Starting phenix.real_space_refine (version: dev) on Wed Apr 6 18:43:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/04_2022/3j9x_6310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/04_2022/3j9x_6310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/04_2022/3j9x_6310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/04_2022/3j9x_6310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/04_2022/3j9x_6310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/04_2022/3j9x_6310.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 70702 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "C" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "E" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "G" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "J" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "K" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "L" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "M" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "O" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "P" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Q" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "S" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "T" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "U" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "V" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "W" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "X" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Y" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "Z" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "a" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "b" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "c" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "d" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "e" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "f" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "g" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "h" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "i" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "j" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "k" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "l" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "m" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "n" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "o" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "p" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "q" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "s" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "t" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "u" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "v" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "w" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "x" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "y" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "z" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "1" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "2" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "3" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "4" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "5" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "6" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "7" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 7134 Classifications: {'DNA': 348} Link IDs: {'rna3p': 347} Chain: "8" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 7134 Classifications: {'DNA': 348} Link IDs: {'rna3p': 347} Time building chain proxies: 28.86, per 1000 atoms: 0.41 Number of scatterers: 70702 At special positions: 0 Unit cell: (199.5, 199.5, 139.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 696 15.00 O 14790 8.00 N 12354 7.00 C 42804 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: 25.37 Conformation dependent library (CDL) restraints added in 6.9 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13688 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 0 sheets defined 89.1% alpha, 0.0% beta 348 base pairs and 405 stacking pairs defined. Time for finding SS restraints: 17.80 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 37 through 66 Proline residue: A 50 - end of helix removed outlier: 3.771A pdb=" N VAL A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 91 removed outlier: 3.668A pdb=" N ALA A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 49 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'C' and resid 9 through 26 removed outlier: 3.647A pdb=" N ASN C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 37 through 66 Proline residue: C 50 - end of helix removed outlier: 3.771A pdb=" N VAL C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 114 through 126 Processing helix chain 'D' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 49 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 37 through 66 Proline residue: E 50 - end of helix removed outlier: 3.771A pdb=" N VAL E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 114 through 126 Processing helix chain 'F' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 49 Proline residue: F 39 - end of helix Processing helix chain 'F' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL F 55 " --> pdb=" O LYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'G' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 37 through 66 Proline residue: G 50 - end of helix removed outlier: 3.772A pdb=" N VAL G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 114 through 126 Processing helix chain 'H' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 49 Proline residue: H 39 - end of helix Processing helix chain 'H' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 111 Processing helix chain 'H' and resid 114 through 126 Processing helix chain 'I' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 37 through 66 Proline residue: I 50 - end of helix removed outlier: 3.771A pdb=" N VAL I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 91 removed outlier: 3.668A pdb=" N ALA