Starting phenix.real_space_refine on Thu Feb 22 17:49:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/02_2024/6rpo_4979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/02_2024/6rpo_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_4979/02_2024/6rpo_4979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/02_2024/6rpo_4979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/02_2024/6rpo_4979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rpo_4979/02_2024/6rpo_4979.pdb" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 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. 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: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 36.49, per 1000 atoms: 0.36 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: 25.83 Conformation dependent library (CDL) restraints added in 12.4 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: 4.82 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: 17.70 Time building geometry restraints manager: 28.90 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 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: 0.980 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: 0.100 Extract box with map and model: 8.150 Check model and map are aligned: 1.110 Set scattering table: 0.720 Process input model: 172.220 Find NCS groups from input model: 5.430 Set up NCS constraints: 1.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 200.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 % Allowed : 2.82 % Favored : 97.18 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 156 HIS 0.003 0.001 HIS 6 158 PHE 0.016 0.003 PHE W 175 TYR 0.013 0.003 TYR 3 210 ARG 0.005 0.001 ARG P 148 *********************** 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 : 8.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 35 TYR cc_start: 0.7559 (t80) cc_final: 0.7156 (t80) REVERT: u 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8601 (t0) REVERT: u 138 ILE cc_start: 0.8590 (mm) cc_final: 0.8361 (mm) REVERT: A 55 TRP cc_start: 0.7929 (m100) cc_final: 0.7721 (m100) REVERT: A 224 GLU cc_start: 0.7721 (tp30) cc_final: 0.7287 (tp30) REVERT: B 36 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.6128 (ptp90) REVERT: B 138 ILE cc_start: 0.8761 (mm) cc_final: 0.8558 (mm) REVERT: C 55 TRP cc_start: 0.7870 (m100) cc_final: 0.7589 (m100) REVERT: D 36 ARG cc_start: 0.6728 (ptp-110) cc_final: 0.6504 (mtp85) REVERT: D 140 ASP cc_start: 0.8587 (t0) cc_final: 0.8202 (t0) REVERT: E 36 ARG cc_start: 0.6728 (ptp-110) cc_final: 0.6504 (mtp85) REVERT: E 140 ASP cc_start: 0.8587 (t0) cc_final: 0.8202 (t0) REVERT: F 35 TYR cc_start: 0.7559 (t80) cc_final: 0.7156 (t80) REVERT: F 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8601 (t0) REVERT: F 138 ILE cc_start: 0.8590 (mm) cc_final: 0.8361 (mm) REVERT: G 55 TRP cc_start: 0.7929 (m100) cc_final: 0.7721 (m100) REVERT: G 224 GLU cc_start: 0.7721 (tp30) cc_final: 0.7287 (tp30) REVERT: H 36 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.6128 (ptp90) REVERT: H 138 ILE cc_start: 0.8761 (mm) cc_final: 0.8558 (mm) REVERT: I 55 TRP cc_start: 0.7870 (m100) cc_final: 0.7589 (m100) REVERT: J 55 TRP cc_start: 0.7869 (m100) cc_final: 0.7591 (m100) REVERT: K 36 ARG cc_start: 0.6720 (ptp-110) cc_final: 0.6495 (mtp85) REVERT: K 140 ASP cc_start: 0.8583 (t0) cc_final: 0.8198 (t0) REVERT: L 35 TYR cc_start: 0.7560 (t80) cc_final: 0.7155 (t80) REVERT: L 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8597 (t0) REVERT: L 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8361 (mm) REVERT: M 55 TRP cc_start: 0.7929 (m100) cc_final: 0.7719 (m100) REVERT: M 224 GLU cc_start: 0.7729 (tp30) cc_final: 0.7285 (tp30) REVERT: N 36 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6122 (ptp90) REVERT: N 138 ILE cc_start: 0.8759 (mm) cc_final: 0.8557 (mm) REVERT: O 36 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6122 (ptp90) REVERT: O 138 ILE cc_start: 0.8759 (mm) cc_final: 0.8557 (mm) REVERT: P 55 TRP cc_start: 0.7869 (m100) cc_final: 0.7591 (m100) REVERT: Q 36 ARG cc_start: 0.6720 (ptp-110) cc_final: 0.6495 (mtp85) REVERT: Q 140 ASP cc_start: 0.8583 (t0) cc_final: 0.8198 (t0) REVERT: R 35 TYR cc_start: 0.7560 (t80) cc_final: 0.7155 (t80) REVERT: R 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8597 (t0) REVERT: R 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8361 (mm) REVERT: S 55 TRP cc_start: 0.7929 (m100) cc_final: 0.7719 (m100) REVERT: S 224 GLU cc_start: 0.7729 (tp30) cc_final: 0.7285 (tp30) REVERT: T 36 ARG cc_start: 0.6732 (ptp-110) cc_final: 0.6508 (mtp85) REVERT: T 140 ASP cc_start: 0.8585 (t0) cc_final: 0.8205 (t0) REVERT: U 35 TYR cc_start: 0.7564 (t80) cc_final: 0.7162 (t80) REVERT: U 68 ASN cc_start: 0.8828 (t0) cc_final: 0.8602 (t0) REVERT: U 138 ILE cc_start: 0.8588 (mm) cc_final: 0.8360 (mm) REVERT: V 55 TRP cc_start: 0.7925 (m100) cc_final: 0.7718 (m100) REVERT: V 224 GLU cc_start: 0.7727 (tp30) cc_final: 0.7285 (tp30) REVERT: W 36 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6123 (ptp90) REVERT: W 138 ILE cc_start: 0.8763 (mm) cc_final: 0.8562 (mm) REVERT: X 55 TRP cc_start: 0.7871 (m100) cc_final: 0.7591 (m100) REVERT: Y 35 TYR cc_start: 0.7560 (t80) cc_final: 0.7155 (t80) REVERT: Y 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8597 (t0) REVERT: Y 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8361 (mm) REVERT: Z 55 TRP cc_start: 0.7929 (m100) cc_final: 0.7719 (m100) REVERT: Z 224 GLU cc_start: 0.7729 (tp30) cc_final: 0.7285 (tp30) REVERT: 0 36 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6122 (ptp90) REVERT: 0 138 ILE cc_start: 0.8759 (mm) cc_final: 0.8557 (mm) REVERT: 1 55 TRP cc_start: 0.7869 (m100) cc_final: 0.7591 (m100) REVERT: 2 36 ARG cc_start: 0.6720 (ptp-110) cc_final: 0.6495 (mtp85) REVERT: 2 140 ASP cc_start: 0.8583 (t0) cc_final: 0.8198 (t0) REVERT: 3 36 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.6128 (ptp90) REVERT: 3 138 ILE cc_start: 0.8761 (mm) cc_final: 0.8558 (mm) REVERT: 4 55 TRP cc_start: 0.7870 (m100) cc_final: 0.7589 (m100) REVERT: 5 36 ARG cc_start: 0.6728 (ptp-110) cc_final: 0.6504 (mtp85) REVERT: 5 140 ASP cc_start: 0.8587 (t0) cc_final: 0.8202 (t0) REVERT: 6 35 TYR cc_start: 0.7559 (t80) cc_final: 0.7156 (t80) REVERT: 6 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8601 (t0) REVERT: 6 138 ILE cc_start: 0.8590 (mm) cc_final: 0.8361 (mm) REVERT: 7 55 TRP cc_start: 0.7929 (m100) cc_final: 0.7721 (m100) REVERT: 7 224 GLU cc_start: 0.7721 (tp30) cc_final: 0.7287 (tp30) REVERT: 8 55 TRP cc_start: 0.7869 (m100) cc_final: 0.7588 (m100) REVERT: 9 36 ARG cc_start: 0.6722 (ptp-110) cc_final: 0.6502 (mtp85) REVERT: 9 140 ASP cc_start: 0.8583 (t0) cc_final: 0.8202 (t0) REVERT: a 35 TYR cc_start: 0.7563 (t80) cc_final: 0.7160 (t80) REVERT: a 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8602 (t0) REVERT: a 138 ILE cc_start: 0.8591 (mm) cc_final: 0.8363 (mm) REVERT: b 55 TRP cc_start: 0.7925 (m100) cc_final: 0.7716 (m100) REVERT: b 224 GLU cc_start: 0.7732 (tp30) cc_final: 0.7288 (tp30) REVERT: c 36 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6127 (ptp90) REVERT: d 36 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6127 (ptp90) REVERT: e 55 TRP cc_start: 0.7869 (m100) cc_final: 0.7588 (m100) REVERT: f 36 ARG cc_start: 0.6722 (ptp-110) cc_final: 0.6502 (mtp85) REVERT: f 140 ASP cc_start: 0.8583 (t0) cc_final: 0.8202 (t0) REVERT: g 35 TYR cc_start: 0.7563 (t80) cc_final: 0.7160 (t80) REVERT: g 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8602 (t0) REVERT: g 138 ILE cc_start: 0.8591 (mm) cc_final: 0.8363 (mm) REVERT: h 55 TRP cc_start: 0.7925 (m100) cc_final: 0.7716 (m100) REVERT: h 224 GLU cc_start: 0.7732 (tp30) cc_final: 0.7288 (tp30) REVERT: i 55 TRP cc_start: 0.7871 (m100) cc_final: 0.7591 (m100) REVERT: j 36 ARG cc_start: 0.6732 (ptp-110) cc_final: 0.6508 (mtp85) REVERT: j 140 ASP cc_start: 0.8585 (t0) cc_final: 0.8205 (t0) REVERT: k 35 TYR cc_start: 0.7564 (t80) cc_final: 0.7162 (t80) REVERT: k 68 ASN cc_start: 0.8828 (t0) cc_final: 0.8602 (t0) REVERT: k 138 ILE cc_start: 0.8588 (mm) cc_final: 0.8360 (mm) REVERT: l 55 TRP cc_start: 0.7925 (m100) cc_final: 0.7718 (m100) REVERT: l 224 GLU cc_start: 0.7727 (tp30) cc_final: 0.7285 (tp30) REVERT: m 36 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6123 (ptp90) REVERT: m 138 ILE cc_start: 0.8763 (mm) cc_final: 0.8562 (mm) REVERT: n 36 ARG cc_start: 0.6722 (ptp-110) cc_final: 0.6502 (mtp85) REVERT: n 140 ASP cc_start: 0.8583 (t0) cc_final: 0.8202 (t0) REVERT: o 35 TYR cc_start: 0.7563 (t80) cc_final: 0.7160 (t80) REVERT: o 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8602 (t0) REVERT: o 138 ILE cc_start: 0.8591 (mm) cc_final: 0.8363 (mm) REVERT: p 55 TRP cc_start: 0.7925 (m100) cc_final: 0.7716 (m100) REVERT: p 224 GLU cc_start: 0.7732 (tp30) cc_final: 0.7288 (tp30) REVERT: q 36 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6127 (ptp90) REVERT: r 55 TRP cc_start: 0.7869 (m100) cc_final: 0.7588 (m100) REVERT: s 35 TYR cc_start: 0.7564 (t80) cc_final: 0.7162 (t80) REVERT: s 68 ASN cc_start: 0.8828 (t0) cc_final: 0.8602 (t0) REVERT: s 138 ILE cc_start: 0.8588 (mm) cc_final: 0.8360 (mm) REVERT: t 55 TRP cc_start: 0.7925 (m100) cc_final: 0.7718 (m100) REVERT: t 224 GLU cc_start: 0.7727 (tp30) cc_final: 0.7285 (tp30) REVERT: v 36 ARG cc_start: 0.6678 (ptp-110) cc_final: 0.6123 (ptp90) REVERT: v 138 ILE cc_start: 0.8763 (mm) cc_final: 0.8562 (mm) REVERT: w 55 TRP cc_start: 0.7871 (m100) cc_final: 0.7591 (m100) REVERT: x 36 ARG cc_start: 0.6732 (ptp-110) cc_final: 0.6508 (mtp85) REVERT: x 140 ASP cc_start: 0.8585 (t0) cc_final: 0.8205 (t0) outliers start: 0 outliers final: 0 residues processed: 1896 average time/residue: 1.8838 time to fit residues: 4797.9802 Evaluate side-chains 1464 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1464 time to evaluate : 8.685 ------------------------------------------------------------------------------- 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: 20.0000 chunk 504 optimal weight: 6.9990 chunk 310 optimal weight: 20.0000 chunk 613 optimal weight: 10.0000 chunk 485 optimal weight: 5.9990 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: 0.7980 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 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 69 HIS F 176 GLN F 181 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 69 HIS L 176 GLN L 181 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 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 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 69 HIS a 176 GLN a 181 GLN ** a 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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 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 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: 528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 105000 Z= 0.273 Angle : 0.646 8.422 142800 Z= 0.336 Chirality : 0.045 0.159 13980 Planarity : 0.006 0.070 18780 Dihedral : 6.733 33.607 13740 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.12 % Favored : 96.38 % Rotamer: Outliers : 1.47 % Allowed : 10.56 % Favored : 87.97 % 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: -2.05 (0.07), residues: 11940 helix: -1.76 (0.15), residues: 720 sheet: -0.16 (0.06), residues: 4980 loop : -2.42 (0.06), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 5 156 HIS 0.003 0.001 HIS G 158 PHE 0.014 0.002 PHE 7 186 TYR 0.016 0.002 TYR m 219 ARG 0.005 0.001 ARG G 95 *********************** 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 1668 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1512 time to evaluate : 8.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: u 35 TYR cc_start: 0.7486 (t80) cc_final: 0.7086 (t80) REVERT: u 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8598 (t0) REVERT: u 138 ILE cc_start: 0.8624 (mm) cc_final: 0.8383 (mm) REVERT: B 40 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8044 (ttmm) REVERT: B 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: C 36 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6171 (ttp80) REVERT: D 36 ARG cc_start: 0.6785 (ptp-110) cc_final: 0.6444 (ptp-110) REVERT: E 36 ARG cc_start: 0.6785 (ptp-110) cc_final: 0.6444 (ptp-110) REVERT: F 35 TYR cc_start: 0.7486 (t80) cc_final: 0.7086 (t80) REVERT: F 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8598 (t0) REVERT: F 138 ILE cc_start: 0.8624 (mm) cc_final: 0.8383 (mm) REVERT: H 40 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8044 (ttmm) REVERT: H 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: I 36 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6171 (ttp80) REVERT: J 36 ARG cc_start: 0.6532 (mtp85) cc_final: 0.6172 (ttp80) REVERT: K 36 ARG cc_start: 0.6777 (ptp-110) cc_final: 0.6435 (ptp-110) REVERT: L 35 TYR cc_start: 0.7487 (t80) cc_final: 0.7085 (t80) REVERT: L 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8596 (t0) REVERT: L 138 ILE cc_start: 0.8621 (mm) cc_final: 0.8383 (mm) REVERT: N 40 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8041 (ttmm) REVERT: N 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: O 40 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8041 (ttmm) REVERT: O 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: P 36 ARG cc_start: 0.6532 (mtp85) cc_final: 0.6172 (ttp80) REVERT: Q 36 ARG cc_start: 0.6777 (ptp-110) cc_final: 0.6435 (ptp-110) REVERT: R 35 TYR cc_start: 0.7487 (t80) cc_final: 0.7084 (t80) REVERT: R 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8596 (t0) REVERT: R 138 ILE cc_start: 0.8621 (mm) cc_final: 0.8383 (mm) REVERT: T 36 ARG cc_start: 0.6783 (ptp-110) cc_final: 0.6441 (ptp-110) REVERT: U 35 TYR cc_start: 0.7491 (t80) cc_final: 0.7091 (t80) REVERT: U 68 ASN