal weight: 8.9990 chunk 343 optimal weight: 0.8980 chunk 922 optimal weight: 7.9990 chunk 754 optimal weight: 9.9990 chunk 305 optimal weight: 0.0970 chunk 1109 optimal weight: 4.9990 chunk 1198 optimal weight: 6.9990 chunk 988 optimal weight: 9.9990 chunk 1100 optimal weight: 30.0000 chunk 378 optimal weight: 9.9990 chunk 890 optimal weight: 0.0050 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 182 ASN ** u 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 179 ASN C 181 GLN C 211 ASN D 171 ASN D 207 ASN D 221 GLN E 190 GLN E 211 ASN E 213 GLN F 190 GLN F 211 ASN F 213 GLN G 45 ASN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** H 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 GLN I 179 ASN I 181 GLN I 211 ASN J 171 ASN J 207 ASN J 221 GLN K 171 ASN K 207 ASN K 221 GLN L 190 GLN L 211 ASN L 213 GLN M 45 ASN M 182 ASN ** M 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 GLN ** O 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 ASN P 51 GLN ** P 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 211 ASN Q 171 ASN Q 207 ASN Q 221 GLN R 211 ASN R 213 GLN S 45 ASN S 182 ASN ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 211 ASN U 213 GLN V 45 ASN V 182 ASN ** V 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 51 GLN X 179 ASN X 181 GLN X 211 ASN Y 171 ASN Y 207 ASN Y 221 GLN Z 45 ASN Z 182 ASN ** Z 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 51 GLN ** 1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 211 ASN 2 171 ASN 2 207 ASN 2 221 GLN 3 211 ASN 3 213 GLN 4 51 GLN ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 211 ASN 5 171 ASN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 5 221 GLN 6 211 ASN 6 213 GLN 7 45 ASN 7 182 ASN ** 7 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 171 ASN 9 207 ASN 9 221 GLN a 211 ASN a 213 GLN b 45 ASN b 182 ASN ** b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 51 GLN ** d 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 GLN e 179 ASN e 181 GLN e 211 ASN f 171 ASN f 207 ASN f 221 GLN g 190 GLN g 211 ASN g 213 GLN h 45 ASN h 182 ASN ** h 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 171 ASN j 207 ASN j 221 GLN k 190 GLN k 211 ASN k 213 GLN l 45 ASN l 182 ASN ** l 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 51 GLN n 179 ASN n 181 GLN n 211 ASN ** o 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 211 ASN o 213 GLN p 45 ASN p 182 ASN ** p 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN r 179 ASN r 181 GLN r 211 ASN ** s 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 176 GLN ** s 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 207 ASN s 221 GLN t 45 ASN t 104 GLN t 176 GLN ** t 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 51 GLN ** w 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 211 ASN x 171 ASN x 207 ASN x 221 GLN y 149 HIS y 190 GLN y 211 ASN y 213 GLN Total number of N/Q/H flips: 130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.015 106750 Z= 0.678 Angle : 0.745 36.662 145180 Z= 0.397 Chirality : 0.048 0.981 14213 Planarity : 0.007 0.154 19093 Dihedral : 5.941 53.263 13969 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.88 % Favored : 95.58 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.02 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.07), residues: 12139 helix: -2.24 (0.12), residues: 662 sheet: -1.95 (0.07), residues: 4709 loop : -2.19 (0.07), residues: 6768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1766 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 450 poor density : 1316 time to evaluate : 9.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 450 outliers final: 170 residues processed: 1621 average time/residue: 1.6723 time to fit residues: 3790.1296 Evaluate side-chains 1410 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1240 time to evaluate : 9.054 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 122 residues processed: 48 average time/residue: 1.6433 time to fit residues: 122.2589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 1096 optimal weight: 6.9990 chunk 834 optimal weight: 0.8980 chunk 576 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 529 optimal weight: 5.9990 chunk 745 optimal weight: 0.0370 chunk 1113 optimal weight: 1.9990 chunk 1179 optimal weight: 0.0000 chunk 581 optimal weight: 6.9990 chunk 1055 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 overall best weight: 1.7866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 181 GLN ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 181 GLN C 211 ASN D 171 ASN D 179 ASN D 207 ASN E 211 ASN E 213 GLN F 211 ASN F 213 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN I 211 ASN J 171 ASN J 179 ASN J 207 ASN K 171 ASN K 179 ASN K 207 ASN L 211 ASN L 213 GLN M 181 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 221 GLN O 179 ASN O 181 GLN O 211 ASN P 179 ASN P 181 GLN P 211 ASN Q 171 ASN Q 179 ASN Q 207 ASN R 211 ASN R 213 GLN S 181 GLN ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN U 211 ASN U 213 GLN V 181 GLN ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 GLN X 211 ASN Y 171 ASN Y 179 ASN Y 207 ASN Z 181 GLN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 221 GLN 1 179 ASN 1 181 GLN 1 211 ASN 2 171 ASN 2 179 ASN 2 207 ASN 3 211 ASN 3 213 GLN 4 179 ASN 4 181 GLN 