I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 111 Processing helix chain 'I' and resid 114 through 126 Processing helix chain 'J' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 49 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL J 55 " --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 111 Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'K' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 37 through 66 Proline residue: K 50 - end of helix removed outlier: 3.772A pdb=" N VAL K 55 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 111 Processing helix chain 'K' and resid 114 through 126 Processing helix chain 'L' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 49 Proline residue: L 39 - end of helix Processing helix chain 'L' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 111 Processing helix chain 'L' and resid 114 through 126 Processing helix chain 'M' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN M 26 " --> pdb=" O ASN M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 37 through 66 Proline residue: M 50 - end of helix removed outlier: 3.771A pdb=" N VAL M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 111 Processing helix chain 'M' and resid 114 through 126 Processing helix chain 'N' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN N 26 " --> pdb=" O ASN N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 49 Proline residue: N 39 - end of helix Processing helix chain 'N' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL N 55 " --> pdb=" O LYS N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA N 74 " --> pdb=" O GLY N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 Processing helix chain 'N' and resid 114 through 126 Processing helix chain 'O' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN O 26 " --> pdb=" O ASN O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 37 through 66 Proline residue: O 50 - end of helix removed outlier: 3.772A pdb=" N VAL O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA O 74 " --> pdb=" O GLY O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 111 Processing helix chain 'O' and resid 114 through 126 Processing helix chain 'P' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN P 26 " --> pdb=" O ASN P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 49 Proline residue: P 39 - end of helix Processing helix chain 'P' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA P 74 " --> pdb=" O GLY P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 111 Processing helix chain 'P' and resid 114 through 126 Processing helix chain 'Q' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN Q 26 " --> pdb=" O ASN Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 37 through 66 Proline residue: Q 50 - end of helix removed outlier: 3.771A pdb=" N VAL Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA Q 74 " --> pdb=" O GLY Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 111 Processing helix chain 'Q' and resid 114 through 126 Processing helix chain 'R' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN R 26 " --> pdb=" O ASN R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 49 Proline residue: R 39 - end of helix Processing helix chain 'R' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL R 55 " --> pdb=" O LYS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA R 74 " --> pdb=" O GLY R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 111 Processing helix chain 'R' and resid 114 through 126 Processing helix chain 'S' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN S 26 " --> pdb=" O ASN S 22 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 37 through 66 Proline residue: S 50 - end of helix removed outlier: 3.772A pdb=" N VAL S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA S 74 " --> pdb=" O GLY S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 111 Processing helix chain 'S' and resid 114 through 126 Processing helix chain 'T' and resid 9 through 26 removed outlier: 3.592A pdb=" N ASN T 26 " --> pdb=" O ASN T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 49 Proline residue: T 39 - end of helix Processing helix chain 'T' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA T 74 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 93 through 111 Processing helix chain 'T' and resid 114 through 126 Processing helix chain 'U' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN U 26 " --> pdb=" O ASN U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 37 through 66 Proline residue: U 50 - end of helix removed outlier: 3.771A pdb=" N VAL U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA U 74 " --> pdb=" O GLY U 70 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 111 Processing helix chain 'U' and resid 114 through 126 Processing helix chain 'V' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN V 26 " --> pdb=" O ASN V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 49 Proline residue: V 39 - end of helix Processing helix chain 'V' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL V 55 " --> pdb=" O LYS V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA V 74 " --> pdb=" O GLY V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 111 Processing helix chain 'V' and resid 114 through 126 Processing helix chain 'W' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 37 Processing helix chain 'W' and resid 37 through 66 Proline residue: W 50 - end of helix removed outlier: 3.771A pdb=" N VAL W 55 " --> pdb=" O LYS W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA W 74 " --> pdb=" O GLY W 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 93 through 111 Processing helix chain 'W' and resid 114 through 126 Processing helix chain 'X' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN X 26 " --> pdb=" O ASN X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 49 Proline residue: X 39 - end of helix Processing helix chain 'X' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA X 74 " --> pdb=" O GLY X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 111 Processing helix chain 'X' and resid 114 