cc_start: 0.8843 (t0) cc_final: 0.8600 (t0) REVERT: U 138 ILE cc_start: 0.8623 (mm) cc_final: 0.8383 (mm) REVERT: W 40 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8041 (ttmm) REVERT: W 224 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: X 36 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6168 (ttp80) REVERT: Y 35 TYR cc_start: 0.7487 (t80) cc_final: 0.7084 (t80) REVERT: Y 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8596 (t0) REVERT: Y 138 ILE cc_start: 0.8621 (mm) cc_final: 0.8383 (mm) REVERT: 0 40 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8041 (ttmm) REVERT: 0 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: 1 36 ARG cc_start: 0.6532 (mtp85) cc_final: 0.6172 (ttp80) REVERT: 2 36 ARG cc_start: 0.6777 (ptp-110) cc_final: 0.6435 (ptp-110) REVERT: 3 40 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8044 (ttmm) REVERT: 3 224 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: 4 36 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6171 (ttp80) REVERT: 5 36 ARG cc_start: 0.6785 (ptp-110) cc_final: 0.6444 (ptp-110) REVERT: 6 35 TYR cc_start: 0.7486 (t80) cc_final: 0.7086 (t80) REVERT: 6 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8598 (t0) REVERT: 6 138 ILE cc_start: 0.8624 (mm) cc_final: 0.8383 (mm) REVERT: 8 36 ARG cc_start: 0.6537 (mtp85) cc_final: 0.6176 (ttp80) REVERT: 9 36 ARG cc_start: 0.6779 (ptp-110) cc_final: 0.6440 (ptp-110) REVERT: a 35 TYR cc_start: 0.7487 (t80) cc_final: 0.7087 (t80) REVERT: a 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8599 (t0) REVERT: a 138 ILE cc_start: 0.8624 (mm) cc_final: 0.8384 (mm) REVERT: c 40 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8045 (ttmm) REVERT: c 224 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: d 40 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8045 (ttmm) REVERT: d 224 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: e 36 ARG cc_start: 0.6537 (mtp85) cc_final: 0.6176 (ttp80) REVERT: f 36 ARG cc_start: 0.6779 (ptp-110) cc_final: 0.6440 (ptp-110) REVERT: g 35 TYR cc_start: 0.7487 (t80) cc_final: 0.7087 (t80) REVERT: g 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8599 (t0) REVERT: g 138 ILE cc_start: 0.8624 (mm) cc_final: 0.8384 (mm) REVERT: i 36 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6168 (ttp80) REVERT: j 36 ARG cc_start: 0.6783 (ptp-110) cc_final: 0.6441 (ptp-110) REVERT: k 35 TYR cc_start: 0.7491 (t80) cc_final: 0.7091 (t80) REVERT: k 68 ASN cc_start: 0.8843 (t0) cc_final: 0.8600 (t0) REVERT: k 138 ILE cc_start: 0.8623 (mm) cc_final: 0.8383 (mm) REVERT: m 40 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8041 (ttmm) REVERT: m 224 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: n 36 ARG cc_start: 0.6779 (ptp-110) cc_final: 0.6440 (ptp-110) REVERT: o 35 TYR cc_start: 0.7487 (t80) cc_final: 0.7087 (t80) REVERT: o 68 ASN cc_start: 0.8841 (t0) cc_final: 0.8599 (t0) REVERT: o 138 ILE cc_start: 0.8624 (mm) cc_final: 0.8384 (mm) REVERT: q 40 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8045 (ttmm) REVERT: q 224 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: r 36 ARG cc_start: 0.6537 (mtp85) cc_final: 0.6176 (ttp80) REVERT: s 35 TYR cc_start: 0.7491 (t80) cc_final: 0.7091 (t80) REVERT: s 68 ASN cc_start: 0.8843 (t0) cc_final: 0.8600 (t0) REVERT: s 138 ILE cc_start: 0.8623 (mm) cc_final: 0.8383 (mm) REVERT: v 40 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8041 (ttmm) REVERT: v 224 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: w 36 ARG cc_start: 0.6529 (mtp85) cc_final: 0.6168 (ttp80) REVERT: x 36 ARG cc_start: 0.6783 (ptp-110) cc_final: 0.6441 (ptp-110) outliers start: 156 outliers final: 48 residues processed: 1596 average time/residue: 1.9098 time to fit residues: 4078.2653 Evaluate side-chains 1476 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1416 time to evaluate : 8.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain S residue 40 LYS Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain Z residue 40 LYS Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 7 residue 40 LYS Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain b residue 40 LYS Chi-restraints excluded: chain b residue 109 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain p residue 40 LYS Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 109 ILE Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 605 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 906 optimal weight: 0.9980 chunk 742 optimal weight: 10.0000 chunk 300 optimal weight: 30.0000 chunk 1091 optimal weight: 8.9990 chunk 1179 optimal weight: 10.0000 chunk 972 optimal weight: 10.0000 chunk 1082 optimal weight: 10.0000 chunk 372 optimal weight: 2.9990 chunk 875 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 182 ASN ** u 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 195 GLN C 181 GLN F 182 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN G 195 GLN I 181 GLN J 181 GLN L 182 ASN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 GLN M 195 GLN P 181 GLN R 182 ASN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 GLN S 195 GLN U 182 ASN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN V 195 GLN X 181 GLN Y 182 ASN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 181 GLN Z 195 GLN 1 181 GLN 4 181 GLN 6 182 ASN ** 6 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 181 GLN 7 195 GLN 8 181 GLN a 182 ASN ** a 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN b 195 GLN e 181 GLN g 182 ASN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 GLN h 195 GLN i 181 GLN k 182 ASN ** k 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 181 GLN l 195 GLN o 182 ASN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN p 195 GLN r 181 GLN s 182 ASN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN t 195 GLN w 181 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 105000 Z= 0.236 Angle : 0.612 8.122 142800 Z= 0.318 Chirality : 0.044 0.155 13980 Planarity : 0.006 0.068 18780 Dihedral : 6.492 34.841 13740 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.12 % Favored : 95.38 % Rotamer: Outliers : 2.57 % Allowed : 10.88 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.43 % 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: -1.68 (0.07), residues: 11940 helix: -0.53 (0.17), residues: 720 sheet: -0.00 (0.07), residues: 4980 loop : -2.21 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP t 156 HIS 0.003 0.001 HIS Z 158 PHE 0.012 0.002 PHE P 175 TYR 0.016 0.002 TYR 5 116 ARG 0.004 0.000 ARG M 36 *********************** 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 1689 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1416 time to evaluate : 9.103 Fit side-chains REVERT: u 35 TYR cc_start: 0.7473 (t80) cc_final: 0.7094 (t80) REVERT: u 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6250 (ttm-80) REVERT: u 68 ASN cc_start: 0.8846 (t0) cc_final: 0.8578 (t0) REVERT: u 138 ILE cc_start: 0.8589 (mm) cc_final: 0.8308 (mm) REVERT: B 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8030 (ttmm) REVERT: B 138 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 224 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: C 44 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 224 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: F 35 TYR cc_start: 0.7473 (t80) cc_final: 0.7094 (t80) REVERT: F 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6250 (ttm-80) REVERT: F 68 ASN cc_start: 0.8846 (t0) cc_final: 0.8578 (t0) REVERT: F 138 ILE cc_start: 0.8589 (mm) cc_final: 0.8308 (mm) REVERT: H 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8030 (ttmm) REVERT: H 138 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8621 (mm) REVERT: H 224 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: I 44 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8376 (p) REVERT: I 224 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: J 44 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8371 (p) REVERT: J 224 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: L 35 TYR cc_start: 0.7475 (t80) cc_final: 0.7095 (t80) REVERT: L 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6252 (ttm-80) REVERT: L 68 ASN cc_start: 0.8847 (t0) cc_final: 0.8577 (t0) REVERT: L 138 ILE cc_start: 0.8584 (mm) cc_final: 0.8305 (mm) REVERT: N 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8028 (ttmm) REVERT: N 138 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8624 (mm) REVERT: N 224 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: O 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8028 (ttmm) REVERT: O 138 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8624 (mm) REVERT: O 224 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: P 44 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8371 (p) REVERT: P 224 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: R 35 TYR cc_start: 0.7475 (t80) cc_final: 0.7095 (t80) REVERT: R 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6252 (ttm-80) REVERT: R 68 ASN cc_start: 0.8847 (t0) cc_final: 0.8577 (t0) REVERT: R 138 ILE cc_start: 0.8584 (mm) cc_final: 0.8305 (mm) REVERT: U 35 TYR cc_start: 0.7477 (t80) cc_final: 0.7101 (t80) REVERT: U 36 ARG cc_start: 0.6609 (ptp-110) cc_final: 0.6249 (ttm-80) REVERT: U 68 ASN cc_start: 0.8850 (t0) cc_final: 0.8581 (t0) REVERT: U 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8308 (mm) REVERT: W 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8027 (ttmm) REVERT: W 138 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8625 (mm) REVERT: W 224 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: X 44 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (p) REVERT: X 224 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: Y 35 TYR cc_start: 0.7475 (t80) cc_final: 0.7095 (t80) REVERT: Y 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6252 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8847 (t0) cc_final: 0.8577 (t0) REVERT: Y 138 ILE cc_start: 0.8584 (mm) cc_final: 0.8305 (mm) REVERT: 0 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8028 (ttmm) REVERT: 0 138 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8624 (mm) REVERT: 0 224 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: 1 44 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8371 (p) REVERT: 1 224 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: 3 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8030 (ttmm) REVERT: 3 138 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8621 (mm) REVERT: 3 224 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: 4 44 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8376 (p) REVERT: 4 224 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: 6 35 TYR cc_start: 0.7473 (t80) cc_final: 0.7094 (t80) REVERT: 6 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6250 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8846 (t0) cc_final: 0.8578 (t0) REVERT: 6 138 ILE cc_start: 0.8589 (mm) cc_final: 0.8308 (mm) REVERT: 8 44 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (p) REVERT: 8 224 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: a 35 TYR cc_start: 0.7473 (t80) cc_final: 0.7096 (t80) REVERT: a 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6248 (ttm-80) REVERT: a 68 ASN cc_start: 0.8846 (t0) cc_final: 0.8581 (t0) REVERT: a 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8307 (mm) REVERT: c 40 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8032 (ttmm) REVERT: c 224 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: d 40 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8032 (ttmm) REVERT: d 224 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: e 44 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (p) REVERT: e 224 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: g 35 TYR cc_start: 0.7473 (t80) cc_final: 0.7096 (t80) REVERT: g 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6248 (ttm-80) REVERT: g 68 ASN cc_start: 0.8847 (t0) cc_final: 0.8581 (t0) REVERT: g 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8307 (mm) REVERT: i 44 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (p) REVERT: i 224 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: k 35 TYR cc_start: 0.7477 (t80) cc_final: 0.7101 (t80) REVERT: k 36 ARG cc_start: 0.6609 (ptp-110) cc_final: 0.6249 (ttm-80) REVERT: k 68 ASN cc_start: 0.8850 (t0) cc_final: 0.8581 (t0) REVERT: k 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8308 (mm) REVERT: m 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8027 (ttmm) REVERT: m 138 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8625 (mm) REVERT: m 224 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: o 35 TYR cc_start: 0.7473 (t80) cc_final: 0.7096 (t80) REVERT: o 36 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6248 (ttm-80) REVERT: o 68 ASN cc_start: 0.8846 (t0) cc_final: 0.8581 (t0) REVERT: o 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8307 (mm) REVERT: q 40 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8032 (ttmm) REVERT: q 224 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: r 44 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (p) REVERT: r 224 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: s 35 TYR cc_start: 0.7477 (t80) cc_final: 0.7101 (t80) REVERT: s 36 ARG cc_start: 0.6609 (ptp-110) cc_final: 0.6249 (ttm-80) REVERT: s 68 ASN cc_start: 0.8850 (t0) cc_final: 0.8581 (t0) REVERT: s 138 ILE cc_start: 0.8587 (mm) cc_final: 0.8308 (mm) REVERT: v 40 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8027 (ttmm) REVERT: v 138 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8626 (mm) REVERT: v 224 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: w 44 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8374 (p) REVERT: w 224 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7051 (tm-30) outliers start: 273 outliers final: 84 residues processed: 1572 average time/residue: 1.8952 time to fit residues: 4002.5988 Evaluate side-chains 1509 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1380 time to evaluate : 8.