4 211 ASN 5 171 ASN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 6 211 ASN 6 213 GLN 7 181 GLN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN 9 171 ASN 9 179 ASN 9 207 ASN a 211 ASN a 213 GLN b 181 GLN ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 GLN d 179 ASN d 181 GLN e 179 ASN e 181 GLN e 211 ASN f 171 ASN f 179 ASN f 207 ASN g 211 ASN g 213 GLN h 181 GLN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 221 GLN j 171 ASN j 179 ASN j 207 ASN k 211 ASN k 213 GLN l 181 GLN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 221 GLN n 179 ASN n 211 ASN ** o 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 211 ASN o 213 GLN p 181 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 221 GLN r 179 ASN r 211 ASN s 176 GLN ** s 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 207 ASN ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 211 ASN w 179 ASN w 181 GLN w 211 ASN x 171 ASN x 179 ASN x 207 ASN y 211 ASN y 213 GLN Total number of N/Q/H flips: 109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.027 106750 Z= 0.653 Angle : 0.674 36.982 145180 Z= 0.361 Chirality : 0.046 0.685 14213 Planarity : 0.006 0.117 19093 Dihedral : 5.573 55.874 13969 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.91 % Favored : 95.56 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.07), residues: 12139 helix: -0.87 (0.15), residues: 662 sheet: -1.80 (0.07), residues: 4677 loop : -2.12 (0.07), residues: 6800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 488 poor density : 1231 time to evaluate : 9.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 488 outliers final: 188 residues processed: 1575 average time/residue: 1.6610 time to fit residues: 3656.4413 Evaluate side-chains 1348 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1160 time to evaluate : 8.913 Switching outliers to nearest non-outliers outliers start: 188 outliers final: 161 residues processed: 27 average time/residue: 1.2083 time to fit residues: 62.1293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 982 optimal weight: 10.0000 chunk 669 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 878 optimal weight: 5.9990 chunk 486 optimal weight: 0.9980 chunk 1006 optimal weight: 1.9990 chunk 815 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 602 optimal weight: 30.0000 chunk 1058 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 213 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN D 176 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN E 211 ASN E 213 GLN F 211 ASN F 213 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 ASN I 181 GLN I 211 ASN J 176 GLN J 179 ASN J 182 ASN J 207 ASN K 176 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN L 211 ASN L 213 GLN M 213 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 221 GLN O 181 GLN O 211 ASN P 211 ASN Q 176 GLN ** Q 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 ASN R 211 ASN R 213 GLN S 213 GLN ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN U 211 ASN U 213 GLN V 213 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 GLN X 179 ASN X 211 ASN Y 176 GLN ** Y 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 207 ASN Z 213 GLN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 221 GLN 1 179 ASN ** 1 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 176 GLN 2 179 ASN 2 182 ASN 2 207 ASN 3 211 ASN 3 213 GLN ** 4 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 GLN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 6 211 ASN 6 213 GLN 7 213 GLN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN 9 176 GLN ** 9 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 207 ASN a 211 ASN a 213 GLN b 213 GLN ** c 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 GLN ** d 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 211 ASN f 176 GLN f 179 ASN f 182 ASN f 207 ASN g 211 ASN g 213 GLN h 213 GLN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 221 GLN j 176 GLN j 179 ASN j 182 ASN j 207 ASN k 211 ASN k 213 GLN l 213 GLN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 221 GLN ** n 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 211 ASN ** o 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 211 ASN o 213 GLN o 230 ASN p 213 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 221 GLN r 179 ASN r 211 ASN s 83 GLN ** s 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 179 ASN s 207 ASN ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN ** t 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 211 ASN ** w 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 211 ASN x 176 GLN x 179 ASN x 182 ASN x 207 ASN y 69 HIS y 211 ASN y 213 GLN Total number of N/Q/H flips: 101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.021 106750 Z= 0.683 Angle : 0.698 36.643 145180 Z= 0.369 Chirality : 0.046 0.532 14213 Planarity : 0.006 0.126 19093 Dihedral : 5.829 52.295 13969 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.13 % Favored : 95.35 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.18 % Twisted General : 0.28 % 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: -2.59 (0.07), residues: 12139 helix: -0.05 (0.16), residues: 662 sheet: -1.56 (0.07), residues: 4357 loop : -2.03 (0.07), residues: 7120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1709 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 478 poor density : 1231 time to evaluate : 9.