through 126 Processing helix chain 'Y' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN Y 26 " --> pdb=" O ASN Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 37 Processing helix chain 'Y' and resid 37 through 66 Proline residue: Y 50 - end of helix removed outlier: 3.772A pdb=" N VAL Y 55 " --> pdb=" O LYS Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 93 through 111 Processing helix chain 'Y' and resid 114 through 126 Processing helix chain 'Z' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN Z 26 " --> pdb=" O ASN Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 49 Proline residue: Z 39 - end of helix Processing helix chain 'Z' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL Z 55 " --> pdb=" O LYS Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA Z 74 " --> pdb=" O GLY Z 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 111 Processing helix chain 'Z' and resid 114 through 126 Processing helix chain 'a' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN a 26 " --> pdb=" O ASN a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 37 Processing helix chain 'a' and resid 37 through 66 Proline residue: a 50 - end of helix removed outlier: 3.773A pdb=" N VAL a 55 " --> pdb=" O LYS a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA a 74 " --> pdb=" O GLY a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 111 Processing helix chain 'a' and resid 114 through 126 Processing helix chain 'b' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN b 26 " --> pdb=" O ASN b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 49 Proline residue: b 39 - end of helix Processing helix chain 'b' and resid 49 through 66 removed outlier: 3.741A pdb=" N VAL b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA b 74 " --> pdb=" O GLY b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 111 Processing helix chain 'b' and resid 114 through 126 Processing helix chain 'c' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN c 26 " --> pdb=" O ASN c 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 37 through 66 Proline residue: c 50 - end of helix removed outlier: 3.772A pdb=" N VAL c 55 " --> pdb=" O LYS c 51 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA c 74 " --> pdb=" O GLY c 70 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 111 Processing helix chain 'c' and resid 114 through 126 Processing helix chain 'd' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN d 26 " --> pdb=" O ASN d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 49 Proline residue: d 39 - end of helix Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL d 55 " --> pdb=" O LYS d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA d 74 " --> pdb=" O GLY d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 111 Processing helix chain 'd' and resid 114 through 126 Processing helix chain 'e' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN e 26 " --> pdb=" O ASN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 26 through 37 Processing helix chain 'e' and resid 37 through 66 Proline residue: e 50 - end of helix removed outlier: 3.771A pdb=" N VAL e 55 " --> pdb=" O LYS e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA e 74 " --> pdb=" O GLY e 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 111 Processing helix chain 'e' and resid 114 through 126 Processing helix chain 'f' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN f 26 " --> pdb=" O ASN f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 49 Proline residue: f 39 - end of helix Processing helix chain 'f' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL f 55 " --> pdb=" O LYS f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA f 74 " --> pdb=" O GLY f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 Processing helix chain 'f' and resid 114 through 126 Processing helix chain 'g' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN g 26 " --> pdb=" O ASN g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 37 through 66 Proline residue: g 50 - end of helix removed outlier: 3.771A pdb=" N VAL g 55 " --> pdb=" O LYS g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA g 74 " --> pdb=" O GLY g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 111 Processing helix chain 'g' and resid 114 through 126 Processing helix chain 'h' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN h 26 " --> pdb=" O ASN h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 26 through 49 Proline residue: h 39 - end of helix Processing helix chain 'h' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL h 55 " --> pdb=" O LYS h 51 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA h 74 " --> pdb=" O GLY h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 111 Processing helix chain 'h' and resid 114 through 126 Processing helix chain 'i' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN i 26 " --> pdb=" O ASN i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 37 Processing helix chain 'i' and resid 37 through 66 Proline residue: i 50 - end of helix removed outlier: 3.771A pdb=" N VAL i 55 " --> pdb=" O LYS i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 111 Processing helix chain 'i' and resid 114 through 126 Processing helix chain 'j' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN j 26 " --> pdb=" O ASN j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 49 Proline residue: j 39 - end of helix Processing helix chain 'j' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL j 55 " --> pdb=" O LYS j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA j 74 " --> pdb=" O GLY j 70 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 111 Processing helix chain 'j' and resid 114 through 126 Processing helix chain 'k' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN k 26 " --> pdb=" O ASN k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 37 Processing helix chain 'k' and resid 37 through 66 Proline residue: k 50 - end of helix removed outlier: 3.771A pdb=" N VAL k 55 " --> pdb=" O LYS k 51 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA k 74 " --> pdb=" O GLY