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain S residue 40 LYS Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 138 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain Z residue 40 LYS Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 138 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 138 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 7 residue 40 LYS Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 8 residue 44 THR Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain b residue 40 LYS Chi-restraints excluded: chain b residue 109 ILE Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain l residue 40 LYS Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain p residue 40 LYS Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain t residue 40 LYS Chi-restraints excluded: chain t residue 109 ILE Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 138 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 44 THR Chi-restraints excluded: chain w residue 224 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1078 optimal weight: 20.0000 chunk 820 optimal weight: 30.0000 chunk 566 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 chunk 521 optimal weight: 7.9990 chunk 733 optimal weight: 8.9990 chunk 1095 optimal weight: 9.9990 chunk 1159 optimal weight: 9.9990 chunk 572 optimal weight: 10.0000 chunk 1038 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN C 181 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN I 181 GLN J 181 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 GLN P 181 GLN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 GLN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN X 181 GLN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 181 GLN 1 181 GLN 4 181 GLN ** 6 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 181 GLN 8 181 GLN ** a 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN e 181 GLN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 GLN i 181 GLN ** k 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 181 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN r 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN w 181 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 105000 Z= 0.380 Angle : 0.713 9.441 142800 Z= 0.373 Chirality : 0.048 0.184 13980 Planarity : 0.007 0.076 18780 Dihedral : 6.994 36.237 13740 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.15 % Favored : 94.35 % Rotamer: Outliers : 2.71 % Allowed : 12.32 % Favored : 84.97 % 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: -1.58 (0.07), residues: 11940 helix: -0.17 (0.18), residues: 720 sheet: -0.04 (0.07), residues: 4980 loop : -2.07 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 156 HIS 0.003 0.001 HIS Z 158 PHE 0.017 0.002 PHE w 186 TYR 0.020 0.003 TYR K 116 ARG 0.006 0.001 ARG Z 95 *********************** 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 1764 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1476 time to evaluate : 9.008 Fit side-chains REVERT: u 35 TYR cc_start: 0.7514 (t80) cc_final: 0.7115 (t80) REVERT: u 36 ARG cc_start: 0.6633 (ptp-110) cc_final: 0.6400 (ttm-80) REVERT: u 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8587 (t0) REVERT: u 224 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: A 38 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: B 36 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6459 (ttp80) REVERT: B 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: C 36 ARG cc_start: 0.6804 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: C 44 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 224 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: D 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7749 (ptmt) REVERT: E 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7749 (ptmt) REVERT: F 35 TYR cc_start: 0.7514 (t80) cc_final: 0.7115 (t80) REVERT: F 36 ARG cc_start: 0.6633 (ptp-110) cc_final: 0.6400 (ttm-80) REVERT: F 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8587 (t0) REVERT: F 224 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: G 38 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: H 36 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6459 (ttp80) REVERT: H 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: I 36 ARG cc_start: 0.6804 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: I 44 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8376 (p) REVERT: I 224 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: J 36 ARG cc_start: 0.6806 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: J 44 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (p) REVERT: J 224 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: K 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7748 (ptmt) REVERT: L 35 TYR cc_start: 0.7516 (t80) cc_final: 0.7114 (t80) REVERT: L 36 ARG cc_start: 0.6634 (ptp-110) cc_final: 0.6400 (ttm-80) REVERT: L 68 ASN cc_start: 0.8825 (t0) cc_final: 0.8585 (t0) REVERT: L 224 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: M 38 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: N 36 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: N 224 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: O 36 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: O 224 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: P 36 ARG cc_start: 0.6806 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: P 44 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (p) REVERT: P 224 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: Q 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7748 (ptmt) REVERT: R 35 TYR cc_start: 0.7516 (t80) cc_final: 0.7114 (t80) REVERT: R 36 ARG cc_start: 0.6634 (ptp-110) cc_final: 0.6400 (ttm-80) REVERT: R 68 ASN cc_start: 0.8825 (t0) cc_final: 0.8585 (t0) REVERT: R 224 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7236 (tm-30) REVERT: S 38 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: T 58 LYS cc_start: 0.7947 (ttpm) cc_final: 0.7747 (ptmt) REVERT: U 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7120 (t80) REVERT: U 36 ARG cc_start: 0.6628 (ptp-110) cc_final: 0.6398 (ttm-80) REVERT: U 68 ASN cc_start: 0.8828 (t0) cc_final: 0.8591 (t0) REVERT: U 224 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: V 38 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8216 (mtt-85) REVERT: W 36 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: W 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: X 36 ARG cc_start: 0.6805 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: X 44 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8374 (p) REVERT: X 224 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: Y 35 TYR cc_start: 0.7516 (t80) cc_final: 0.7114 (t80) REVERT: Y 36 ARG cc_start: 0.6634 (ptp-110) cc_final: 0.6400 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8825 (t0) cc_final: 0.8585 (t0) REVERT: Y 224 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: Z 38 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: 0 36 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: 0 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: 1 36 ARG cc_start: 0.6806 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: 1 44 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8373 (p) REVERT: 1 224 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: 2 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7748 (ptmt) REVERT: 3 36 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6459 (ttp80) REVERT: 3 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6914 (tm-30) REVERT: 4 36 ARG cc_start: 0.6804 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: 4 44 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8376 (p) REVERT: 4 224 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: 5 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7749 (ptmt) REVERT: 6 35 TYR cc_start: 0.7514 (t80) cc_final: 0.7114 (t80) REVERT: 6 36 ARG cc_start: 0.6633 (ptp-110) cc_final: 0.6400 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8587 (t0) REVERT: 6 224 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: 7 38 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: 8 36 ARG cc_start: 0.6813 (tmm-80) cc_final: 0.6567 (ttt90) REVERT: 8 44 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8370 (p) REVERT: 8 224 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: 9 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7750 (ptmt) REVERT: a 35 TYR cc_start: 0.7516 (t80) cc_final: 0.7115 (t80) REVERT: a 36 ARG cc_start: 0.6634 (ptp-110) cc_final: 0.6399 (ttm-80) REVERT: a 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8590 (t0) REVERT: a 224 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: b 38 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8212 (mtt-85) REVERT: c 36 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6457 (ttp80) REVERT: c 224 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: d 36 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6457 (ttp80) REVERT: d 224 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: e 36 ARG cc_start: 0.6813 (tmm-80) cc_final: 0.6567 (ttt90) REVERT: e 44 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8370 (p) REVERT: e 224 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: f 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7750 (ptmt) REVERT: g 35 TYR cc_start: 0.7516 (t80) cc_final: 0.7116 (t80) REVERT: g 36 ARG cc_start: 0.6634 (ptp-110) cc_final: 0.6399 (ttm-80) REVERT: g 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8590 (t0) REVERT: g 224 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: h 38 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8212 (mtt-85) REVERT: i 36 ARG cc_start: 0.6805 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: i 44 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8374 (p) REVERT: i 224 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: j 58 LYS cc_start: 0.7947 (ttpm) cc_final: 0.7747 (ptmt) REVERT: k 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7120 (t80) REVERT: k 36 ARG cc_start: 0.6628 (ptp-110) cc_final: 0.6397 (ttm-80) REVERT: k 68 ASN cc_start: 0.8828 (t0) cc_final: 0.8591 (t0) REVERT: k 224 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: l 38 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8216 (mtt-85) REVERT: m 36 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: m 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: n 58 LYS cc_start: 0.7951 (ttpm) cc_final: 0.7750 (ptmt) REVERT: o 35 TYR cc_start: 0.7516 (t80) cc_final: 0.7115 (t80) REVERT: o 36 ARG cc_start: 0.6634 (ptp-110) cc_final: 0.6399 (ttm-80) REVERT: o 68 ASN cc_start: 0.8826 (t0) cc_final: 0.8590 (t0) REVERT: o 224 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: p 38 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8212 (mtt-85) REVERT: q 36 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6457 (ttp80) REVERT: q 224 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: r 36 ARG cc_start: 0.6813 (tmm-80) cc_final: 0.6567 (ttt90) REVERT: r 44 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8370 (p) REVERT: r 224 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: s 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7120 (t80) REVERT: s 36 ARG cc_start: 0.6628 (ptp-110) cc_final: 0.6397 (ttm-80) REVERT: s 68 ASN cc_start: 0.8828 (t0) cc_final: 0.8591 (t0) REVERT: s 224 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: t 38 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8216 (mtt-85) REVERT: v 36 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: v 224 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: w 36 ARG cc_start: 0.6805 (tmm-80) cc_final: 0.6560 (ttt90) REVERT: w 44 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8374 (p) REVERT: w 224 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: x 58 LYS cc_start: 0.7947 (ttpm) cc_final: 0.7747 (ptmt) outliers start: 288 outliers final: 87 residues processed: 1620 average time/residue: 1.9837 time to fit residues: 4300.5378 Evaluate side-chains 1611 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1464 time to evaluate : 8.