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 478 outliers final: 201 residues processed: 1553 average time/residue: 1.7815 time to fit residues: 3865.4401 Evaluate side-chains 1381 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1180 time to evaluate : 9.391 Switching outliers to nearest non-outliers outliers start: 201 outliers final: 164 residues processed: 37 average time/residue: 1.5581 time to fit residues: 95.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 396 optimal weight: 10.0000 chunk 1061 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 692 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 1180 optimal weight: 30.0000 chunk 979 optimal weight: 6.9990 chunk 546 optimal weight: 0.0870 chunk 98 optimal weight: 8.9990 chunk 390 optimal weight: 0.7980 chunk 619 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 213 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 211 ASN D 176 GLN D 181 GLN D 207 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN F 149 HIS ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN G 69 HIS ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN H 149 HIS ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 ASN I 181 GLN I 211 ASN J 176 GLN J 181 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 ASN K 176 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN L 149 HIS ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN ** M 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 HIS ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 221 GLN O 179 ASN O 181 GLN O 211 ASN P 211 ASN Q 176 GLN Q 181 GLN Q 207 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN ** S 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 213 GLN ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 HIS ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN U 149 HIS ** U 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 213 GLN ** V 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 213 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 149 HIS ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 GLN X 179 ASN X 211 ASN Y 176 GLN Y 181 GLN Y 207 ASN Z 213 GLN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 149 HIS ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 221 GLN 1 179 ASN ** 1 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 176 GLN 2 181 GLN ** 2 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 207 ASN 3 149 HIS ** 3 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 213 GLN ** 4 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 GLN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 6 149 HIS ** 6 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 213 GLN 7 213 GLN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 149 HIS ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN 9 176 GLN 9 181 GLN 9 207 ASN a 149 HIS ** a 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 GLN ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 213 GLN ** c 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 149 HIS ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 GLN d 179 ASN e 179 ASN e 181 GLN e 211 ASN f 176 GLN f 181 GLN ** f 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 207 ASN g 149 HIS ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 213 GLN ** h 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 213 GLN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 149 HIS ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 221 GLN j 176 GLN j 181 GLN ** j 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 207 ASN ** k 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN l 213 GLN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 149 HIS ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 221 GLN n 179 ASN n 211 ASN ** o 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 149 HIS ** o 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 213 GLN p 213 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 149 HIS ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 221 GLN r 179 ASN r 211 ASN s 83 GLN ** s 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 192 GLN s 207 ASN ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 149 HIS t 181 GLN ** t 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 179 ASN w 211 ASN x 176 GLN ** x 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 207 ASN ** y 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 213 GLN Total number of N/Q/H flips: 111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.020 106750 Z= 0.668 Angle : 0.676 35.103 145180 Z= 0.359 Chirality : 0.046 0.517 14213 Planarity : 0.006 0.122 19093 Dihedral : 5.717 51.488 13969 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.12 % Favored : 95.36 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.07), residues: 12139 helix: 0.65 (0.16), residues: 662 sheet: -1.45 (0.07), residues: 4337 loop : -1.99 (0.07), residues: 7140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 413 poor density : 1147 time to evaluate : 9.