Starting phenix.real_space_refine (version: dev) on Mon Dec 19 04:39:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/12_2022/6rpo_4979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/12_2022/6rpo_4979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/12_2022/6rpo_4979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/12_2022/6rpo_4979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/12_2022/6rpo_4979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/12_2022/6rpo_4979.pdb" } resolution = 2.39 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= 0.000 sd= 0.019 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 "u ARG 50": "NH1" <-> "NH2" Residue "u PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 75": "OD1" <-> "OD2" Residue "u ASP 76": "OD1" <-> "OD2" Residue "u PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 95": "NH1" <-> "NH2" Residue "u PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 114": "NH1" <-> "NH2" Residue "u ARG 148": "NH1" <-> "NH2" Residue "u ARG 160": "NH1" <-> "NH2" Residue "u ASP 169": "OD1" <-> "OD2" Residue "u GLU 208": "OE1" <-> "OE2" Residue "u TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 215": "NH1" <-> "NH2" Residue "u ARG 223": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ASP 169": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ASP 169": "OD1" <-> "OD2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 160": "NH1" <-> "NH2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "G ASP 76": "OD1" <-> "OD2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 114": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 215": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 75": "OD1" <-> "OD2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "H PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H ARG 160": "NH1" <-> "NH2" Residue "H ASP 169": "OD1" <-> "OD2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "H TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "I PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I ARG 160": "NH1" <-> "NH2" Residue "I ASP 169": "OD1" <-> "OD2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 215": "NH1" <-> "NH2" Residue "I ARG 223": "NH1" <-> "NH2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "J ASP 76": "OD1" <-> "OD2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 114": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J ARG 160": "NH1" <-> "NH2" Residue "J ASP 169": "OD1" <-> "OD2" Residue "J GLU 208": "OE1" <-> "OE2" Residue "J TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 215": "NH1" <-> "NH2" Residue "J ARG 223": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "K PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 95": "NH1" <-> "NH2" Residue "K PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K ARG 160": "NH1" <-> "NH2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "K GLU 208": "OE1" <-> "OE2" Residue "K TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 215": "NH1" <-> "NH2" Residue "K ARG 223": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L ARG 160": "NH1" <-> "NH2" Residue "L ASP 169": "OD1" <-> "OD2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "L TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 215": "NH1" <-> "NH2" Residue "L ARG 223": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M ARG 148": "NH1" <-> "NH2" Residue "M ARG 160": "NH1" <-> "NH2" Residue "M ASP 169": "OD1" <-> "OD2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M ARG 223": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 75": "OD1" <-> "OD2" Residue "N ASP 76": "OD1" <-> "OD2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 95": "NH1" <-> "NH2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "N ARG 160": "NH1" <-> "NH2" Residue "N ASP 169": "OD1" <-> "OD2" Residue "N GLU 208": "OE1" <-> "OE2" Residue "N TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 215": "NH1" <-> "NH2" Residue "N ARG 223": "NH1" <-> "NH2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 75": "OD1" <-> "OD2" Residue "O ASP 76": "OD1" <-> "OD2" Residue "O PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 95": "NH1" <-> "NH2" Residue "O PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 148": "NH1" <-> "NH2" Residue "O ARG 160": "NH1" <-> "NH2" Residue "O ASP 169": "OD1" <-> "OD2" Residue "O GLU 208": "OE1" <-> "OE2" Residue "O TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 215": "NH1" <-> "NH2" Residue "O ARG 223": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 75": "OD1" <-> "OD2" Residue "P ASP 76": "OD1" <-> "OD2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 148": "NH1" <-> "NH2" Residue "P ARG 160": "NH1" <-> "NH2" Residue "P ASP 169": "OD1" <-> "OD2" Residue "P GLU 208": "OE1" <-> "OE2" Residue "P TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 215": "NH1" <-> "NH2" Residue "P ARG 223": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 75": "OD1" <-> "OD2" Residue "Q ASP 76": "OD1" <-> "OD2" Residue "Q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 148": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q ASP 169": "OD1" <-> "OD2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 215": "NH1" <-> "NH2" Residue "Q ARG 223": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 75": "OD1" <-> "OD2" Residue "R ASP 76": "OD1" <-> "OD2" Residue "R PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R ARG 148": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ASP 169": "OD1" <-> "OD2" Residue "R GLU 208": "OE1" <-> "OE2" Residue "R TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 215": "NH1" <-> "NH2" Residue "R ARG 223": "NH1" <-> "NH2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "S PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 75": "OD1" <-> "OD2" Residue "S ASP 76": "OD1" <-> "OD2" Residue "S PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 114": "NH1" <-> "NH2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ASP 169": "OD1" <-> "OD2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 215": "NH1" <-> "NH2" Residue "S ARG 223": "NH1" <-> "NH2" Residue "T ARG 50": "NH1" <-> "NH2" Residue "T PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 75": "OD1" <-> "OD2" Residue "T ASP 76": "OD1" <-> "OD2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 114": "NH1" <-> "NH2" Residue "T ARG 148": "NH1" <-> "NH2" Residue "T ARG 160": "NH1" <-> "NH2" Residue "T ASP 169": "OD1" <-> "OD2" Residue "T GLU 208": "OE1" <-> "OE2" Residue "T TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 