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain u residue 224 GLU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 224 GLU Chi-restraints excluded: chain M residue 109 ILE Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 224 GLU Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain U residue 224 GLU Chi-restraints excluded: chain V residue 109 ILE Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain Y residue 224 GLU Chi-restraints excluded: chain Z residue 109 ILE Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 44 THR Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 6 residue 224 GLU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 8 residue 44 THR Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain 9 residue 89 LEU Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain b residue 109 ILE Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 138 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain g residue 224 GLU Chi-restraints excluded: chain h residue 109 ILE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain j residue 89 LEU Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain k residue 224 GLU Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain o residue 224 GLU Chi-restraints excluded: chain p residue 109 ILE Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 138 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain s residue 224 GLU Chi-restraints excluded: chain t residue 109 ILE Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 44 THR Chi-restraints excluded: chain w residue 224 GLU Chi-restraints excluded: chain x residue 89 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 966 optimal weight: 20.0000 chunk 658 optimal weight: 7.9990 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: 20.0000 chunk 1 optimal weight: 10.0000 chunk 592 optimal weight: 9.9990 chunk 1041 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN C 181 GLN D 179 ASN E 179 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN I 181 GLN J 181 GLN K 179 ASN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 GLN P 181 GLN Q 179 ASN S 181 GLN T 179 ASN V 181 GLN X 181 GLN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 181 GLN 1 181 GLN 2 179 ASN 4 181 GLN 5 179 ASN 7 181 GLN 8 181 GLN 9 179 ASN b 181 GLN e 181 GLN f 179 ASN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 GLN i 181 GLN j 179 ASN l 181 GLN n 179 ASN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN r 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN w 181 GLN x 179 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 105000 Z= 0.433 Angle : 0.744 10.236 142800 Z= 0.391 Chirality : 0.050 0.201 13980 Planarity : 0.007 0.077 18780 Dihedral : 7.141 37.769 13740 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.72 % Favored : 94.77 % Rotamer: Outliers : 2.63 % Allowed : 12.43 % Favored : 84.94 % 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: -1.54 (0.07), residues: 11940 helix: -0.11 (0.18), residues: 720 sheet: -0.03 (0.07), residues: 4980 loop : -2.04 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 156 HIS 0.004 0.001 HIS M 158 PHE 0.017 0.003 PHE i 186 TYR 0.022 0.003 TYR D 116 ARG 0.007 0.001 ARG b 95 *********************** 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 1725 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1446 time to evaluate : 9.056 Fit side-chains REVERT: u 35 TYR cc_start: 0.7524 (t80) cc_final: 0.7129 (t80) REVERT: u 36 ARG cc_start: 0.6636 (ptp-110) cc_final: 0.6287 (ttm-80) REVERT: u 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8606 (t0) REVERT: A 38 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8198 (mtt-85) REVERT: B 36 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: B 224 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: C 224 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: D 138 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (mm) REVERT: E 138 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (mm) REVERT: F 35 TYR cc_start: 0.7524 (t80) cc_final: 0.7129 (t80) REVERT: F 36 ARG cc_start: 0.6636 (ptp-110) cc_final: 0.6287 (ttm-80) REVERT: F 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8606 (t0) REVERT: G 38 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8198 (mtt-85) REVERT: H 36 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: H 224 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: I 224 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: J 224 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: K 138 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8489 (mm) REVERT: L 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7127 (t80) REVERT: L 36 ARG cc_start: 0.6637 (ptp-110) cc_final: 0.6286 (ttm-80) REVERT: L 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8604 (t0) REVERT: M 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8196 (mtt-85) REVERT: N 36 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: N 224 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: O 36 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: O 224 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: P 224 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: Q 138 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8489 (mm) REVERT: R 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7127 (t80) REVERT: R 36 ARG cc_start: 0.6637 (ptp-110) cc_final: 0.6286 (ttm-80) REVERT: R 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8604 (t0) REVERT: S 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8196 (mtt-85) REVERT: T 138 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8489 (mm) REVERT: U 35 TYR cc_start: 0.7526 (t80) cc_final: 0.7133 (t80) REVERT: U 36 ARG cc_start: 0.6629 (ptp-110) cc_final: 0.6283 (ttm-80) REVERT: U 68 ASN cc_start: 0.8819 (t0) cc_final: 0.8610 (t0) REVERT: V 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8193 (mtt-85) REVERT: W 36 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6664 (ttp80) REVERT: W 224 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: X 224 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: Y 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7127 (t80) REVERT: Y 36 ARG cc_start: 0.6637 (ptp-110) cc_final: 0.6286 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8604 (t0) REVERT: Z 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8196 (mtt-85) REVERT: 0 36 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: 0 224 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: 1 224 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: 2 138 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8489 (mm) REVERT: 3 36 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6666 (ttp80) REVERT: 3 224 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: 4 224 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7256 (tm-30) REVERT: 5 138 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8489 (mm) REVERT: 6 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7129 (t80) REVERT: 6 36 ARG cc_start: 0.6636 (ptp-110) cc_final: 0.6287 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8606 (t0) REVERT: 7 38 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8198 (mtt-85) REVERT: 8 224 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: 9 138 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8488 (mm) REVERT: a 35 TYR cc_start: 0.7522 (t80) cc_final: 0.7128 (t80) REVERT: a 36 ARG cc_start: 0.6635 (ptp-110) cc_final: 0.6287 (ttm-80) REVERT: a 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8609 (t0) REVERT: b 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8190 (mtt-85) REVERT: c 36 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6661 (ttp80) REVERT: c 224 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: d 36 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6661 (ttp80) REVERT: d 224 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: e 224 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: f 138 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8488 (mm) REVERT: g 35 TYR cc_start: 0.7522 (t80) cc_final: 0.7128 (t80) REVERT: g 36 ARG cc_start: 0.6635 (ptp-110) cc_final: 0.6287 (ttm-80) REVERT: g 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8609 (t0) REVERT: h 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8190 (mtt-85) REVERT: i 224 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: j 138 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8489 (mm) REVERT: k 35 TYR cc_start: 0.7526 (t80) cc_final: 0.7133 (t80) REVERT: k 36 ARG cc_start: 0.6630 (ptp-110) cc_final: 0.6283 (ttm-80) REVERT: k 68 ASN cc_start: 0.8819 (t0) cc_final: 0.8610 (t0) REVERT: l 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8193 (mtt-85) REVERT: m 36 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6664 (ttp80) REVERT: m 224 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: n 138 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8488 (mm) REVERT: o 35 TYR cc_start: 0.7522 (t80) cc_final: 0.7128 (t80) REVERT: o 36 ARG cc_start: 0.6635 (ptp-110) cc_final: 0.6287 (ttm-80) REVERT: o 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8609 (t0) REVERT: p 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8190 (mtt-85) REVERT: q 36 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6661 (ttp80) REVERT: q 224 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: r 224 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: s 35 TYR cc_start: 0.7526 (t80) cc_final: 0.7133 (t80) REVERT: s 36 ARG cc_start: 0.6630 (ptp-110) cc_final: 0.6283 (ttm-80) REVERT: s 68 ASN cc_start: 0.8820 (t0) cc_final: 0.8610 (t0) REVERT: t 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8193 (mtt-85) REVERT: v 36 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6664 (ttp80) REVERT: v 224 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: w 224 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: x 138 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8489 (mm) outliers start: 279 outliers final: 87 residues processed: 1590 average time/residue: 1.9590 time to fit residues: 4145.7751 Evaluate side-chains 1593 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1458 time to evaluate : 8.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain 9 residue 89 LEU Chi-restraints excluded: chain 9 residue 120 VAL Chi-restraints excluded: chain 9 residue 138 ILE Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 138 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain j residue 89 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 138 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 138 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 224 GLU Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 120 VAL Chi-restraints excluded: chain x residue 138 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 390 optimal weight: 20.0000 chunk 1044 optimal weight: 0.0470 chunk 229 optimal weight: 6.9990 chunk 681 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 chunk 1161 optimal weight: 8.9990 chunk 963 optimal weight: 20.0000 chunk 537 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 609 optimal weight: 10.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN C 51 GLN C 171 ASN C 181 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN I 51 GLN I 171 ASN I 181 GLN J 51 GLN J 171 ASN J 181 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 GLN P 51 GLN P 171 ASN P 181 GLN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 GLN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN X 51 GLN X 171 ASN X 181 GLN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 181 GLN 1 51 GLN 1 171 ASN 1 181 GLN 4 51 GLN 4 171 ASN 4 181 GLN 7 181 GLN 8 51 GLN 8 171 ASN 8 181 GLN b 181 GLN e 51 GLN e 171 ASN e 181 GLN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 GLN i 51 GLN i 171 ASN i 181 GLN l 181 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN r 51 GLN r 171 ASN r 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN w 51 GLN w 171 ASN w 181 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 105000 Z= 0.266 Angle : 0.637 8.900 142800 Z= 0.332 Chirality : 0.045 0.174 13980 Planarity : 0.006 0.067 18780 Dihedral : 6.685 34.421 13740 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.36 % Favored : 95.14 % Rotamer: Outliers : 2.14 % Allowed : 13.05 % Favored : 84.81 % 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: -1.25 (0.07), residues: 11940 helix: 0.16 (0.18), residues: 720 sheet: 0.25 (0.07), residues: 4620 loop : -1.83 (0.07), residues: 6600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP j 156 HIS 0.002 0.001 HIS t 158 PHE 0.013 0.002 PHE 4 175 TYR 0.018 0.002 TYR 5 116 ARG 0.004 0.001 ARG A 148 *********************** 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 1718 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1491 time to evaluate : 9.237 Fit side-chains REVERT: u 35 TYR cc_start: 0.7500 (t80) cc_final: 0.7106 (t80) REVERT: u 36 ARG cc_start: 0.6657 (ptp-110) cc_final: 0.6349 (ttm-80) REVERT: u 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8581 (t0) REVERT: A 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: B 36 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: B 40 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7962 (ttmm) REVERT: B 224 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: C 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: D 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8398 (mm) REVERT: E 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8398 (mm) REVERT: F 35 TYR cc_start: 0.7501 (t80) cc_final: 0.7106 (t80) REVERT: F 36 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6349 (ttm-80) REVERT: F 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8581 (t0) REVERT: G 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: H 36 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: H 40 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7962 (ttmm) REVERT: H 224 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: I 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: J 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: K 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (mm) REVERT: L 35 TYR cc_start: 0.7502 (t80) cc_final: 0.7104 (t80) REVERT: L 36 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6347 (ttm-80) REVERT: L 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8580 (t0) REVERT: M 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: N 36 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6436 (ttp80) REVERT: N 40 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7961 (ttmm) REVERT: N 224 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: O 36 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6436 (ttp80) REVERT: O 40 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7961 (ttmm) REVERT: O 224 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: P 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: Q 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (mm) REVERT: R 35 TYR cc_start: 0.7502 (t80) cc_final: 0.7104 (t80) REVERT: R 36 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6347 (ttm-80) REVERT: R 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8580 (t0) REVERT: S 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: T 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8399 (mm) REVERT: U 35 TYR cc_start: 0.7505 (t80) cc_final: 0.7113 (t80) REVERT: U 36 ARG cc_start: 0.6653 (ptp-110) cc_final: 0.6347 (ttm-80) REVERT: U 68 ASN cc_start: 0.8820 (t0) cc_final: 0.8584 (t0) REVERT: V 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8213 (mtt-85) REVERT: W 36 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6435 (ttp80) REVERT: W 40 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7958 (ttmm) REVERT: W 224 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: X 224 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: Y 35 TYR cc_start: 0.7502 (t80) cc_final: 0.7104 (t80) REVERT: Y 36 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.6347 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8580 (t0) REVERT: Z 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: 0 36 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6436 (ttp80) REVERT: 0 40 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7961 (ttmm) REVERT: 0 224 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: 1 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: 2 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (mm) REVERT: 3 36 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: 3 40 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7962 (ttmm) REVERT: 3 224 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: 4 224 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: 5 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (mm) REVERT: 6 35 TYR cc_start: 0.7500 (t80) cc_final: 0.7106 (t80) REVERT: 6 36 ARG cc_start: 0.6657 (ptp-110) cc_final: 0.6349 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8582 (t0) REVERT: 7 38 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: 8 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: 9 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (mm) REVERT: a 35 TYR cc_start: 0.7500 (t80) cc_final: 0.7107 (t80) REVERT: a 36 ARG cc_start: 0.6657 (ptp-110) cc_final: 0.6350 (ttm-80) REVERT: a 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8583 (t0) REVERT: b 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: c 36 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: c 40 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7962 (ttmm) REVERT: c 224 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: d 36 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: d 40 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7962 (ttmm) REVERT: d 224 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: e 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: f 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (mm) REVERT: g 35 TYR cc_start: 0.7500 (t80) cc_final: 0.7107 (t80) REVERT: g 36 ARG cc_start: 0.6657 (ptp-110) cc_final: 0.6350 (ttm-80) REVERT: g 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8583 (t0) REVERT: h 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: i 224 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: j 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (mm) REVERT: k 35 TYR cc_start: 0.7505 (t80) cc_final: 0.7112 (t80) REVERT: k 36 ARG cc_start: 0.6653 (ptp-110) cc_final: 0.6348 (ttm-80) REVERT: k 68 ASN cc_start: 0.8820 (t0) cc_final: 0.8584 (t0) REVERT: l 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8213 (mtt-85) REVERT: m 36 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6435 (ttp80) REVERT: m 40 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7959 (ttmm) REVERT: m 224 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: n 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (mm) REVERT: o 35 TYR cc_start: 0.7500 (t80) cc_final: 0.7107 (t80) REVERT: o 36 ARG cc_start: 0.6657 (ptp-110) cc_final: 0.6350 (ttm-80) REVERT: o 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8583 (t0) REVERT: p 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: q 36 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6438 (ttp80) REVERT: q 40 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7962 (ttmm) REVERT: q 224 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: r 224 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: s 35 TYR cc_start: 0.7505 (t80) cc_final: 0.7112 (t80) REVERT: s 36 ARG cc_start: 0.6653 (ptp-110) cc_final: 0.6347 (ttm-80) REVERT: s 68 ASN cc_start: 0.8819 (t0) cc_final: 0.8584 (t0) REVERT: t 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8213 (mtt-85) REVERT: v 36 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6435 (ttp80) REVERT: v 40 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7958 (ttmm) REVERT: v 224 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: w 224 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: x 138 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (mm) outliers start: 227 outliers final: 119 residues processed: 1587 average time/residue: 1.9895 time to fit residues: 4198.8225 Evaluate side-chains 1642 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1475 time to evaluate : 8.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 89 LEU Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 159 LYS Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 138 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 89 LEU Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 138 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 138 ILE Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 159 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 138 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 138 ILE Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 159 LYS Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 89 LEU Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain 9 residue 120 VAL Chi-restraints excluded: chain 9 residue 138 ILE Chi-restraints excluded: chain 9 residue 159 LYS Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 138 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 138 ILE Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 159 LYS Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain i residue 138 ILE Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 138 ILE Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 89 LEU Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain n residue 159 LYS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 89 LEU Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 138 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 138 ILE Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 89 LEU Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 138 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 138 ILE Chi-restraints excluded: chain w residue 224 GLU Chi-restraints excluded: chain x residue 120 VAL Chi-restraints excluded: chain x residue 138 ILE Chi-restraints excluded: chain x residue 159 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1119 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 661 optimal weight: 9.9990 chunk 847 optimal weight: 10.0000 chunk 656 optimal weight: 8.9990 chunk 977 optimal weight: 20.0000 chunk 648 optimal weight: 20.0000 chunk 1156 optimal weight: 9.9990 chunk 723 optimal weight: 20.0000 chunk 705 optimal weight: 3.9990 chunk 533 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 207 ASN A 181 GLN C 181 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN G 181 GLN I 181 GLN J 181 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 ASN M 181 GLN P 181 GLN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN S 181 GLN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 207 ASN V 181 GLN X 181 GLN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 207 ASN Z 181 GLN 1 181 GLN 4 181 GLN 6 207 ASN 7 181 GLN 8 181 GLN a 207 ASN b 181 GLN e 181 GLN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 207 ASN h 181 GLN i 181 GLN k 207 ASN l 181 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 207 ASN p 181 GLN r 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 207 ASN t 181 GLN w 181 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 105000 Z= 0.372 Angle : 0.707 9.552 142800 Z= 0.371 Chirality : 0.048 0.188 13980 Planarity : 0.007 0.076 18780 Dihedral : 7.020 38.282 13740 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.92 % Favored : 94.57 % Rotamer: Outliers : 2.03 % Allowed : 13.42 % Favored : 84.55 % 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: -1.46 (0.07), residues: 11940 helix: 0.02 (0.18), residues: 720 sheet: 0.02 (0.07), residues: 4980 loop : -2.00 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP 5 156 HIS 0.003 0.001 HIS t 158 PHE 0.015 0.002 PHE J 186 TYR 0.021 0.003 TYR 9 116 ARG 0.005 0.001 ARG p 95 *********************** REFINEMENT MACRO_CYCLE 7 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 1731 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1515 time to evaluate : 8.919 Fit side-chains REVERT: u 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7117 (t80) REVERT: u 36 ARG cc_start: 0.6674 (ptp-110) cc_final: 0.6395 (ttm-80) REVERT: u 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8601 (t0) REVERT: A 38 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8203 (mtt-85) REVERT: B 36 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6562 (ttp80) REVERT: B 224 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: C 224 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: D 138 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mm) REVERT: E 138 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mm) REVERT: F 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7117 (t80) REVERT: F 36 ARG cc_start: 0.6674 (ptp-110) cc_final: 0.6395 (ttm-80) REVERT: F 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8601 (t0) REVERT: G 38 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8203 (mtt-85) REVERT: H 36 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6562 (ttp80) REVERT: H 224 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: I 224 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: J 37 TRP cc_start: 0.8551 (t60) cc_final: 0.8307 (t60) REVERT: J 224 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: K 138 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mm) REVERT: L 35 TYR cc_start: 0.7522 (t80) cc_final: 0.7117 (t80) REVERT: L 36 ARG cc_start: 0.6673 (ptp-110) cc_final: 0.6396 (ttm-80) REVERT: L 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8598 (t0) REVERT: M 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8202 (mtt-85) REVERT: N 36 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6561 (ttp80) REVERT: N 224 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: O 36 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6560 (ttp80) REVERT: O 224 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: P 37 TRP cc_start: 0.8551 (t60) cc_final: 0.8306 (t60) REVERT: P 224 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: Q 138 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mm) REVERT: R 35 TYR cc_start: 0.7522 (t80) cc_final: 0.7117 (t80) REVERT: R 36 ARG cc_start: 0.6672 (ptp-110) cc_final: 0.6396 (ttm-80) REVERT: R 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8599 (t0) REVERT: S 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8203 (mtt-85) REVERT: T 138 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8436 (mm) REVERT: U 35 TYR cc_start: 0.7525 (t80) cc_final: 0.7125 (t80) REVERT: U 36 ARG cc_start: 0.6666 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: U 68 ASN cc_start: 0.8818 (t0) cc_final: 0.8604 (t0) REVERT: V 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8198 (mtt-85) REVERT: W 36 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6559 (ttp80) REVERT: W 224 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: X 224 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: Y 35 TYR cc_start: 0.7522 (t80) cc_final: 0.7117 (t80) REVERT: Y 36 ARG cc_start: 0.6672 (ptp-110) cc_final: 0.6396 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8598 (t0) REVERT: Z 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8202 (mtt-85) REVERT: 0 36 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6561 (ttp80) REVERT: 0 224 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: 1 37 TRP cc_start: 0.8551 (t60) cc_final: 0.8307 (t60) REVERT: 1 224 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: 2 138 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mm) REVERT: 3 36 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6562 (ttp80) REVERT: 3 224 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: 4 224 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: 5 138 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mm) REVERT: 6 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7116 (t80) REVERT: 6 36 ARG cc_start: 0.6674 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8601 (t0) REVERT: 7 38 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8203 (mtt-85) REVERT: 8 224 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: 9 138 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8440 (mm) REVERT: a 35 TYR cc_start: 0.7520 (t80) cc_final: 0.7119 (t80) REVERT: a 36 ARG cc_start: 0.6670 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: a 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8603 (t0) REVERT: b 38 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8195 (mtt-85) REVERT: c 36 