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 413 outliers final: 213 residues processed: 1477 average time/residue: 1.8008 time to fit residues: 3657.1025 Evaluate side-chains 1297 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1084 time to evaluate : 9.167 Switching outliers to nearest non-outliers outliers start: 213 outliers final: 178 residues processed: 35 average time/residue: 1.5335 time to fit residues: 89.6151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 1138 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 672 optimal weight: 10.0000 chunk 862 optimal weight: 0.2980 chunk 667 optimal weight: 0.8980 chunk 993 optimal weight: 10.0000 chunk 659 optimal weight: 5.9990 chunk 1175 optimal weight: 1.9990 chunk 735 optimal weight: 5.9990 chunk 716 optimal weight: 10.0000 chunk 542 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 213 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 181 GLN D 176 GLN D 179 ASN D 182 ASN D 207 ASN E 211 ASN E 213 GLN F 211 ASN F 213 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN H 181 GLN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN J 176 GLN ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 ASN K 176 GLN K 179 ASN K 182 ASN K 207 ASN L 211 ASN L 213 GLN ** M 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 221 GLN O 181 GLN Q 176 GLN Q 179 ASN Q 182 ASN Q 207 ASN R 211 ASN R 213 GLN ** S 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 213 GLN ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN U 211 ASN U 213 GLN ** V 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 213 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 GLN Y 176 GLN Y 179 ASN Y 182 ASN Y 207 ASN Z 213 GLN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 221 GLN 1 179 ASN ** 1 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 176 GLN ** 2 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 207 ASN 3 211 ASN 3 213 GLN ** 4 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 GLN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 6 211 ASN 6 213 GLN 7 213 GLN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN 9 176 GLN 9 179 ASN 9 182 ASN 9 207 ASN ** a 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 GLN b 213 GLN ** c 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 GLN d 179 ASN d 181 GLN e 179 ASN e 181 GLN f 176 GLN ** f 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 207 ASN ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 213 GLN ** h 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 213 GLN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 221 GLN j 176 GLN ** j 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 207 ASN ** k 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN l 213 GLN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 221 GLN n 179 ASN o 85 ASN ** o 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 213 GLN p 213 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 221 GLN r 179 ASN s 83 GLN ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 179 ASN s 192 GLN s 207 ASN t 104 GLN ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN ** t 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 149 HIS ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 211 ASN ** v 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 179 ASN x 176 GLN ** x 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 207 ASN y 211 ASN y 213 GLN Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.028 106750 Z= 0.648 Angle : 0.640 35.457 145180 Z= 0.341 Chirality : 0.044 0.479 14213 Planarity : 0.006 0.177 19093 Dihedral : 5.396 51.130 13969 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.02 % Favored : 95.46 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.21 % 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: -2.27 (0.07), residues: 12139 helix: 1.20 (0.17), residues: 662 sheet: -1.27 (0.07), residues: 4337 loop : -1.98 (0.07), residues: 7140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1466 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1097 time to evaluate : 10.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 369 outliers final: 181 residues processed: 1402 average time/residue: 1.7614 time to fit residues: 3412.3772 Evaluate side-chains 1230 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1049 time to evaluate : 9.135 Switching outliers to nearest non-outliers outliers start: 181 outliers final: 165 residues processed: 16 average time/residue: 0.9946 time to fit residues: 38.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 727 optimal weight: 3.9990 chunk 469 optimal weight: 0.0970 chunk 702 optimal weight: 5.9990 chunk 354 optimal weight: 0.1980 chunk 231 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 747 optimal weight: 0.9990 chunk 801 optimal weight: 9.9990 chunk 581 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 924 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN A 213 GLN u 190 GLN u 213 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 181 GLN C 211 ASN D 176 GLN D 207 ASN E 211 ASN E 213 GLN F 211 ASN F 213 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN H 181 GLN H 182 ASN ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN I 211 ASN J 176 GLN ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 ASN K 176 GLN K 207 ASN L 211 ASN L 213 GLN M 181 GLN M 213 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 221 GLN O 181 GLN O 211 ASN O 221 