215": "NH1" <-> "NH2" Residue "T ARG 223": "NH1" <-> "NH2" Residue "U ARG 50": "NH1" <-> "NH2" Residue "U PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 75": "OD1" <-> "OD2" Residue "U ASP 76": "OD1" <-> "OD2" Residue "U PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 114": "NH1" <-> "NH2" Residue "U ARG 148": "NH1" <-> "NH2" Residue "U ARG 160": "NH1" <-> "NH2" Residue "U ASP 169": "OD1" <-> "OD2" Residue "U GLU 208": "OE1" <-> "OE2" Residue "U TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 215": "NH1" <-> "NH2" Residue "U ARG 223": "NH1" <-> "NH2" Residue "V ARG 50": "NH1" <-> "NH2" Residue "V PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 75": "OD1" <-> "OD2" Residue "V ASP 76": "OD1" <-> "OD2" Residue "V PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 95": "NH1" <-> "NH2" Residue "V PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 114": "NH1" <-> "NH2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "V ASP 169": "OD1" <-> "OD2" Residue "V GLU 208": "OE1" <-> "OE2" Residue "V TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 215": "NH1" <-> "NH2" Residue "V ARG 223": "NH1" <-> "NH2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 75": "OD1" <-> "OD2" Residue "W ASP 76": "OD1" <-> "OD2" Residue "W PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "W ARG 148": "NH1" <-> "NH2" Residue "W ARG 160": "NH1" <-> "NH2" Residue "W ASP 169": "OD1" <-> "OD2" Residue "W GLU 208": "OE1" <-> "OE2" Residue "W TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 215": "NH1" <-> "NH2" Residue "W ARG 223": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 75": "OD1" <-> "OD2" Residue "X ASP 76": "OD1" <-> "OD2" Residue "X PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 114": "NH1" <-> "NH2" Residue "X ARG 148": "NH1" <-> "NH2" Residue "X ARG 160": "NH1" <-> "NH2" Residue "X ASP 169": "OD1" <-> "OD2" Residue "X GLU 208": "OE1" <-> "OE2" Residue "X TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 215": "NH1" <-> "NH2" Residue "X ARG 223": "NH1" <-> "NH2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 75": "OD1" <-> "OD2" Residue "Y ASP 76": "OD1" <-> "OD2" Residue "Y PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 95": "NH1" <-> "NH2" Residue "Y PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 114": "NH1" <-> "NH2" Residue "Y ARG 148": "NH1" <-> "NH2" Residue "Y ARG 160": "NH1" <-> "NH2" Residue "Y ASP 169": "OD1" <-> "OD2" Residue "Y GLU 208": "OE1" <-> "OE2" Residue "Y TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 215": "NH1" <-> "NH2" Residue "Y ARG 223": "NH1" <-> "NH2" Residue "Z ARG 50": "NH1" <-> "NH2" Residue "Z PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 75": "OD1" <-> "OD2" Residue "Z ASP 76": "OD1" <-> "OD2" Residue "Z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 95": "NH1" <-> "NH2" Residue "Z PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z ARG 148": "NH1" <-> "NH2" Residue "Z ARG 160": "NH1" <-> "NH2" Residue "Z ASP 169": "OD1" <-> "OD2" Residue "Z GLU 208": "OE1" <-> "OE2" Residue "Z TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 215": "NH1" <-> "NH2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 75": "OD1" <-> "OD2" Residue "0 ASP 76": "OD1" <-> "OD2" Residue "0 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 95": "NH1" <-> "NH2" Residue "0 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 114": "NH1" <-> "NH2" Residue "0 ARG 148": "NH1" <-> "NH2" Residue "0 ARG 160": "NH1" <-> "NH2" Residue "0 ASP 169": "OD1" <-> "OD2" Residue "0 GLU 208": "OE1" <-> "OE2" Residue "0 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 215": "NH1" <-> "NH2" Residue "0 ARG 223": "NH1" <-> "NH2" Residue "1 ARG 50": "NH1" <-> "NH2" Residue "1 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 75": "OD1" <-> "OD2" Residue "1 ASP 76": "OD1" <-> "OD2" Residue "1 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 95": "NH1" <-> "NH2" Residue "1 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 114": "NH1" <-> "NH2" Residue "1 ARG 148": "NH1" <-> "NH2" Residue "1 ARG 160": "NH1" <-> "NH2" Residue "1 ASP 169": "OD1" <-> "OD2" Residue "1 GLU 208": "OE1" <-> "OE2" Residue "1 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 215": "NH1" <-> "NH2" Residue "1 ARG 223": "NH1" <-> "NH2" Residue "2 ARG 50": "NH1" <-> "NH2" Residue "2 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 75": "OD1" <-> "OD2" Residue "2 ASP 76": "OD1" <-> "OD2" Residue "2 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 95": "NH1" <-> "NH2" Residue "2 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 114": "NH1" <-> "NH2" Residue "2 ARG 148": "NH1" <-> "NH2" Residue "2 ARG 160": "NH1" <-> "NH2" Residue "2 ASP 169": "OD1" <-> "OD2" Residue "2 GLU 208": "OE1" <-> "OE2" Residue "2 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 215": "NH1" <-> "NH2" Residue "2 ARG 223": "NH1" <-> "NH2" Residue "3 ARG 50": "NH1" <-> "NH2" Residue "3 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 75": "OD1" <-> "OD2" Residue "3 ASP 76": "OD1" <-> "OD2" Residue "3 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 95": "NH1" <-> "NH2" Residue "3 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 114": "NH1" <-> "NH2" Residue "3 ARG 148": "NH1" <-> "NH2" Residue "3 ARG 160": "NH1" <-> "NH2" Residue "3 ASP 169": "OD1" <-> "OD2" Residue "3 GLU 208": "OE1" <-> "OE2" Residue "3 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 215": "NH1" <-> "NH2" Residue "3 ARG 223": "NH1" <-> "NH2" Residue "4 ARG 50": "NH1" <-> "NH2" Residue "4 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 75": "OD1" <-> "OD2" Residue "4 ASP 76": "OD1" <-> "OD2" Residue "4 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 95": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 114": "NH1" <-> "NH2" Residue "4 ARG 148": "NH1" <-> "NH2" Residue "4 ARG 160": "NH1" <-> "NH2" Residue "4 ASP 169": "OD1" <-> "OD2" Residue "4 GLU 208": "OE1" <-> "OE2" Residue "4 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 215": "NH1" <-> "NH2" Residue "4 ARG 223": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 75": "OD1" <-> "OD2" Residue "5 ASP 76": "OD1" <-> "OD2" Residue "5 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 95": "NH1" <-> "NH2" Residue "5 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 114": "NH1" <-> "NH2" Residue "5 ARG 148": "NH1" <-> "NH2" Residue "5 ARG 160": "NH1" <-> "NH2" Residue "5 ASP 169": "OD1" <-> "OD2" Residue "5 GLU 208": "OE1" <-> "OE2" Residue "5 