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6560 (ttp80) REVERT: c 224 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: d 36 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6560 (ttp80) REVERT: d 224 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: e 224 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: f 138 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8437 (mm) REVERT: g 35 TYR cc_start: 0.7520 (t80) cc_final: 0.7119 (t80) REVERT: g 36 ARG cc_start: 0.6670 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: g 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8603 (t0) REVERT: h 38 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8195 (mtt-85) REVERT: i 224 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: j 138 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8436 (mm) REVERT: k 35 TYR cc_start: 0.7525 (t80) cc_final: 0.7125 (t80) REVERT: k 36 ARG cc_start: 0.6667 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: k 68 ASN cc_start: 0.8818 (t0) cc_final: 0.8605 (t0) REVERT: l 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8199 (mtt-85) REVERT: m 36 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6559 (ttp80) REVERT: m 224 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: n 138 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8437 (mm) REVERT: o 35 TYR cc_start: 0.7520 (t80) cc_final: 0.7119 (t80) REVERT: o 36 ARG cc_start: 0.6670 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: o 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8603 (t0) REVERT: p 38 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8195 (mtt-85) REVERT: q 36 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6560 (ttp80) REVERT: q 224 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: r 224 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: s 35 TYR cc_start: 0.7525 (t80) cc_final: 0.7125 (t80) REVERT: s 36 ARG cc_start: 0.6666 (ptp-110) cc_final: 0.6394 (ttm-80) REVERT: s 68 ASN cc_start: 0.8818 (t0) cc_final: 0.8604 (t0) REVERT: t 38 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8199 (mtt-85) REVERT: v 36 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6558 (ttp80) REVERT: v 224 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: w 224 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7065 (tm-30) REVERT: x 138 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8436 (mm) outliers start: 216 outliers final: 120 residues processed: 1623 average time/residue: 2.0445 time to fit residues: 4415.2015 Evaluate side-chains 1674 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1506 time to evaluate : 8.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 89 LEU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 159 LYS Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 138 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 138 ILE Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 138 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 138 ILE Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 159 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 138 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 138 ILE Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 5 residue 89 LEU Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 159 LYS Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 8 residue 138 ILE Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain 9 residue 89 LEU Chi-restraints excluded: chain 9 residue 120 VAL Chi-restraints excluded: chain 9 residue 138 ILE Chi-restraints excluded: chain 9 residue 159 LYS Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 138 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 138 ILE Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 159 LYS Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain i residue 138 ILE Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain j residue 89 LEU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 138 ILE Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 89 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain n residue 159 LYS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 138 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 138 ILE Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 138 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 138 ILE Chi-restraints excluded: chain w residue 224 GLU Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 120 VAL Chi-restraints excluded: chain x residue 138 ILE Chi-restraints excluded: chain x residue 159 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 715 optimal weight: 3.9990 chunk 461 optimal weight: 7.9990 chunk 690 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 735 optimal weight: 9.9990 chunk 787 optimal weight: 5.9990 chunk 571 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 909 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 207 ASN A 181 GLN C 181 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN G 181 GLN I 181 GLN J 181 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 207 ASN M 181 GLN P 181 GLN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN S 181 GLN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 207 ASN V 181 GLN X 181 GLN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 207 ASN Z 181 GLN 1 181 GLN 4 181 GLN 6 207 ASN 7 181 GLN 8 181 GLN a 207 ASN b 181 GLN e 181 GLN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 207 ASN h 181 GLN i 181 GLN k 207 ASN l 181 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 207 ASN p 181 GLN r 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 207 ASN t 181 GLN w 181 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 105000 Z= 0.287 Angle : 0.654 8.986 142800 Z= 0.341 Chirality : 0.046 0.174 13980 Planarity : 0.006 0.067 18780 Dihedral : 6.746 34.120 13740 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.94 % Favored : 95.56 % Rotamer: Outliers : 1.92 % Allowed : 13.57 % Favored : 84.51 % 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: -1.42 (0.07), residues: 11940 helix: 0.07 (0.18), residues: 720 sheet: 0.07 (0.07), residues: 4980 loop : -2.00 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP w 55 HIS 0.002 0.001 HIS Q 69 PHE 0.013 0.002 PHE 1 175 TYR 0.018 0.002 TYR 5 116 ARG 0.004 0.001 ARG S 95 *********************** REFINEMENT MACRO_CYCLE 8 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 1692 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1488 time to evaluate : 9.006 Fit side-chains REVERT: u 35 TYR cc_start: 0.7509 (t80) cc_final: 0.7081 (t80) REVERT: u 36 ARG cc_start: 0.6693 (ptp-110) cc_final: 0.6354 (ttm-80) REVERT: u 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8588 (t0) REVERT: A 38 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8211 (mtt-85) REVERT: B 36 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6290 (ttp80) REVERT: B 224 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: C 37 TRP cc_start: 0.8558 (t60) cc_final: 0.8298 (t60) REVERT: C 40 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7880 (ttpt) REVERT: C 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: D 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8408 (mm) REVERT: E 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8408 (mm) REVERT: F 35 TYR cc_start: 0.7509 (t80) cc_final: 0.7081 (t80) REVERT: F 36 ARG cc_start: 0.6693 (ptp-110) cc_final: 0.6355 (ttm-80) REVERT: F 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8587 (t0) REVERT: G 38 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: H 36 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6290 (ttp80) REVERT: H 224 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: I 37 TRP cc_start: 0.8558 (t60) cc_final: 0.8298 (t60) REVERT: I 40 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7883 (ttpt) REVERT: I 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: J 37 TRP cc_start: 0.8559 (t60) cc_final: 0.8298 (t60) REVERT: J 40 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7880 (ttpt) REVERT: J 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: K 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8408 (mm) REVERT: L 35 TYR cc_start: 0.7510 (t80) cc_final: 0.7080 (t80) REVERT: L 36 ARG cc_start: 0.6692 (ptp-110) cc_final: 0.6354 (ttm-80) REVERT: L 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8586 (t0) REVERT: M 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8210 (mtt-85) REVERT: N 36 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6288 (ttp80) REVERT: N 224 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: O 36 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6288 (ttp80) REVERT: O 224 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: P 37 TRP cc_start: 0.8559 (t60) cc_final: 0.8298 (t60) REVERT: P 40 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7880 (ttpt) REVERT: P 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: Q 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8408 (mm) REVERT: R 35 TYR cc_start: 0.7510 (t80) cc_final: 0.7080 (t80) REVERT: R 36 ARG cc_start: 0.6691 (ptp-110) cc_final: 0.6353 (ttm-80) REVERT: R 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8585 (t0) REVERT: S 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8211 (mtt-85) REVERT: T 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8409 (mm) REVERT: U 35 TYR cc_start: 0.7515 (t80) cc_final: 0.7088 (t80) REVERT: U 36 ARG cc_start: 0.6688 (ptp-110) cc_final: 0.6353 (ttm-80) REVERT: U 68 ASN cc_start: 0.8818 (t0) cc_final: 0.8591 (t0) REVERT: V 38 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8206 (mtt-85) REVERT: W 36 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6288 (ttp80) REVERT: W 224 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: X 37 TRP cc_start: 0.8562 (t60) cc_final: 0.8301 (t60) REVERT: X 40 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7877 (ttpt) REVERT: X 224 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: Y 35 TYR cc_start: 0.7510 (t80) cc_final: 0.7080 (t80) REVERT: Y 36 ARG cc_start: 0.6692 (ptp-110) cc_final: 0.6354 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8585 (t0) REVERT: Z 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8211 (mtt-85) REVERT: 0 36 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6288 (ttp80) REVERT: 0 224 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: 1 37 TRP cc_start: 0.8559 (t60) cc_final: 0.8298 (t60) REVERT: 1 40 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7880 (ttpt) REVERT: 1 224 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: 2 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8408 (mm) REVERT: 3 36 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6290 (ttp80) REVERT: 3 224 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: 4 37 TRP cc_start: 0.8558 (t60) cc_final: 0.8298 (t60) REVERT: 4 40 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7883 (ttpt) REVERT: 4 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: 5 138 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8408 (mm) REVERT: 6 35 TYR cc_start: 0.7509 (t80) cc_final: 0.7081 (t80) REVERT: 6 36 ARG cc_start: 0.6693 (ptp-110) cc_final: 0.6355 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8587 (t0) REVERT: 7 38 ARG cc_start: 0.8446 (mtp85) cc_final: 0.8211 (mtt-85) REVERT: 8 37 TRP cc_start: 0.8561 (t60) cc_final: 0.8301 (t60) REVERT: 8 40 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7886 (ttpt) REVERT: 8 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: 9 138 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8410 (mm) REVERT: a 35 TYR cc_start: 0.7511 (t80) cc_final: 0.7085 (t80) REVERT: a 36 ARG cc_start: 0.6692 (ptp-110) cc_final: 0.6356 (ttm-80) REVERT: a 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8589 (t0) REVERT: b 38 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8202 (mtt-85) REVERT: c 36 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6488 (ttp80) REVERT: c 224 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: d 36 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6488 (ttp80) REVERT: d 224 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: e 37 TRP cc_start: 0.8562 (t60) cc_final: 0.8302 (t60) REVERT: e 40 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7886 (ttpt) REVERT: e 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: f 138 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8410 (mm) REVERT: g 35 TYR cc_start: 0.7510 (t80) cc_final: 0.7085 (t80) REVERT: g 36 ARG cc_start: 0.6692 (ptp-110) cc_final: 0.6356 (ttm-80) REVERT: g 68 ASN cc_start: 0.8816 (t0) cc_final: 0.8589 (t0) REVERT: h 38 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8202 (mtt-85) REVERT: i 37 TRP cc_start: 0.8562 (t60) cc_final: 0.8302 (t60) REVERT: i 40 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7877 (ttpt) REVERT: i 224 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: j 138 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8410 (mm) REVERT: k 35 TYR cc_start: 0.7515 (t80) cc_final: 0.7088 (t80) REVERT: k 36 ARG cc_start: 0.6687 (ptp-110) cc_final: 0.6353 (ttm-80) REVERT: k 68 ASN cc_start: 0.8819 (t0) cc_final: 0.8591 (t0) REVERT: l 38 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8206 (mtt-85) REVERT: m 36 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: m 224 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: n 138 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8410 (mm) REVERT: o 35 TYR cc_start: 0.7511 (t80) cc_final: 0.7085 (t80) REVERT: o 36 ARG cc_start: 0.6692 (ptp-110) cc_final: 0.6356 (ttm-80) REVERT: o 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8589 (t0) REVERT: p 38 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8202 (mtt-85) REVERT: q 36 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6488 (ttp80) REVERT: q 224 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: r 37 TRP cc_start: 0.8561 (t60) cc_final: 0.8301 (t60) REVERT: r 40 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7886 (ttpt) REVERT: r 224 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: s 35 TYR cc_start: 0.7515 (t80) cc_final: 0.7088 (t80) REVERT: s 36 ARG cc_start: 0.6688 (ptp-110) cc_final: 0.6353 (ttm-80) REVERT: s 68 ASN cc_start: 0.8818 (t0) cc_final: 0.8590 (t0) REVERT: t 38 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8206 (mtt-85) REVERT: v 36 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: v 224 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: w 37 TRP cc_start: 0.8562 (t60) cc_final: 0.8302 (t60) REVERT: w 40 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7877 (ttpt) REVERT: w 224 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: x 138 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8410 (mm) outliers start: 204 outliers final: 96 residues processed: 1584 average time/residue: 1.9998 time to fit residues: 4209.5497 Evaluate side-chains 1597 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1453 time to evaluate : 8.