GLN P 211 ASN Q 176 GLN Q 207 ASN R 211 ASN R 213 GLN S 181 GLN S 190 GLN S 213 GLN ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN U 211 ASN U 213 GLN V 181 GLN V 190 GLN V 213 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 GLN X 211 ASN X 221 GLN Y 176 GLN Y 207 ASN Z 190 GLN Z 213 GLN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 221 GLN 1 211 ASN 2 176 GLN 2 179 ASN 2 182 ASN 2 207 ASN 3 211 ASN 3 213 GLN 4 179 ASN 4 211 ASN 5 176 GLN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 207 ASN 6 211 ASN 6 213 GLN 7 190 GLN 7 213 GLN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN 9 176 GLN 9 207 ASN a 211 ASN a 213 GLN b 213 GLN ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 179 ASN e 179 ASN e 181 GLN e 211 ASN e 221 GLN f 176 GLN f 179 ASN ** f 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 ASN f 207 ASN g 211 ASN g 213 GLN h 181 GLN h 213 GLN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 221 GLN j 176 GLN j 179 ASN j 182 ASN j 207 ASN k 45 ASN ** k 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN l 190 GLN l 213 GLN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 221 GLN n 179 ASN n 211 ASN o 45 ASN o 211 ASN o 213 GLN p 190 GLN p 213 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 221 GLN r 211 ASN r 221 GLN s 83 GLN ** s 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 192 GLN s 207 ASN ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 179 ASN ** t 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 211 ASN ** v 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 230 ASN w 179 ASN w 211 ASN x 176 GLN x 179 ASN x 182 ASN x 207 ASN y 211 ASN y 213 GLN Total number of N/Q/H flips: 121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.025 106750 Z= 0.644 Angle : 0.624 35.591 145180 Z= 0.333 Chirality : 0.044 0.479 14213 Planarity : 0.006 0.138 19093 Dihedral : 5.144 49.955 13969 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.93 % Favored : 95.56 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.10 % Twisted General : 0.22 % 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: -2.33 (0.07), residues: 12139 helix: 1.63 (0.18), residues: 662 sheet: -1.36 (0.07), residues: 4676 loop : -2.04 (0.07), residues: 6801 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 340 poor density : 1177 time to evaluate : 9.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 340 outliers final: 185 residues processed: 1458 average time/residue: 1.7889 time to fit residues: 3606.8334 Evaluate side-chains 1277 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1092 time to evaluate : 9.118 Switching outliers to nearest non-outliers outliers start: 185 outliers final: 167 residues processed: 18 average time/residue: 1.1877 time to fit residues: 46.4951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 1069 optimal weight: 9.9990 chunk 1126 optimal weight: 0.9990 chunk 1027 optimal weight: 7.9990 chunk 1095 optimal weight: 4.9990 chunk 659 optimal weight: 7.9990 chunk 477 optimal weight: 8.9990 chunk 860 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 990 optimal weight: 30.0000 chunk 1036 optimal weight: 4.9990 chunk 1091 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 69 HIS ** u 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 213 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 221 GLN D 83 GLN D 176 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 207 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN G 213 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** H 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 GLN J 176 GLN ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 ASN K 83 GLN K 176 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN K 207 ASN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN M 69 HIS M 181 GLN M 213 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 221 GLN Q 83 GLN Q 176 GLN ** Q 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 GLN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 192 GLN Q 207 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN S 69 HIS S 181 GLN S 213 GLN ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 213 GLN V 69 HIS V 181 GLN V 213 GLN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Y 176 GLN ** Y 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 181 GLN ** Y 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 192 GLN Y 207 ASN Z 69 HIS ** Z 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 213 GLN ** 0 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 211 ASN 1 221 GLN 2 176 GLN 2 179 ASN 2 181 GLN 2 207 ASN ** 3 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 213 GLN 4 179 ASN 4 181 GLN 4 211 ASN 4 221 GLN 5 83 GLN 5 176 GLN ** 5 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 192 GLN 5 207 ASN ** 6 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 213 GLN 7 69 HIS ** 7 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 213 GLN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 83 GLN 9 176 GLN ** 9 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 181 GLN ** 9 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 192 GLN 9 207 ASN ** a 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 GLN b 69 HIS ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 213 GLN ** c 