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 215": "NH1" <-> "NH2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "6 ARG 50": "NH1" <-> "NH2" Residue "6 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 75": "OD1" <-> "OD2" Residue "6 ASP 76": "OD1" <-> "OD2" Residue "6 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 148": "NH1" <-> "NH2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 ASP 169": "OD1" <-> "OD2" Residue "6 GLU 208": "OE1" <-> "OE2" Residue "6 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 215": "NH1" <-> "NH2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "7 ARG 50": "NH1" <-> "NH2" Residue "7 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 75": "OD1" <-> "OD2" Residue "7 ASP 76": "OD1" <-> "OD2" Residue "7 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 95": "NH1" <-> "NH2" Residue "7 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 114": "NH1" <-> "NH2" Residue "7 ARG 148": "NH1" <-> "NH2" Residue "7 ARG 160": "NH1" <-> "NH2" Residue "7 ASP 169": "OD1" <-> "OD2" Residue "7 GLU 208": "OE1" <-> "OE2" Residue "7 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 215": "NH1" <-> "NH2" Residue "7 ARG 223": "NH1" <-> "NH2" Residue "8 ARG 50": "NH1" <-> "NH2" Residue "8 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 75": "OD1" <-> "OD2" Residue "8 ASP 76": "OD1" <-> "OD2" Residue "8 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 95": "NH1" <-> "NH2" Residue "8 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 114": "NH1" <-> "NH2" Residue "8 ARG 148": "NH1" <-> "NH2" Residue "8 ARG 160": "NH1" <-> "NH2" Residue "8 ASP 169": "OD1" <-> "OD2" Residue "8 GLU 208": "OE1" <-> "OE2" Residue "8 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 215": "NH1" <-> "NH2" Residue "8 ARG 223": "NH1" <-> "NH2" Residue "9 ARG 50": "NH1" <-> "NH2" Residue "9 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 75": "OD1" <-> "OD2" Residue "9 ASP 76": "OD1" <-> "OD2" Residue "9 PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 95": "NH1" <-> "NH2" Residue "9 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 ARG 148": "NH1" <-> "NH2" Residue "9 ARG 160": "NH1" <-> "NH2" Residue "9 ASP 169": "OD1" <-> "OD2" Residue "9 GLU 208": "OE1" <-> "OE2" Residue "9 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 215": "NH1" <-> "NH2" Residue "9 ARG 223": "NH1" <-> "NH2" Residue "a ARG 50": "NH1" <-> "NH2" Residue "a PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 75": "OD1" <-> "OD2" Residue "a ASP 76": "OD1" <-> "OD2" Residue "a PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 95": "NH1" <-> "NH2" Residue "a PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 114": "NH1" <-> "NH2" Residue "a ARG 148": "NH1" <-> "NH2" Residue "a ARG 160": "NH1" <-> "NH2" Residue "a ASP 169": "OD1" <-> "OD2" Residue "a GLU 208": "OE1" <-> "OE2" Residue "a TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 215": "NH1" <-> "NH2" Residue "a ARG 223": "NH1" <-> "NH2" Residue "b ARG 50": "NH1" <-> "NH2" Residue "b PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 75": "OD1" <-> "OD2" Residue "b ASP 76": "OD1" <-> "OD2" Residue "b PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b ARG 160": "NH1" <-> "NH2" Residue "b ASP 169": "OD1" <-> "OD2" Residue "b GLU 208": "OE1" <-> "OE2" Residue "b TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 215": "NH1" <-> "NH2" Residue "b ARG 223": "NH1" <-> "NH2" Residue "c ARG 50": "NH1" <-> "NH2" Residue "c PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 75": "OD1" <-> "OD2" Residue "c ASP 76": "OD1" <-> "OD2" Residue "c PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 95": "NH1" <-> "NH2" Residue "c PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 114": "NH1" <-> "NH2" Residue "c ARG 148": "NH1" <-> "NH2" Residue "c ARG 160": "NH1" <-> "NH2" Residue "c ASP 169": "OD1" <-> "OD2" Residue "c GLU 208": "OE1" <-> "OE2" Residue "c TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 215": "NH1" <-> "NH2" Residue "c ARG 223": "NH1" <-> "NH2" Residue "d ARG 50": "NH1" <-> "NH2" Residue "d PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 75": "OD1" <-> "OD2" Residue "d ASP 76": "OD1" <-> "OD2" Residue "d PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 95": "NH1" <-> "NH2" Residue "d PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d ARG 148": "NH1" <-> "NH2" Residue "d ARG 160": "NH1" <-> "NH2" Residue "d ASP 169": "OD1" <-> "OD2" Residue "d GLU 208": "OE1" <-> "OE2" Residue "d TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 215": "NH1" <-> "NH2" Residue "d ARG 223": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 75": "OD1" <-> "OD2" Residue "e ASP 76": "OD1" <-> "OD2" Residue "e PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 95": "NH1" <-> "NH2" Residue "e PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 148": "NH1" <-> "NH2" Residue "e ARG 160": "NH1" <-> "NH2" Residue "e ASP 169": "OD1" <-> "OD2" Residue "e GLU 208": "OE1" <-> "OE2" Residue "e TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 215": "NH1" <-> "NH2" Residue "e ARG 223": "NH1" <-> "NH2" Residue "f ARG 50": "NH1" <-> "NH2" Residue "f PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 75": "OD1" <-> "OD2" Residue "f ASP 76": "OD1" <-> "OD2" Residue "f PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 95": "NH1" <-> "NH2" Residue "f PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 114": "NH1" <-> "NH2" Residue "f ARG 148": "NH1" <-> "NH2" Residue "f ARG 160": "NH1" <-> "NH2" Residue "f ASP 169": "OD1" <-> "OD2" Residue "f GLU 208": "OE1" <-> "OE2" Residue "f TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 215": "NH1" <-> "NH2" Residue "f ARG 223": "NH1" <-> "NH2" Residue "g ARG 50": "NH1" <-> "NH2" Residue "g PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 75": "OD1" <-> "OD2" Residue "g ASP 76": "OD1" <-> "OD2" Residue "g PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 114": "NH1" <-> "NH2" Residue "g ARG 148": "NH1" <-> "NH2" Residue "g ARG 160": "NH1" <-> "NH2" Residue "g ASP 169": "OD1" <-> "OD2" Residue "g GLU 208": "OE1" <-> "OE2" Residue "g TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 215": "NH1" <-> "NH2" Residue "g ARG 223": "NH1" <-> "NH2" Residue "h ARG 50": "NH1" <-> "NH2" Residue "h PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 75": "OD1" <-> "OD2" Residue "h ASP 76": "OD1" <-> "OD2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 95": "NH1" <-> "NH2" Residue "h PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 114": "NH1" <-> "NH2" Residue "h ARG 148": "NH1" <-> "NH2" Residue "h ARG 160": "NH1" <-> "NH2" Residue "h ASP 169": "OD1" <-> "OD2" Residue "h GLU 208": "OE1" <-> "OE2" Residue "h TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 215": "NH1" <-> "NH2" Residue "h ARG 223": "NH1" <-> "NH2" Residue "i ARG 50": "NH1" <-> "NH2" Residue "i PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 75": "OD1" <-> "OD2" Residue "i ASP 76": "OD1" <-> "OD2" Residue "i PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 95": "NH1" <-> "NH2" Residue "i PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 114": "NH1" <-> "NH2" Residue "i ARG 148": "NH1" <-> "NH2" Residue "i ARG 160": "NH1" <-> "NH2" Residue "i ASP 169": "OD1" <-> "OD2" Residue "i GLU 208": "OE1" <-> "OE2" Residue "i TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 215": "NH1" <-> "NH2" Residue "i ARG 223": "NH1" <-> "NH2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "j PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "j ASP 76": "OD1" <-> "OD2" Residue "j PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 95": "NH1" <-> "NH2" Residue "j PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 114": "NH1" <-> "NH2" Residue "j ARG 148": "NH1" <-> "NH2" Residue "j ARG 160": "NH1" <-> "NH2" Residue "j ASP 169": "OD1" <-> "OD2" Residue "j GLU 208": "OE1" <-> "OE2" Residue "j TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 215": "NH1" <-> "NH2" Residue "j ARG 223": "NH1" <-> "NH2" Residue "k ARG 50": "NH1" <-> "NH2" Residue "k PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 75": "OD1" <-> "OD2" Residue "k ASP 76": "OD1" <-> "OD2" Residue "k PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 114": "NH1" <-> "NH2" Residue "k ARG 148": "NH1" <-> "NH2" Residue "k ARG 160": "NH1" <-> "NH2" Residue "k ASP 169": "OD1" <-> "OD2" Residue "k GLU 208": "OE1" <-> "OE2" Residue "k TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 215": "NH1" <-> "NH2" Residue "k ARG 223": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 75": "OD1" <-> "OD2" Residue "l ASP 76": "OD1" <-> "OD2" Residue "l PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 95": "NH1" <-> "NH2" Residue "l PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "l ARG 148": "NH1" <-> "NH2" Residue "l ARG 160": "NH1" <-> "NH2" Residue "l ASP 169": "OD1" <-> "OD2" Residue "l GLU 208": "OE1" <-> "OE2" Residue "l TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 215": "NH1" <-> "NH2" Residue "l ARG 223": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 75": "OD1" <-> "OD2" Residue "m ASP 76": "OD1" <-> "OD2" Residue "m PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 95": "NH1" <-> "NH2" Residue "m PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "m ARG 148": "NH1" <-> "NH2" Residue "m ARG 160": "NH1" <-> "NH2" Residue "m ASP 169": "OD1" <-> "OD2" Residue "m GLU 208": "OE1" <-> "OE2" Residue "m TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 215": "NH1" <-> "NH2" Residue "m ARG 223": "NH1" <-> "NH2" Residue "n ARG 50": "NH1" <-> "NH2" Residue "n PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 75": "OD1" <-> "OD2" Residue "n ASP 76": "OD1" <-> "OD2" Residue "n PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 95": "NH1" <-> "NH2" Residue "n PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 114": "NH1" <-> "NH2" Residue "n ARG 148": "NH1" <-> "NH2" Residue "n ARG 160": "NH1" <-> "NH2" Residue "n ASP 169": "OD1" <-> "OD2" Residue "n GLU 208": "OE1" <-> "OE2" Residue "n TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 215": "NH1" <-> "NH2" Residue "n ARG 223": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 75": "OD1" <-> "OD2" Residue "o ASP 76": "OD1" <-> "OD2" Residue "o PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 95": "NH1" <-> "NH2" Residue "o PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 114": "NH1" <-> "NH2" Residue "o ARG 148": "NH1" <-> "NH2" Residue "o ARG 160": "NH1" <-> "NH2" Residue "o ASP 169": "OD1" <-> "OD2" Residue "o GLU 208": "OE1" <-> "OE2" Residue "o TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 215": "NH1" <-> "NH2" Residue "o ARG 223": "NH1" <-> "NH2" Residue "p ARG 50": "NH1" <-> "NH2" Residue "p PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 75": "OD1" <-> "OD2" Residue "p ASP 76": "OD1" <-> "OD2" Residue "p PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 95": "NH1" <-> "NH2" Residue "p PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 114": "NH1" <-> "NH2" Residue "p ARG 148": "NH1" <-> "NH2" Residue "p ARG 160": "NH1" <-> "NH2" Residue "p ASP 169": "OD1" <-> "OD2" Residue "p GLU 208": "OE1" <-> "OE2" Residue "p TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 215": "NH1" <-> "NH2" Residue "p ARG 223": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 75": "OD1" <-> "OD2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 95": "NH1" <-> "NH2" Residue "q PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q ARG 148": "NH1" <-> "NH2" Residue "q ARG 160": "NH1" <-> "NH2" Residue "q ASP 169": "OD1" <-> "OD2" Residue "q GLU 208": "OE1" <-> "OE2" Residue "q TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 215": "NH1" <-> "NH2" Residue "q ARG 223": "NH1" <-> "NH2" Residue "r ARG 50": "NH1" <-> "NH2" Residue "r PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 75": "OD1" <-> "OD2" Residue "r ASP 76": "OD1" <-> "OD2" Residue "r PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 114": "NH1" <-> "NH2" Residue "r ARG 148": "NH1" <-> "NH2" Residue "r ARG 160": "NH1" <-> "NH2" Residue "r ASP 169": "OD1" <-> "OD2" Residue "r GLU 208": "OE1" <-> "OE2" Residue "r TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 215": "NH1" <-> "NH2" Residue "r ARG 223": "NH1" <-> "NH2" Residue "s ARG 50": "NH1" <-> "NH2" Residue "s PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 75": "OD1" <-> "OD2" Residue "s ASP 76": "OD1" <-> "OD2" Residue "s PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "s PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 148": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ASP 169": "OD1" <-> "OD2" Residue "s GLU 208": "OE1" <-> "OE2" Residue "s TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 215": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "t ARG 50": "NH1" <-> "NH2" Residue "t PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 75": "OD1" <-> "OD2" Residue "t ASP 76": "OD1" <-> "OD2" Residue "t PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 95": "NH1" <-> "NH2" Residue "t PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 114": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t ARG 160": "NH1" <-> "NH2" Residue "t ASP 169": "OD1" <-> "OD2" Residue "t GLU 208": "OE1" <-> "OE2" Residue "t TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 215": "NH1" <-> "NH2" Residue "t ARG 223": "NH1" <-> "NH2" Residue "v ARG 50": "NH1" <-> "NH2" Residue "v PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 75": "OD1" <-> "OD2" Residue "v ASP 76": "OD1" <-> "OD2" Residue "v PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 95": "NH1" <-> "NH2" Residue "v PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 114": "NH1" <-> "NH2" Residue "v ARG 148": "NH1" <-> "NH2" Residue "v ARG 160": "NH1" <-> "NH2" Residue "v ASP 169": "OD1" <-> "OD2" Residue "v GLU 208": "OE1" <-> "OE2" Residue "v TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 215": "NH1" <-> "NH2" Residue "v ARG 223": "NH1" <-> "NH2" Residue "w ARG 50": "NH1" <-> "NH2" Residue "w PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 75": "OD1" <-> "OD2" Residue "w ASP 76": "OD1" <-> "OD2" Residue "w PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 95": "NH1" <-> "NH2" Residue "w PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 114": "NH1" <-> "NH2" Residue "w ARG 148": "NH1" <-> "NH2" Residue "w ARG 160": "NH1" <-> "NH2" Residue "w ASP 169": "OD1" <-> "OD2" Residue "w GLU 208": "OE1" <-> "OE2" Residue "w TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 215": "NH1" <-> "NH2" Residue "w ARG 223": "NH1" <-> "NH2" Residue "x ARG 50": "NH1" <-> "NH2" Residue "x PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 75": "OD1" <-> "OD2" Residue "x ASP 76": "OD1" <-> "OD2" Residue "x PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 95": "NH1" <-> "NH2" Residue "x PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 114": "NH1" <-> "NH2" Residue "x ARG 148": "NH1" <-> "NH2" Residue "x ARG 160": "NH1" <-> "NH2" Residue "x ASP 169": "OD1" <-> "OD2" Residue "x GLU 208": "OE1" <-> "OE2" Residue "x TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 215": "NH1" <-> "NH2" Residue "x ARG 223": "NH1" <-> "NH2" Time to flip residues: 0.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 101400 Number of models: 1 Model: "" Number of chains: 60 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: "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: "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} Time building chain proxies: 39.93, per 1000 atoms: 0.39 Number of scatterers: 101400 At special positions: 0 Unit cell: (213.06, 213.06, 213.06, 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 60 16.00 O 17280 8.00 N 18060 7.00 C 66000 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: 27.76 Conformation dependent library (CDL) restraints added in 10.5 seconds 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22560 Finding SS restraints... Secondary structure from input PDB file: 120 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' 300 hydrogen bonds defined for protein. 900 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: 16.40 Time building geometry restraints manager: 30.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 30552 1.33 - 1.45: 19404 1.45 - 1.56: 54924 1.56 - 1.68: 0 1.68 - 1.79: 120 Bond restraints: 105000 Sorted by residual: bond pdb=" C ARG N 106 " pdb=" N LEU N 107 " ideal model delta sigma weight residual 1.333 1.275 0.058 2.74e-02 1.33e+03 4.45e+00 bond pdb=" C ARG d 106 " pdb=" N LEU d 107 " ideal model delta sigma weight residual 1.333 1.275 0.058 2.74e-02 1.33e+03 4.45e+00 bond pdb=" C ARG W 106 " pdb=" N LEU W 107 " ideal model delta sigma weight residual 1.333 1.275 0.058 2.74e-02 1.33e+03 4.45e+00 bond pdb=" C ARG H 106 " pdb=" N LEU H 107 " ideal model delta sigma weight residual 1.333 1.275 0.058 2.74e-02 1.33e+03 4.45e+00 bond pdb=" C ARG c 106 " pdb=" N LEU c 107 " ideal model delta sigma weight residual 1.333 1.275 0.058 2.74e-02 1.33e+03 4.45e+00 ... (remaining 104995 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.37: 3960 106.37 - 113.32: 50760 113.32 - 120.27: 40008 120.27 - 127.22: 46572 127.22 - 134.17: 1500 Bond angle restraints: 142800 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 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 angle pdb=" N THR J 153 " pdb=" CA THR J 153 " pdb=" C THR J 153 " ideal model delta sigma weight residual 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 angle pdb=" N THR I 153 " pdb=" CA THR I 153 " pdb=" C THR I 153 " ideal model delta sigma weight residual 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 angle pdb=" N THR w 153 " pdb=" CA THR w 153 " pdb=" C THR w 153 " ideal model delta sigma weight residual 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 angle pdb=" N THR 4 153 " pdb=" CA THR 4 153 " pdb=" C THR 4 153 " ideal model delta sigma weight residual 109.81 120.29 -10.48 2.21e+00 2.05e-01 2.25e+01 ... (remaining 142795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 54840 17.80 - 35.60: 4596 35.60 - 53.41: 1164 53.41 - 71.21: 180 71.21 - 89.01: 180 Dihedral angle restraints: 60960 sinusoidal: 25680 harmonic: 35280 Sorted by residual: dihedral pdb=" CA THR Z 153 " pdb=" C THR Z 153 " pdb=" N PRO Z 154 " pdb=" CA PRO Z 154 " ideal model delta harmonic sigma weight residual 180.00 143.80 36.20 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA THR M 153 " pdb=" C THR M 153 " pdb=" N PRO M 154 " pdb=" CA PRO M 154 " ideal model delta harmonic sigma weight residual 180.00 143.80 36.20 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA THR S 153 " pdb=" C THR S 153 " pdb=" N PRO S 154 " pdb=" CA PRO S 154 " ideal model delta harmonic sigma weight residual 180.00 143.80 36.20 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 60957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 9984 0.054 - 0.107: 3444 0.107 - 0.161: 432 0.161 - 0.215: 0 0.215 - 0.268: 120 Chirality restraints: 13980 Sorted by residual: chirality pdb=" CB ILE Q 151 " pdb=" CA ILE Q 151 " pdb=" CG1 ILE Q 151 " pdb=" CG2 ILE Q 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE T 151 " pdb=" CA ILE T 151 " pdb=" CG1 ILE T 151 " pdb=" CG2 ILE T 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE x 151 " pdb=" CA ILE x 151 " pdb=" CG1 ILE x 151 " pdb=" CG2 ILE x 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 13977 not shown) Planarity restraints: 18780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR p 153 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO p 154 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO p 154 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO p 154 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR h 153 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO h 154 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO h 154 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO h 154 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 153 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO G 154 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 154 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 154 " -0.043 5.00e-02 4.00e+02 ... (remaining 18777 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 31920 2.84 - 3.36: 79482 3.36 - 3.87: 184188 3.87 - 4.39: 213996 4.39 - 4.90: 349530 Nonbonded interactions: 859116 Sorted by model distance: nonbonded pdb=" O THR 5 153 " pdb=" OG1 THR 5 153 " model vdw 2.326 2.440 nonbonded pdb=" O THR j 153 " pdb=" OG1 THR j 153 " model vdw 2.326 2.440 nonbonded pdb=" O THR 2 153 " pdb=" OG1 THR 2 153 " model vdw 2.326 2.440 nonbonded pdb=" O THR 9 153 " pdb=" OG1 THR 9 153 " model vdw 2.326 2.440 nonbonded pdb=" O THR f 153 " pdb=" OG1 THR f 153 " model vdw 2.326 2.440 ... (remaining 859111 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' } 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 60 5.16 5 C 66000 2.51 5 N 18060 2.21 5 O 17280 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 10.960 Check model and map are aligned: 1.120 Convert atoms to be neutral: 0.650 Process input model: 163.480 Find NCS groups from input model: 5.160 Set up NCS constraints: 1.190 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: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 0.061 105000 Z= 0.404 Angle : 0.922 10.482 142800 Z= 0.525 Chirality : 0.055 0.268 13980 Planarity : 0.007 0.075 18780 Dihedral : 15.023 89.011 38400 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.72 % Favored : 95.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.54 % 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: -2.67 (0.06), residues: 11940 helix: -3.84 (0.09), residues: 720 sheet: -0.47 (0.06), residues: 4620 loop : -2.61 (0.06), residues: 6600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1896 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1896 time to evaluate : 9.300 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: 0 outliers final: 0 residues processed: 1896 average time/residue: 1.7796 time to fit residues: 4569.1403 Evaluate side-chains 1440 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1440 time to evaluate : 9.072 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 12.1399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1013 optimal weight: 2.9990 chunk 909 optimal weight: 0.6980 chunk 504 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 613 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 chunk 940 optimal weight: 30.0000 chunk 363 optimal weight: 20.0000 chunk 571 optimal weight: 9.9990 chunk 700 optimal weight: 30.0000 chunk 1089 optimal weight: 0.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 45 ASN u 51 GLN u 62 ASN u 68 ASN u 69 HIS u 176 GLN u 181 GLN u 213 GLN u 221 GLN A 45 ASN A 51 GLN A 62 ASN A 69 HIS A 176 GLN A 179 ASN A 195 GLN A 213 GLN A 221 GLN B 45 ASN B 62 ASN B 69 HIS B 149 HIS B 176 GLN B 182 ASN B 213 GLN B 221 GLN C 45 ASN C 51 GLN C 62 ASN C 69 HIS C 176 GLN C 181 GLN C 182 ASN C 213 GLN C 221 GLN D 45 ASN D 51 GLN D 62 ASN D 69 HIS D 176 GLN D 179 ASN D 181 GLN D 190 GLN D 213 GLN D 221 GLN E 45 ASN E 51 GLN E 62 ASN E 69 HIS E 176 GLN E 179 ASN E 181 GLN E 190 GLN E 213 GLN E 221 GLN F 45 ASN F 51 GLN F 62 ASN F 68 ASN F 69 HIS F 176 GLN F 181 GLN F 213 GLN F 221 GLN G 45 ASN G 51 GLN G 62 ASN G 69 HIS G 176 GLN G 179 ASN G 195 GLN G 213 GLN G 221 GLN H 45 ASN H 62 ASN H 69 HIS H 149 HIS H 176 GLN H 182 ASN H 213 GLN H 221 GLN I 45 ASN I 51 GLN I 62 ASN I 69 HIS I 176 GLN I 181 GLN I 182 ASN I 213 GLN I 221 GLN J 45 ASN J 51 GLN J 62 ASN J 69 HIS J 176 GLN J 181 GLN J 182 ASN J 213 GLN J 221 GLN K 45 ASN K 51 GLN K 62 ASN K 69 HIS K 176 GLN K 179 ASN K 181 GLN K 190 GLN K 213 GLN K 221 GLN L 45 ASN L 51 GLN L 62 ASN L 68 ASN L 69 HIS L 176 GLN L 181 GLN L 213 GLN L 221 GLN M 45 ASN M 51 GLN M 62 ASN M 69 HIS M 176 GLN M 179 ASN M 195 GLN M 213 GLN M 221 GLN N 45 ASN N 62 ASN N 69 HIS N 149 HIS N 176 GLN N 182 ASN N 213 GLN N 221 GLN O 45 ASN O 62 ASN O 69 HIS O 149 HIS O 176 GLN O 182 ASN O 213 GLN O 221 GLN P 45 ASN P 51 GLN P 62 ASN P 69 HIS P 176 GLN P 181 GLN P 182 ASN P 213 GLN P 221 GLN Q 45 ASN Q 51 GLN Q 62 ASN Q 69 HIS Q 176 GLN Q 179 ASN Q 181 GLN Q 190 GLN Q 213 GLN Q 221 GLN R 45 ASN R 51 GLN R 62 ASN R 68 ASN R 69 HIS R 176 GLN R 181 GLN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN R 221 GLN S 45 ASN S 51 GLN S 62 ASN S 69 HIS S 176 GLN S 179 ASN S 195 GLN S 213 GLN S 221 GLN T 45 ASN T 51 GLN T 62 ASN T 69 HIS T 176 GLN T 179 ASN T 181 GLN T 190 GLN T 213 GLN T 221 GLN U 45 ASN U 51 GLN U 62 ASN U 68 ASN U 69 HIS U 176 GLN U 181 GLN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 213 GLN U 221 GLN V 45 ASN V 51 GLN V 62 ASN V 69 HIS V 176 GLN V 179 ASN V 195 GLN V 213 GLN V 221 GLN W 45 ASN W 62 ASN W 69 HIS W 149 HIS W 176 GLN W 182 ASN W 213 GLN W 221 GLN X 45 ASN X 51 GLN X 62 ASN X 69 HIS X 176 GLN X 181 GLN X 182 ASN X 213 GLN X 221 GLN Y 45 ASN Y 51 GLN Y 62 ASN Y 68 ASN Y 69 HIS Y 176 GLN Y 181 GLN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 213 GLN Y 221 GLN Z 45 ASN Z 51 GLN Z 62 ASN Z 69 HIS Z 176 GLN Z 179 ASN Z 195 GLN Z 213 GLN Z 221 GLN 0 45 ASN 0 62 ASN 0 69 HIS 0 149 HIS 0 176 GLN 0 182 ASN 0 213 GLN 0 221 GLN 1 45 ASN 1 51 GLN 1 62 ASN 1 69 HIS 1 176 GLN 1 181 GLN 1 182 ASN 1 213 GLN 1 221 GLN 2 45 ASN 2 51 GLN 2 62 ASN 2 69 HIS 2 176 GLN 2 179 ASN 2 181 GLN 2 190 GLN 2 213 GLN 2 221 GLN 3 45 ASN 3 62 ASN 3 69 HIS 3 149 HIS 3 176 GLN 3 182 ASN 3 213 GLN 3 221 GLN 4 45 ASN 4 51 GLN 4 62 ASN 4 69 HIS 4 176 GLN 4 181 GLN 4 182 ASN 4 213 GLN 4 221 GLN 5 45 ASN 5 51 GLN 5 62 ASN 5 69 HIS 5 176 GLN 5 179 ASN 5 181 GLN 5 190 GLN 5 213 GLN 5 221 GLN 6 45 ASN 6 51 GLN 6 62 ASN 6 68 ASN 6 69 HIS 6 176 GLN 6 181 GLN ** 6 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 213 GLN 6 221 GLN 7 45 ASN 7 51 GLN 7 62 ASN 7 69 HIS 7 176 GLN 7 179 ASN 7 195 GLN 7 213 GLN 7 221 GLN 8 45 ASN 8 51 GLN 8 62 ASN 8 69 HIS 8 176 GLN 8 181 GLN 8 182 ASN 8 213 GLN 8 221 GLN 9 45 ASN 9 51 GLN 9 62 ASN 9 69 HIS 9 176 GLN 9 179 ASN 9 181 GLN 9 190 GLN 9 213 GLN 9 221 GLN a 45 ASN a 51 GLN a 62 ASN a 68 ASN a 69 HIS a 176 