k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 111 Processing helix chain 'k' and resid 114 through 126 Processing helix chain 'l' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN l 26 " --> pdb=" O ASN l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 49 Proline residue: l 39 - end of helix Processing helix chain 'l' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL l 55 " --> pdb=" O LYS l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA l 74 " --> pdb=" O GLY l 70 " (cutoff:3.500A) Processing helix chain 'l' and resid 93 through 111 Processing helix chain 'l' and resid 114 through 126 Processing helix chain 'm' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN m 26 " --> pdb=" O ASN m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 37 through 66 Proline residue: m 50 - end of helix removed outlier: 3.770A pdb=" N VAL m 55 " --> pdb=" O LYS m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 70 through 91 removed outlier: 3.668A pdb=" N ALA m 74 " --> pdb=" O GLY m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 111 Processing helix chain 'm' and resid 114 through 126 Processing helix chain 'n' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN n 26 " --> pdb=" O ASN n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 49 Proline residue: n 39 - end of helix Processing helix chain 'n' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL n 55 " --> pdb=" O LYS n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA n 74 " --> pdb=" O GLY n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 111 Processing helix chain 'n' and resid 114 through 126 Processing helix chain 'o' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN o 26 " --> pdb=" O ASN o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 37 Processing helix chain 'o' and resid 37 through 66 Proline residue: o 50 - end of helix removed outlier: 3.772A pdb=" N VAL o 55 " --> pdb=" O LYS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA o 74 " --> pdb=" O GLY o 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 93 through 111 Processing helix chain 'o' and resid 114 through 126 Processing helix chain 'p' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN p 26 " --> pdb=" O ASN p 22 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 49 Proline residue: p 39 - end of helix Processing helix chain 'p' and resid 49 through 66 removed outlier: 3.741A pdb=" N VAL p 55 " --> pdb=" O LYS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA p 74 " --> pdb=" O GLY p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 111 Processing helix chain 'p' and resid 114 through 126 Processing helix chain 'q' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN q 26 " --> pdb=" O ASN q 22 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 37 Processing helix chain 'q' and resid 37 through 66 Proline residue: q 50 - end of helix removed outlier: 3.772A pdb=" N VAL q 55 " --> pdb=" O LYS q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA q 74 " --> pdb=" O GLY q 70 " (cutoff:3.500A) Processing helix chain 'q' and resid 93 through 111 Processing helix chain 'q' and resid 114 through 126 Processing helix chain 'r' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN r 26 " --> pdb=" O ASN r 22 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 49 Proline residue: r 39 - end of helix Processing helix chain 'r' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL r 55 " --> pdb=" O LYS r 51 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA r 74 " --> pdb=" O GLY r 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 93 through 111 Processing helix chain 'r' and resid 114 through 126 Processing helix chain 's' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN s 26 " --> pdb=" O ASN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 26 through 37 Processing helix chain 's' and resid 37 through 66 Proline residue: s 50 - end of helix removed outlier: 3.772A pdb=" N VAL s 55 " --> pdb=" O LYS s 51 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA s 74 " --> pdb=" O GLY s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 93 through 111 Processing helix chain 's' and resid 114 through 126 Processing helix chain 't' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN t 26 " --> pdb=" O ASN t 22 " (cutoff:3.500A) Processing helix chain 't' and resid 26 through 49 Proline residue: t 39 - end of helix Processing helix chain 't' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL t 55 " --> pdb=" O LYS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA t 74 " --> pdb=" O GLY t 70 " (cutoff:3.500A) Processing helix chain 't' and resid 93 through 111 Processing helix chain 't' and resid 114 through 126 Processing helix chain 'u' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN u 26 " --> pdb=" O ASN u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 37 Processing helix chain 'u' and resid 37 through 66 Proline residue: u 50 - end of helix removed outlier: 3.771A pdb=" N VAL u 55 " --> pdb=" O LYS u 51 " (cutoff:3.500A) Processing helix chain 'u' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA u 74 " --> pdb=" O GLY u 70 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 111 Processing helix chain 'u' and resid 114 through 126 Processing helix chain 'v' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN v 26 " --> pdb=" O ASN v 22 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 49 Proline residue: v 39 - end of helix Processing helix chain 'v' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL v 55 " --> pdb=" O LYS v 51 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA v 74 " --> pdb=" O GLY v 70 " (cutoff:3.500A) Processing helix chain 'v' and resid 93 through 111 Processing helix chain 'v' and resid 114 through 126 Processing helix chain 'w' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN w 26 " --> pdb=" O ASN w 22 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 37 Processing helix chain 'w' and resid 37 through 66 Proline residue: w 50 - end of helix removed outlier: 3.773A pdb=" N VAL w 55 " --> pdb=" O LYS