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 GLN d 179 ASN d 221 GLN e 179 ASN f 176 GLN f 179 ASN f 207 ASN ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 213 GLN h 69 HIS h 181 GLN h 213 GLN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 176 GLN j 179 ASN j 181 GLN j 207 ASN ** k 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN l 69 HIS ** l 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 213 GLN ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 221 GLN ** o 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 213 GLN p 69 HIS ** p 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 213 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 83 GLN ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 192 GLN s 207 ASN ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 211 ASN ** t 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 179 ASN w 221 GLN x 176 GLN x 179 ASN x 181 GLN x 207 ASN ** y 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 213 GLN Total number of N/Q/H flips: 104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.011 106750 Z= 0.624 Angle : 0.694 35.651 145180 Z= 0.364 Chirality : 0.047 0.621 14213 Planarity : 0.006 0.112 19093 Dihedral : 5.757 50.002 13969 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.16 % Favored : 95.32 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.66 % Twisted General : 0.22 % 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: -2.19 (0.07), residues: 12139 helix: 1.39 (0.17), residues: 668 sheet: -1.17 (0.07), residues: 4337 loop : -1.97 (0.07), residues: 7134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1137 time to evaluate : 9.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 362 outliers final: 201 residues processed: 1420 average time/residue: 1.8131 time to fit residues: 3525.6540 Evaluate side-chains 1325 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1124 time to evaluate : 8.871 Switching outliers to nearest non-outliers outliers start: 201 outliers final: 182 residues processed: 19 average time/residue: 1.6308 time to fit residues: 56.3520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 719 optimal weight: 8.9990 chunk 1158 optimal weight: 5.9990 chunk 707 optimal weight: 2.9990 chunk 549 optimal weight: 0.9990 chunk 805 optimal weight: 0.0000 chunk 1215 optimal weight: 3.9990 chunk 1118 optimal weight: 6.9990 chunk 967 optimal weight: 7.9990 chunk 100 optimal weight: 30.0000 chunk 747 optimal weight: 0.0060 chunk 593 optimal weight: 3.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 179 ASN D 83 GLN D 176 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 207 ASN E 211 ASN E 213 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN G 181 GLN G 213 GLN H 51 GLN H 181 GLN H 213 GLN H 221 GLN I 181 GLN J 83 GLN J 176 GLN J 192 GLN J 207 ASN K 176 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN M 181 GLN N 51 GLN N 213 GLN O 181 GLN Q 83 GLN Q 176 GLN ** Q 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 192 GLN Q 207 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN S 181 GLN T 51 GLN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** U 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 213 GLN V 181 GLN V 213 GLN W 51 GLN ** W 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 213 GLN Y 83 GLN Y 176 GLN ** Y 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 192 GLN Y 207 ASN ** Z 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 213 GLN 0 51 GLN 0 213 GLN 1 179 ASN 2 83 GLN 2 176 GLN 2 179 ASN 2 192 GLN 2 207 ASN ** 3 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 213 GLN 5 176 GLN 5 179 ASN 5 207 ASN ** 6 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 213 GLN ** 7 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 213 GLN 8 51 GLN ** 8 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 213 GLN 9 83 GLN 9 176 GLN ** 9 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 192 GLN 9 207 ASN a 211 ASN a 213 GLN ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 213 GLN c 51 GLN c 179 ASN c 182 ASN ** c 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 213 GLN d 179 ASN f 83 GLN f 176 GLN f 179 ASN ** f 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 192 GLN f 207 ASN g 211 ASN g 213 GLN h 181 GLN i 51 GLN ** i 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 213 GLN j 83 GLN j 176 GLN j 179 ASN j 192 GLN j 207 ASN ** k 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN ** l 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 213 GLN m 51 GLN m 213 GLN n 179 ASN ** o 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 213 GLN ** p 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN q 213 GLN r 179 ASN s 83 GLN ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 192 GLN s 207 ASN ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 221 GLN ** v 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 179 ASN x 83 GLN x 176 GLN x 179 ASN x 192 GLN x 207 ASN ** y 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 211 ASN y 213 GLN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.012 106750 Z= 0.567 Angle : 0.639 35.684 145180 Z= 0.337 Chirality : 0.045 0.615 14213 Planarity : 0.006 0.114 19093 Dihedral : 5.335 49.198 13969 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.37 % Favored : 95.12 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.10 % Twisted General : 0.20 % 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: -2.08 (0.07), residues: 12139 helix: 1.62 (0.17), residues: 662 sheet: -1.04 (0.07), residues: 4336 loop : -1.95 (0.07), residues: 7141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24278 Ramachandran restraints generated. 