GLN a 181 GLN a 213 GLN a 221 GLN b 45 ASN b 51 GLN b 62 ASN b 69 HIS b 176 GLN b 179 ASN b 195 GLN b 213 GLN b 221 GLN c 45 ASN c 62 ASN c 69 HIS c 149 HIS c 176 GLN c 182 ASN c 213 GLN c 221 GLN d 45 ASN d 62 ASN d 69 HIS d 149 HIS d 176 GLN d 182 ASN d 213 GLN d 221 GLN e 45 ASN e 51 GLN e 62 ASN e 69 HIS e 176 GLN e 181 GLN e 182 ASN e 213 GLN e 221 GLN f 45 ASN f 51 GLN f 62 ASN f 69 HIS f 176 GLN f 179 ASN f 181 GLN f 190 GLN f 213 GLN f 221 GLN g 45 ASN g 51 GLN g 62 ASN g 68 ASN g 69 HIS g 176 GLN g 181 GLN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 213 GLN g 221 GLN h 45 ASN h 51 GLN h 62 ASN h 69 HIS h 176 GLN h 179 ASN h 195 GLN h 213 GLN h 221 GLN i 45 ASN i 51 GLN i 62 ASN i 69 HIS i 176 GLN i 181 GLN i 182 ASN i 213 GLN i 221 GLN j 45 ASN j 51 GLN j 62 ASN j 69 HIS j 176 GLN j 179 ASN j 181 GLN j 190 GLN j 213 GLN j 221 GLN k 45 ASN k 51 GLN k 62 ASN k 68 ASN k 69 HIS k 176 GLN k 181 GLN ** k 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 213 GLN k 221 GLN l 45 ASN l 51 GLN l 62 ASN l 69 HIS l 176 GLN l 179 ASN l 195 GLN l 213 GLN l 221 GLN m 45 ASN m 62 ASN m 69 HIS m 149 HIS m 176 GLN m 182 ASN m 213 GLN m 221 GLN n 45 ASN n 51 GLN n 62 ASN n 69 HIS n 176 GLN n 179 ASN n 181 GLN n 190 GLN n 213 GLN n 221 GLN o 45 ASN o 51 GLN o 62 ASN o 68 ASN o 69 HIS o 176 GLN o 181 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 213 GLN o 221 GLN p 45 ASN p 51 GLN p 62 ASN p 69 HIS p 176 GLN p 179 ASN p 195 GLN p 213 GLN p 221 GLN q 45 ASN q 62 ASN q 69 HIS q 149 HIS q 176 GLN q 182 ASN q 213 GLN q 221 GLN r 45 ASN r 51 GLN r 62 ASN r 69 HIS r 176 GLN r 181 GLN r 182 ASN r 213 GLN r 221 GLN s 45 ASN s 51 GLN s 62 ASN s 68 ASN s 69 HIS s 176 GLN s 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 213 GLN s 221 GLN t 45 ASN t 51 GLN t 62 ASN t 69 HIS t 176 GLN t 179 ASN t 195 GLN t 213 GLN t 221 GLN v 45 ASN v 62 ASN v 69 HIS v 149 HIS v 176 GLN v 182 ASN v 213 GLN v 221 GLN w 45 ASN w 51 GLN w 62 ASN w 69 HIS w 176 GLN w 181 GLN w 182 ASN w 213 GLN w 221 GLN x 45 ASN x 51 GLN x 62 ASN x 69 HIS x 176 GLN x 179 ASN x 181 GLN x 190 GLN x 213 GLN x 221 GLN Total number of N/Q/H flips: 540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 105000 Z= 0.194 Angle : 0.585 8.004 142800 Z= 0.304 Chirality : 0.043 0.140 13980 Planarity : 0.006 0.064 18780 Dihedral : 6.315 31.622 13740 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.02 % Favored : 96.48 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.07), residues: 11940 helix: -1.79 (0.15), residues: 720 sheet: -0.11 (0.06), residues: 4980 loop : -2.45 (0.06), residues: 6240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1620 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1512 time to evaluate : 9.112 Fit side-chains outliers start: 108 outliers final: 24 residues processed: 1560 average time/residue: 1.8418 time to fit residues: 3888.8195 Evaluate side-chains 1392 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1368 time to evaluate : 9.011 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 2.1782 time to fit residues: 45.9310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 605 optimal weight: 0.0670 chunk 338 optimal weight: 20.0000 chunk 906 optimal weight: 5.9990 chunk 742 optimal weight: 5.9990 chunk 300 optimal weight: 30.0000 chunk 1091 optimal weight: 9.9990 chunk 1179 optimal weight: 10.0000 chunk 972 optimal weight: 9.9990 chunk 1082 optimal weight: 5.9990 chunk 372 optimal weight: 0.8980 chunk 875 optimal weight: 10.0000 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 182 ASN A 181 GLN B 51 GLN C 181 GLN F 182 ASN G 181 GLN H 51 GLN I 181 GLN J 181 GLN L 182 ASN M 181 GLN N 51 GLN O 51 GLN P 181 GLN R 182 ASN S 181 GLN U 182 ASN V 181 GLN W 51 GLN X 181 GLN Y 182 ASN Z 181 GLN 0 51 GLN 1 181 GLN 3 51 GLN 4 181 GLN 6 182 ASN 7 181 GLN 8 181 GLN a 182 ASN b 181 GLN c 51 GLN d 51 GLN e 181 GLN g 182 ASN h 181 GLN i 181 GLN k 182 ASN l 181 GLN m 51 GLN o 182 ASN p 181 GLN q 51 GLN r 181 GLN s 182 ASN t 181 GLN v 51 GLN w 181 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 105000 Z= 0.205 Angle : 0.588 8.072 142800 Z= 0.305 Chirality : 0.043 0.152 13980 Planarity : 0.005 0.064 18780 Dihedral : 6.251 34.622 13740 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.57 % Favored : 95.93 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.07), residues: 11940 helix: -0.47 (0.17), residues: 720 sheet: 0.03 (0.07), residues: 4980 loop : -2.27 (0.06), residues: 6240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1425 time to evaluate : 9.155 Fit side-chains outliers start: 240 outliers final: 60 residues processed: 1533 average time/residue: 1.8483 time to fit residues: 3849.0679 Evaluate side-chains 1476 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1416 time to evaluate : 9.170 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 48 residues processed: 12 average time/residue: 1.9325 time to fit residues: 43.3165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1078 optimal weight: 1.9990 chunk 820 optimal weight: 30.0000 chunk 566 optimal weight: 0.8980 chunk 120 optimal weight: 30.0000 chunk 521 optimal weight: 4.9990 chunk 733 optimal weight: 2.9990 chunk 1095 optimal weight: 20.0000 chunk 1159 optimal weight: 20.0000 chunk 572 optimal weight: 8.9990 chunk 1038 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 181 GLN A 182 ASN C 181 GLN G 179 ASN G 181 GLN G 182 ASN I 181 GLN J 181 GLN M 179 ASN M 181 GLN M 182 ASN P 181 GLN S 179 ASN S 181 GLN S 182 ASN V 179 ASN V 181 GLN V 182 ASN X 181 GLN Z 179 ASN Z 181 GLN Z 182 ASN 1 181 GLN 4 181 GLN 7 179 ASN 7 181 GLN 7 182 ASN 8 181 GLN b 179 ASN b 181 GLN b 182 ASN e 181 GLN h 179 ASN h 181 GLN h 182 ASN i 181 GLN l 179 ASN l 181 GLN l 182 ASN p 179 ASN p 181 GLN p 182 ASN r 181 GLN t 179 ASN t 181 GLN t 182 ASN w 181 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 105000 Z= 0.180 Angle : 0.561 7.873 142800 Z= 0.291 Chirality : 0.042 0.138 13980 Planarity : 0.005 0.060 18780 Dihedral : 5.948 31.117 13740 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.52 % Favored : 95.98 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.07), residues: 11940 helix: 0.13 (0.18), residues: 720 sheet: 0.10 (0.07), residues: 4980 loop : -2.14 (0.07), residues: 6240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1452 time to evaluate : 9.078 Fit side-chains outliers start: 241 outliers final: 84 residues processed: 1573 average time/residue: 1.8350 time to fit residues: 3919.0887 Evaluate side-chains 1489 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1405 time to evaluate : 9.060 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 60 residues processed: 24 average time/residue: 2.0158 time to fit residues: 75.