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 159 LYS Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 138 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 138 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 159 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 138 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 159 LYS Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain 9 residue 120 VAL Chi-restraints excluded: chain 9 residue 138 ILE Chi-restraints excluded: chain 9 residue 159 LYS Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 138 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 159 LYS Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 138 ILE Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain n residue 159 LYS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 138 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 138 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 224 GLU Chi-restraints excluded: chain x residue 120 VAL Chi-restraints excluded: chain x residue 138 ILE Chi-restraints excluded: chain x residue 159 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1052 optimal weight: 4.9990 chunk 1108 optimal weight: 20.0000 chunk 1010 optimal weight: 0.8980 chunk 1077 optimal weight: 10.0000 chunk 1107 optimal weight: 10.0000 chunk 648 optimal weight: 9.9990 chunk 469 optimal weight: 10.0000 chunk 846 optimal weight: 0.9990 chunk 330 optimal weight: 40.0000 chunk 973 optimal weight: 3.9990 chunk 1019 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN C 181 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN I 181 GLN J 181 GLN ** L 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 GLN P 181 GLN P 230 ASN ** R 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 GLN ** U 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 181 GLN X 181 GLN X 230 ASN ** Y 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 181 GLN 1 181 GLN 4 181 GLN 7 181 GLN 8 181 GLN b 181 GLN e 181 GLN ** g 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 181 GLN i 181 GLN i 230 ASN l 181 GLN ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 181 GLN r 181 GLN ** s 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 181 GLN w 181 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 105000 Z= 0.212 Angle : 0.600 8.572 142800 Z= 0.313 Chirality : 0.044 0.157 13980 Planarity : 0.005 0.064 18780 Dihedral : 6.420 35.523 13740 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.22 % Favored : 95.28 % Rotamer: Outliers : 1.46 % Allowed : 13.94 % Favored : 84.60 % 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: -1.34 (0.07), residues: 11940 helix: 0.21 (0.19), residues: 720 sheet: 0.15 (0.07), residues: 4980 loop : -1.97 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 55 HIS 0.002 0.001 HIS m 69 PHE 0.012 0.002 PHE Y 175 TYR 0.016 0.002 TYR E 116 ARG 0.003 0.000 ARG 7 95 *********************** REFINEMENT MACRO_CYCLE 9 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 1667 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1512 time to evaluate : 8.960 Fit side-chains REVERT: u 35 TYR cc_start: 0.7466 (t80) cc_final: 0.7042 (t80) REVERT: u 36 ARG cc_start: 0.6685 (ptp-110) cc_final: 0.6340 (ttm-80) REVERT: u 68 ASN cc_start: 0.8793 (t0) cc_final: 0.8526 (t0) REVERT: A 38 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8217 (mtt-85) REVERT: B 36 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: B 40 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7953 (ttmm) REVERT: B 224 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: C 40 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7779 (ttpt) REVERT: C 224 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: D 138 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8281 (mm) REVERT: E 138 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8281 (mm) REVERT: F 35 TYR cc_start: 0.7466 (t80) cc_final: 0.7041 (t80) REVERT: F 36 ARG cc_start: 0.6685 (ptp-110) cc_final: 0.6340 (ttm-80) REVERT: F 68 ASN cc_start: 0.8792 (t0) cc_final: 0.8526 (t0) REVERT: G 38 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8217 (mtt-85) REVERT: H 36 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: H 40 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7954 (ttmm) REVERT: H 224 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: I 40 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7782 (ttpt) REVERT: I 224 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: J 40 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7777 (ttpt) REVERT: J 224 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: K 138 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (mm) REVERT: L 35 TYR cc_start: 0.7468 (t80) cc_final: 0.7043 (t80) REVERT: L 36 ARG cc_start: 0.6685 (ptp-110) cc_final: 0.6338 (ttm-80) REVERT: L 68 ASN cc_start: 0.8793 (t0) cc_final: 0.8525 (t0) REVERT: M 38 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8216 (mtt-85) REVERT: N 36 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6286 (ttp80) REVERT: N 40 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7949 (ttmm) REVERT: N 224 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: O 36 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6286 (ttp80) REVERT: O 40 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7950 (ttmm) REVERT: O 224 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: P 40 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7777 (ttpt) REVERT: P 224 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: Q 36 ARG cc_start: 0.6632 (ptm160) cc_final: 0.5974 (ptp90) REVERT: Q 138 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8282 (mm) REVERT: R 35 TYR cc_start: 0.7467 (t80) cc_final: 0.7042 (t80) REVERT: R 36 ARG cc_start: 0.6685 (ptp-110) cc_final: 0.6338 (ttm-80) REVERT: R 68 ASN cc_start: 0.8793 (t0) cc_final: 0.8525 (t0) REVERT: S 38 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8217 (mtt-85) REVERT: T 138 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (mm) REVERT: U 35 TYR cc_start: 0.7471 (t80) cc_final: 0.7049 (t80) REVERT: U 36 ARG cc_start: 0.6679 (ptp-110) cc_final: 0.6338 (ttm-80) REVERT: U 68 ASN cc_start: 0.8794 (t0) cc_final: 0.8530 (t0) REVERT: V 38 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8215 (mtt-85) REVERT: W 36 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6285 (ttp80) REVERT: W 40 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7947 (ttmm) REVERT: W 224 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: X 40 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7774 (ttpt) REVERT: X 224 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: Y 35 TYR cc_start: 0.7467 (t80) cc_final: 0.7043 (t80) REVERT: Y 36 ARG cc_start: 0.6685 (ptp-110) cc_final: 0.6338 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8793 (t0) cc_final: 0.8525 (t0) REVERT: Z 38 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8216 (mtt-85) REVERT: 0 36 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6286 (ttp80) REVERT: 0 40 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7950 (ttmm) REVERT: 0 224 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: 1 40 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7777 (ttpt) REVERT: 1 224 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: 2 36 ARG cc_start: 0.6633 (ptm160) cc_final: 0.5974 (ptp90) REVERT: 2 138 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8283 (mm) REVERT: 3 36 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: 3 40 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7953 (ttmm) REVERT: 3 224 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: 4 40 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7783 (ttpt) REVERT: 4 224 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: 5 138 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8281 (mm) REVERT: 6 35 TYR cc_start: 0.7466 (t80) cc_final: 0.7042 (t80) REVERT: 6 36 ARG cc_start: 0.6685 (ptp-110) cc_final: 0.6339 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8792 (t0) cc_final: 0.8526 (t0) REVERT: 7 38 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8217 (mtt-85) REVERT: 8 40 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7784 (ttpt) REVERT: 8 224 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: 9 138 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8283 (mm) REVERT: a 35 TYR cc_start: 0.7467 (t80) cc_final: 0.7046 (t80) REVERT: a 36 ARG cc_start: 0.6684 (ptp-110) cc_final: 0.6339 (ttm-80) REVERT: a 68 ASN cc_start: 0.8792 (t0) cc_final: 0.8529 (t0) REVERT: b 38 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8213 (mtt-85) REVERT: c 36 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6293 (ttp80) REVERT: c 40 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7955 (ttmm) REVERT: c 224 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: d 36 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6293 (ttp80) REVERT: d 40 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7955 (ttmm) REVERT: d 224 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6688 (tm-30) REVERT: e 40 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7784 (ttpt) REVERT: e 224 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: f 138 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8283 (mm) REVERT: g 35 TYR cc_start: 0.7467 (t80) cc_final: 0.7046 (t80) REVERT: g 36 ARG cc_start: 0.6684 (ptp-110) cc_final: 0.6339 (ttm-80) REVERT: g 68 ASN cc_start: 0.8792 (t0) cc_final: 0.8529 (t0) REVERT: h 38 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8213 (mtt-85) REVERT: i 40 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7774 (ttpt) REVERT: i 224 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: j 138 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (mm) REVERT: k 35 TYR cc_start: 0.7471 (t80) cc_final: 0.7049 (t80) REVERT: k 36 ARG cc_start: 0.6679 (ptp-110) cc_final: 0.6338 (ttm-80) REVERT: k 68 ASN cc_start: 0.8794 (t0) cc_final: 0.8530 (t0) REVERT: l 38 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8215 (mtt-85) REVERT: m 36 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6285 (ttp80) REVERT: m 40 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7947 (ttmm) REVERT: m 224 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: n 138 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (mm) REVERT: o 35 TYR cc_start: 0.7467 (t80) cc_final: 0.7046 (t80) REVERT: o 36 ARG cc_start: 0.6684 (ptp-110) cc_final: 0.6339 (ttm-80) REVERT: o 68 ASN cc_start: 0.8792 (t0) cc_final: 0.8529 (t0) REVERT: p 38 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8213 (mtt-85) REVERT: q 36 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6293 (ttp80) REVERT: q 40 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7956 (ttmm) REVERT: q 224 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: r 40 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7784 (ttpt) REVERT: r 224 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: s 35 TYR cc_start: 0.7471 (t80) cc_final: 0.7049 (t80) REVERT: s 36 ARG cc_start: 0.6679 (ptp-110) cc_final: 0.6337 (ttm-80) REVERT: s 68 ASN cc_start: 0.8795 (t0) cc_final: 0.8530 (t0) REVERT: t 38 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8215 (mtt-85) REVERT: v 36 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6285 (ttp80) REVERT: v 40 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7947 (ttmm) REVERT: v 224 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: w 40 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7774 (ttpt) REVERT: w 224 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: x 138 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8284 (mm) outliers start: 155 outliers final: 82 residues processed: 1585 average time/residue: 2.0354 time to fit residues: 4317.0621 Evaluate side-chains 1606 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1476 time to evaluate : 8.