12139 Oldfield, 0 Emsley, 12139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1089 time to evaluate : 9.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 268 outliers final: 170 residues processed: 1334 average time/residue: 1.7135 time to fit residues: 3187.4169 Evaluate side-chains 1215 residues out of total 10797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1045 time to evaluate : 9.045 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 167 residues processed: 3 average time/residue: 1.8465 time to fit residues: 19.8967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1220 random chunks: chunk 768 optimal weight: 20.0000 chunk 1030 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 892 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 969 optimal weight: 0.0770 chunk 405 optimal weight: 7.9990 chunk 995 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN B 213 GLN C 179 ASN ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** E 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN G 181 GLN G 190 GLN G 213 GLN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** H 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 GLN ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN ** J 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 ASN K 176 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 ASN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 GLN M 181 GLN N 190 GLN N 213 GLN ** O 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 GLN ** Q 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 181 GLN ** Q 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 207 ASN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN ** S 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 213 GLN ** U 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 213 GLN ** V 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 213 GLN W 190 GLN W 213 GLN ** X 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 176 GLN ** Y 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 181 GLN ** Y 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 207 ASN ** Z 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 213 GLN 0 213 GLN 1 149 HIS ** 1 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 176 GLN 2 179 ASN 2 181 GLN 2 207 ASN ** 3 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 213 GLN 4 149 HIS ** 4 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 GLN 5 179 ASN 5 207 ASN ** 6 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 213 GLN ** 7 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN 7 213 GLN 8 213 GLN 9 176 GLN ** 9 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 181 GLN ** 9 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 207 ASN ** a 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 GLN ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 213 GLN ** c 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 213 GLN ** d 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 181 GLN ** e 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 176 GLN ** f 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 207 ASN ** g 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 213 GLN h 181 GLN i 213 GLN j 176 GLN j 179 ASN j 181 GLN j 207 ASN ** k 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN ** l 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 213 GLN m 213 GLN n 179 ASN ** n 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 213 GLN ** p 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 213 GLN ** r 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 83 GLN ** s 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 192 GLN s 207 ASN ** t 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 192 GLN ** v 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 179 ASN ** w 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 176 GLN ** x 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 207 ASN ** y 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 213 GLN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.120895 restraints weight = 118539.221| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.14 r_work: 0.3160 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.008 106750 Z= 0.642 Angle : 0.714 35.778 145180 Z= 0.372 Chirality : 0.049 0.634 14213 Planarity : 0.007 0.141 19093 Dihedral : 5.895 49.713 13969 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.14 % Favored : 95.35 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.18 % Twisted General : 0.21 % 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: -2.17 (0.07), residues: 12139 helix: 1.23 (0.17), residues: 668 sheet: -1.15 (0.07), residues: 4336 loop : -1.95 (0.07), residues: 7135 =============================================================================== Job complete usr+sys time: 45857.98 seconds wall clock time: 792 minutes 55.06 seconds (47575.06 seconds total)