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 966 optimal weight: 9.9990 chunk 658 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 863 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 989 optimal weight: 20.0000 chunk 801 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 592 optimal weight: 9.9990 chunk 1041 optimal weight: 7.9990 chunk 292 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 207 ASN A 179 ASN A 181 GLN A 182 ASN C 181 GLN D 195 GLN E 195 GLN F 207 ASN G 179 ASN G 181 GLN G 182 ASN I 181 GLN J 181 GLN K 195 GLN L 207 ASN M 179 ASN M 181 GLN M 182 ASN P 181 GLN Q 195 GLN ** Q 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN S 179 ASN S 181 GLN S 182 ASN T 195 GLN ** T 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 207 ASN V 179 ASN V 181 GLN V 182 ASN X 181 GLN Y 207 ASN Z 179 ASN Z 181 GLN Z 182 ASN 1 181 GLN 2 195 GLN 4 181 GLN 5 195 GLN 6 207 ASN 7 179 ASN 7 181 GLN 7 182 ASN 8 181 GLN 9 195 GLN ** 9 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 ASN b 179 ASN b 181 GLN b 182 ASN e 181 GLN f 195 GLN g 207 ASN h 179 ASN h 181 GLN h 182 ASN i 181 GLN j 195 GLN k 207 ASN l 179 ASN l 181 GLN l 182 ASN n 195 GLN o 207 ASN p 179 ASN p 181 GLN p 182 ASN r 181 GLN s 207 ASN t 179 ASN t 181 GLN t 182 ASN w 181 GLN x 195 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 105000 Z= 0.428 Angle : 0.737 9.759 142800 Z= 0.387 Chirality : 0.049 0.192 13980 Planarity : 0.007 0.078 18780 Dihedral : 7.038 38.951 13740 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.70 % Favored : 94.80 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.07), residues: 11940 helix: 0.31 (0.19), residues: 660 sheet: 0.00 (0.07), residues: 4980 loop : -2.02 (0.07), residues: 6300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1769 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1476 time to evaluate : 9.357 Fit side-chains outliers start: 293 outliers final: 132 residues processed: 1619 average time/residue: 1.8978 time to fit residues: 4152.5941 Evaluate side-chains 1601 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1469 time to evaluate : 9.101 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 84 residues processed: 48 average time/residue: 1.7315 time to fit residues: 126.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 390 optimal weight: 0.3980 chunk 1044 optimal weight: 10.0000 chunk 229 optimal weight: 0.4980 chunk 681 optimal weight: 20.0000 chunk 286 optimal weight: 2.9990 chunk 1161 optimal weight: 10.0000 chunk 963 optimal weight: 5.9990 chunk 537 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 609 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 179 ASN u 182 ASN A 181 GLN C 181 GLN D 179 ASN D 195 GLN E 179 ASN E 195 GLN F 179 ASN F 182 ASN G 181 GLN I 181 GLN J 181 GLN K 179 ASN K 195 GLN L 179 ASN L 182 ASN M 181 GLN P 181 GLN Q 179 ASN Q 195 GLN R 179 ASN R 182 ASN S 181 GLN T 179 ASN T 195 GLN U 179 ASN U 182 ASN V 181 GLN X 181 GLN Y 179 ASN Y 182 ASN Z 181 GLN 1 181 GLN 2 179 ASN 2 195 GLN 4 181 GLN 5 179 ASN 5 195 GLN 6 179 ASN 6 182 ASN 7 181 GLN 8 181 GLN 9 179 ASN 9 195 GLN a 179 ASN a 182 ASN b 181 GLN e 181 GLN f 179 ASN f 195 GLN g 179 ASN g 182 ASN h 181 GLN i 181 GLN j 179 ASN j 195 GLN k 179 ASN k 182 ASN l 181 GLN n 179 ASN n 195 GLN o 179 ASN o 182 ASN p 181 GLN r 181 GLN s 179 ASN s 182 ASN t 181 GLN w 181 GLN x 179 ASN x 195 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 105000 Z= 0.190 Angle : 0.580 8.557 142800 Z= 0.301 Chirality : 0.043 0.152 13980 Planarity : 0.005 0.063 18780 Dihedral : 6.125 30.550 13740 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.63 % Favored : 95.86 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.33 (0.07), residues: 11940 helix: 0.38 (0.19), residues: 720 sheet: 0.14 (0.07), residues: 4980 loop : -1.98 (0.07), residues: 6240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23880 Ramachandran restraints generated. 11940 Oldfield, 0 Emsley, 11940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1413 time to evaluate : 9.124 Fit side-chains outliers start: 133 outliers final: 73 residues processed: 1525 average time/residue: 1.8925 time to fit residues: 3919.2662 Evaluate side-chains 1480 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1407 time to evaluate : 9.137 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 61 residues processed: 12 average time/residue: 1.9524 time to fit residues: 43.6583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3001 > 50: distance: 26 - 27: 4.512 distance: 26 - 29: 4.624 distance: 27 - 28: 4.708 distance: 27 - 32: 5.223 distance: 29 - 30: 4.873 distance: 29 - 31: 4.437 distance: 33 - 34: 3.721 distance: 33 - 36: 3.351 distance: 34 - 35: 12.065 distance: 34 - 41: 3.514 distance: 36 - 37: 9.499 distance: 37 - 38: 10.512 distance: 38 - 39: 8.162 distance: 39 - 40: 15.488 distance: 41 - 42: 3.127 distance: 42 - 45: 3.252 distance: 45 - 46: 4.376 distance: 45 - 47: 7.750 distance: 48 - 49: 8.140 distance: 49 - 50: 4.544 distance: 49 - 52: 6.261 distance: 50 - 51: 12.112 distance: 50 - 57: 4.043 distance: 52 - 53: 7.822 distance: 53 - 54: 5.397 distance: 54 - 56: 6.219 distance: 58 - 61: 3.470 distance: 59 - 60: 3.299 distance: 61 - 62: 5.593 distance: 62 - 63: 4.815 distance: 62 - 64: 6.435 distance: 63 - 65: 7.259 distance: 64 - 66: 7.183 distance: 65 - 67: 6.070 distance: 66 - 67: 5.008 distance: 68 - 69: 3.402 distance: 69 - 72: 3.218 distance: 70 - 71: 3.455 distance: 70 - 77: 4.255 distance: 73 - 74: 7.975 distance: 74 - 75: 5.257 distance: 74 - 76: 7.850 distance: 77 - 78: 5.329 distance: 77 - 83: 4.293 distance: 78 - 79: 5.910 distance: 78 - 81: 8.662 distance: 79 - 84: 5.176 distance: 81 - 82: 6.390 distance: 82 - 83: 4.060 distance: 84 - 85: 6.845 distance: 85 - 86: 7.798 distance: 85 - 88: 6.123 distance: 86 - 87: 11.141 distance: 86 - 95: 7.075 distance: 88 - 89: 3.647 distance: 89 - 90: 4.657 distance: 90 - 91: 3.258 distance: 91 - 92: 6.683 distance: 92 - 93: 6.104 distance: 92 - 94: 7.501 distance: 96 - 97: 5.060 distance: 97 - 98: 10.618 distance: 97 - 103: 5.781 distance: 99 - 100: 4.446 distance: 100 - 102: 11.211 distance: 103 - 104: 8.321 distance: 103 - 109: 7.939 distance: 104 - 105: 27.342 distance: 104 - 107: 23.834 distance: 105 - 106: 4.573 distance: 105 - 110: 32.013 distance: 107 - 108: 13.128 distance: 108 - 109: 17.217