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain I residue 224 GLU Chi-restraints excluded: chain J residue 224 GLU Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain P residue 224 GLU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 159 LYS Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 153 THR Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain X residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 1 residue 224 GLU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 159 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 4 residue 224 GLU Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 8 residue 224 GLU Chi-restraints excluded: chain 9 residue 120 VAL Chi-restraints excluded: chain 9 residue 138 ILE Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 138 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 153 THR Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 138 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 153 THR Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain e residue 224 GLU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain i residue 224 GLU Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 138 ILE Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 138 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain r residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 153 THR Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain w residue 224 GLU Chi-restraints excluded: chain x residue 138 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1074 optimal weight: 7.9990 chunk 707 optimal weight: 7.9990 chunk 1139 optimal weight: 20.0000 chunk 695 optimal weight: 10.0000 chunk 540 optimal weight: 30.0000 chunk 792 optimal weight: 4.9990 chunk 1195 optimal weight: 9.9990 chunk 1100 optimal weight: 30.0000 chunk 951 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 735 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN C 181 GLN G 181 GLN I 181 GLN J 181 GLN M 181 GLN P 181 GLN S 181 GLN V 181 GLN X 181 GLN Z 181 GLN 1 181 GLN 4 181 GLN 7 181 GLN 8 181 GLN b 181 GLN e 181 GLN h 181 GLN i 181 GLN l 181 GLN p 181 GLN r 181 GLN t 181 GLN w 181 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 105000 Z= 0.371 Angle : 0.709 9.391 142800 Z= 0.372 Chirality : 0.048 0.198 13980 Planarity : 0.007 0.071 18780 Dihedral : 6.949 36.226 13740 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.85 % Favored : 94.65 % Rotamer: Outliers : 1.40 % Allowed : 14.11 % Favored : 84.49 % 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: -1.44 (0.07), residues: 11940 helix: 0.01 (0.18), residues: 720 sheet: 0.02 (0.07), residues: 4980 loop : -1.97 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP I 55 HIS 0.003 0.001 HIS 7 158 PHE 0.015 0.002 PHE I 186 TYR 0.021 0.003 TYR j 116 ARG 0.005 0.001 ARG M 95 ********************** REFINEMENT MACRO_CYCLE 10 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 1625 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1476 time to evaluate : 8.857 Fit side-chains REVERT: u 35 TYR cc_start: 0.7517 (t80) cc_final: 0.7092 (t80) REVERT: u 36 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.6392 (ttm-80) REVERT: u 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8589 (t0) REVERT: B 36 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6203 (ttp80) REVERT: B 224 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: C 37 TRP cc_start: 0.8569 (t60) cc_final: 0.8302 (t60) REVERT: D 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: E 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: F 35 TYR cc_start: 0.7517 (t80) cc_final: 0.7092 (t80) REVERT: F 36 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.6392 (ttm-80) REVERT: F 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8589 (t0) REVERT: H 36 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6203 (ttp80) REVERT: H 224 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: I 37 TRP cc_start: 0.8569 (t60) cc_final: 0.8302 (t60) REVERT: J 37 TRP cc_start: 0.8570 (t60) cc_final: 0.8303 (t60) REVERT: K 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: L 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7094 (t80) REVERT: L 36 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6393 (ttm-80) REVERT: L 68 ASN cc_start: 0.8813 (t0) cc_final: 0.8587 (t0) REVERT: N 36 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6201 (ttp80) REVERT: N 224 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6894 (tm-30) REVERT: O 36 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6201 (ttp80) REVERT: O 224 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: P 37 TRP cc_start: 0.8570 (t60) cc_final: 0.8303 (t60) REVERT: Q 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: R 35 TYR cc_start: 0.7520 (t80) cc_final: 0.7094 (t80) REVERT: R 36 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6393 (ttm-80) REVERT: R 68 ASN cc_start: 0.8813 (t0) cc_final: 0.8587 (t0) REVERT: T 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: U 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7100 (t80) REVERT: U 36 ARG cc_start: 0.6675 (ptp-110) cc_final: 0.6391 (ttm-80) REVERT: U 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8594 (t0) REVERT: W 36 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6199 (ttp80) REVERT: W 224 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: X 37 TRP cc_start: 0.8571 (t60) cc_final: 0.8305 (t60) REVERT: Y 35 TYR cc_start: 0.7519 (t80) cc_final: 0.7093 (t80) REVERT: Y 36 ARG cc_start: 0.6682 (ptp-110) cc_final: 0.6393 (ttm-80) REVERT: Y 68 ASN cc_start: 0.8813 (t0) cc_final: 0.8587 (t0) REVERT: 0 36 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6201 (ttp80) REVERT: 0 224 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: 1 37 TRP cc_start: 0.8570 (t60) cc_final: 0.8303 (t60) REVERT: 2 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: 3 36 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6203 (ttp80) REVERT: 3 224 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: 4 37 TRP cc_start: 0.8569 (t60) cc_final: 0.8302 (t60) REVERT: 5 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8415 (mm) REVERT: 6 35 TYR cc_start: 0.7518 (t80) cc_final: 0.7093 (t80) REVERT: 6 36 ARG cc_start: 0.6681 (ptp-110) cc_final: 0.6392 (ttm-80) REVERT: 6 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8589 (t0) REVERT: 8 37 TRP cc_start: 0.8572 (t60) cc_final: 0.8306 (t60) REVERT: 9 138 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8417 (mm) REVERT: a 35 TYR cc_start: 0.7518 (t80) cc_final: 0.7095 (t80) REVERT: a 36 ARG cc_start: 0.6680 (ptp-110) cc_final: 0.6393 (ttm-80) REVERT: a 68 ASN cc_start: 0.8814 (t0) cc_final: 0.8592 (t0) REVERT: c 36 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6205 (ttp80) REVERT: c 224 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: d 36 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6205 (ttp80) REVERT: d 224 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: e 37 TRP cc_start: 0.8572 (t60) cc_final: 0.8306 (t60) REVERT: f 138 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8417 (mm) REVERT: g 35 TYR cc_start: 0.7518 (t80) cc_final: 0.7095 (t80) REVERT: g 36 ARG cc_start: 0.6680 (ptp-110) cc_final: 0.6393 (ttm-80) REVERT: g 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8592 (t0) REVERT: i 37 TRP cc_start: 0.8571 (t60) cc_final: 0.8305 (t60) REVERT: j 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8416 (mm) REVERT: k 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7100 (t80) REVERT: k 36 ARG cc_start: 0.6675 (ptp-110) cc_final: 0.6391 (ttm-80) REVERT: k 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8594 (t0) REVERT: m 36 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6198 (ttp80) REVERT: m 224 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: n 138 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8417 (mm) REVERT: o 35 TYR cc_start: 0.7518 (t80) cc_final: 0.7095 (t80) REVERT: o 36 ARG cc_start: 0.6680 (ptp-110) cc_final: 0.6392 (ttm-80) REVERT: o 68 ASN cc_start: 0.8815 (t0) cc_final: 0.8592 (t0) REVERT: q 36 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6212 (ttp80) REVERT: q 224 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: r 37 TRP cc_start: 0.8572 (t60) cc_final: 0.8306 (t60) REVERT: s 35 TYR cc_start: 0.7523 (t80) cc_final: 0.7100 (t80) REVERT: s 36 ARG cc_start: 0.6675 (ptp-110) cc_final: 0.6391 (ttm-80) REVERT: s 68 ASN cc_start: 0.8817 (t0) cc_final: 0.8593 (t0) REVERT: v 36 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6198 (ttp80) REVERT: v 224 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6891 (tm-30) REVERT: w 37 TRP cc_start: 0.8572 (t60) cc_final: 0.8303 (t60) REVERT: x 138 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8416 (mm) outliers start: 149 outliers final: 85 residues processed: 1536 average time/residue: 2.0270 time to fit residues: 4118.3467 Evaluate side-chains 1597 residues out of total 10620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1476 time to evaluate : 8.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 181 GLN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain H residue 36 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 159 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain N residue 36 ARG Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 109 ILE Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 224 GLU Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 224 GLU Chi-restraints excluded: chain Q residue 120 VAL Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 159 LYS Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 159 LYS Chi-restraints excluded: chain U residue 44 THR Chi-restraints excluded: chain U residue 181 GLN Chi-restraints excluded: chain W residue 36 ARG Chi-restraints excluded: chain W residue 44 THR Chi-restraints excluded: chain W residue 109 ILE Chi-restraints excluded: chain W residue 143 ILE Chi-restraints excluded: chain W residue 224 GLU Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 181 GLN Chi-restraints excluded: chain 0 residue 36 ARG Chi-restraints excluded: chain 0 residue 44 THR Chi-restraints excluded: chain 0 residue 109 ILE Chi-restraints excluded: chain 0 residue 143 ILE Chi-restraints excluded: chain 0 residue 224 GLU Chi-restraints excluded: chain 2 residue 120 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 159 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 109 ILE Chi-restraints excluded: chain 3 residue 143 ILE Chi-restraints excluded: chain 3 residue 224 GLU Chi-restraints excluded: chain 5 residue 120 VAL Chi-restraints excluded: chain 5 residue 138 ILE Chi-restraints excluded: chain 5 residue 159 LYS Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 181 GLN Chi-restraints excluded: chain 9 residue 120 VAL Chi-restraints excluded: chain 9 residue 138 ILE Chi-restraints excluded: chain 9 residue 159 LYS Chi-restraints excluded: chain a residue 44 THR Chi-restraints excluded: chain a residue 181 GLN Chi-restraints excluded: chain c residue 36 ARG Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 109 ILE Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain c residue 224 GLU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 109 ILE Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 224 GLU Chi-restraints excluded: chain f residue 120 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 159 LYS Chi-restraints excluded: chain g residue 44 THR Chi-restraints excluded: chain g residue 181 GLN Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 138 ILE Chi-restraints excluded: chain j residue 159 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 181 GLN Chi-restraints excluded: chain m residue 36 ARG Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 109 ILE Chi-restraints excluded: chain m residue 143 ILE Chi-restraints excluded: chain m residue 224 GLU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 138 ILE Chi-restraints excluded: chain n residue 159 LYS Chi-restraints excluded: chain o residue 44 THR Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain q residue 36 ARG Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 109 ILE Chi-restraints excluded: chain q residue 143 ILE Chi-restraints excluded: chain q residue 224 GLU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 181 GLN Chi-restraints excluded: chain v residue 36 ARG Chi-restraints excluded: chain v residue 44 THR Chi-restraints excluded: chain v residue 109 ILE Chi-restraints excluded: chain v residue 143 ILE Chi-restraints excluded: chain v residue 224 GLU Chi-restraints excluded: chain x residue 120 VAL Chi-restraints excluded: chain x residue 138 ILE Chi-restraints excluded: chain x residue 159 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 583 optimal weight: 20.0000 chunk 756 optimal weight: 20.0000 chunk 1014 optimal weight: 0.3980 chunk 291 optimal weight: 0.9980 chunk 877 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 264 optimal weight: 6.9990 chunk 953 optimal weight: 3.9990 chunk 399 optimal weight: 9.9990 chunk 979 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN C 181 GLN G 181 GLN I 181 GLN J 181 GLN M 181 GLN P 181 GLN S 181 GLN V 181 GLN X 181 GLN Z 181 GLN 1 181 GLN 4 181 GLN 7 181 GLN 8 181 GLN b 181 GLN e 181 GLN h 181 GLN i 181 GLN l 181 GLN p 181 GLN r 181 GLN t 181 GLN w 181 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.116368 restraints weight = 91697.300| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.46 r_work: 0.2974 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 105000 Z= 0.226 Angle : 0.613 8.782 142800 Z= 0.320 Chirality : 0.044 0.158 13980 Planarity : 0.006 0.065 18780 Dihedral : 6.472 34.370 13740 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.71 % Favored : 95.79 % Rotamer: Outliers : 1.51 % Allowed : 14.08 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.36 (0.07), residues: 11940 helix: 0.19 (0.19), residues: 720 sheet: 0.10 (0.07), residues: 4980 loop : -1.96 (0.07), residues: 6240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP X 55 HIS 0.002 0.001 HIS x 69 PHE 0.012 0.002 PHE r 175 TYR 0.016 0.002 TYR j 116 ARG 0.003 0.000 ARG G 95 =============================================================================== Job complete usr+sys time: 51544.28 seconds wall clock time: 889 minutes 34.92 seconds (53374.92 seconds total)