w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 70 through 91 removed outlier: 3.667A pdb=" N ALA w 74 " --> pdb=" O GLY w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 93 through 111 Processing helix chain 'w' and resid 114 through 126 Processing helix chain 'x' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN x 26 " --> pdb=" O ASN x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 26 through 49 Proline residue: x 39 - end of helix Processing helix chain 'x' and resid 49 through 66 removed outlier: 3.741A pdb=" N VAL x 55 " --> pdb=" O LYS x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA x 74 " --> pdb=" O GLY x 70 " (cutoff:3.500A) Processing helix chain 'x' and resid 93 through 111 Processing helix chain 'x' and resid 114 through 126 Processing helix chain 'y' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN y 26 " --> pdb=" O ASN y 22 " (cutoff:3.500A) Processing helix chain 'y' and resid 26 through 37 Processing helix chain 'y' and resid 37 through 66 Proline residue: y 50 - end of helix removed outlier: 3.771A pdb=" N VAL y 55 " --> pdb=" O LYS y 51 " (cutoff:3.500A) Processing helix chain 'y' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA y 74 " --> pdb=" O GLY y 70 " (cutoff:3.500A) Processing helix chain 'y' and resid 93 through 111 Processing helix chain 'y' and resid 114 through 126 Processing helix chain 'z' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN z 26 " --> pdb=" O ASN z 22 " (cutoff:3.500A) Processing helix chain 'z' and resid 26 through 49 Proline residue: z 39 - end of helix Processing helix chain 'z' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) Processing helix chain 'z' and resid 70 through 91 removed outlier: 3.648A pdb=" N ALA z 74 " --> pdb=" O GLY z 70 " (cutoff:3.500A) Processing helix chain 'z' and resid 93 through 111 Processing helix chain 'z' and resid 114 through 126 Processing helix chain '1' and resid 9 through 26 removed outlier: 3.645A pdb=" N ASN 1 26 " --> pdb=" O ASN 1 22 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 37 Processing helix chain '1' and resid 37 through 66 Proline residue: 1 50 - end of helix removed outlier: 3.771A pdb=" N VAL 1 55 " --> pdb=" O LYS 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 91 removed outlier: 3.666A pdb=" N ALA 1 74 " --> pdb=" O GLY 1 70 " (cutoff:3.500A) Processing helix chain '1' and resid 93 through 111 Processing helix chain '1' and resid 114 through 126 Processing helix chain '2' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN 2 26 " --> pdb=" O ASN 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 49 Proline residue: 2 39 - end of helix Processing helix chain '2' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA 2 74 " --> pdb=" O GLY 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 93 through 111 Processing helix chain '2' and resid 114 through 126 Processing helix chain '3' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN 3 26 " --> pdb=" O ASN 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 37 Processing helix chain '3' and resid 37 through 66 Proline residue: 3 50 - end of helix removed outlier: 3.772A pdb=" N VAL 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 91 removed outlier: 3.665A pdb=" N ALA 3 74 " --> pdb=" O GLY 3 70 " (cutoff:3.500A) Processing helix chain '3' and resid 93 through 111 Processing helix chain '3' and resid 114 through 126 Processing helix chain '4' and resid 9 through 26 removed outlier: 3.591A pdb=" N ASN 4 26 " --> pdb=" O ASN 4 22 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 49 Proline residue: 4 39 - end of helix Processing helix chain '4' and resid 49 through 66 removed outlier: 3.742A pdb=" N VAL 4 55 " --> pdb=" O LYS 4 51 " (cutoff:3.500A) Processing helix chain '4' and resid 70 through 91 removed outlier: 3.647A pdb=" N ALA 4 74 " --> pdb=" O GLY 4 70 " (cutoff:3.500A) Processing helix chain '4' and resid 93 through 111 Processing helix chain '4' and resid 114 through 126 Processing helix chain '5' and resid 9 through 26 removed outlier: 3.646A pdb=" N ASN 5 26 " --> pdb=" O ASN 5 22 " (cutoff:3.500A) Processing helix chain '5' and resid 26 through 37 Processing helix chain '5' and resid 37 through 66 Proline residue: 5 50 - end of helix removed outlier: 3.773A pdb=" N VAL 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 70 through 91 removed outlier: 3.665A pdb=" N ALA 5 74 " --> pdb=" O GLY 5 70 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 111 Processing helix chain '5' and resid 114 through 126 Processing helix chain '6' and resid 9 through 26 removed outlier: 3.590A pdb=" N ASN 6 26 " --> pdb=" O ASN 6 22 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 49 Proline residue: 6 39 - end of helix Processing helix chain '6' and resid 49 through 66 removed outlier: 3.743A pdb=" N VAL 6 55 " --> pdb=" O LYS 6 51 " (cutoff:3.500A) Processing helix chain '6' and resid 70 through 91 removed outlier: 3.646A pdb=" N ALA 6 74 " --> pdb=" O GLY 6 70 " (cutoff:3.500A) Processing helix chain '6' and resid 93 through 111 Processing helix chain '6' and resid 114 through 126 4872 hydrogen bonds defined for protein. 14616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 696 hydrogen bonds 1392 hydrogen bond angles 0 basepair planarities 348 basepair parallelities 405 stacking parallelities Total time for adding SS restraints: 25.06 Time building geometry restraints manager: 27.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 13087 1.32 - 1.44: 20992 1.44 - 1.56: 38073 1.56 - 1.67: 1390 1.67 - 1.79: 116 Bond restraints: 73658 Sorted by residual: bond pdb=" CA ILE E 124 " pdb=" CB ILE E 124 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.05e-02 9.07e+03 2.20e+01 bond pdb=" CA ILE s 124 " pdb=" CB ILE s 124 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.05e-02 9.07e+03 2.16e+01 bond pdb=" CA ILE e 124 " pdb=" CB ILE e 124 " ideal model delta sigma weight residual 1.545 1.497 0.048 1.05e-02 9.07e+03 2.12e+01 bond pdb=" CA ILE u 124 " pdb=" CB ILE u 124 " ideal model delta sigma weight residual 1.545 1.497 0.048 1.05e-02 9.07e+03 2.12e+01 bond pdb=" CA ILE w 124 " pdb=" CB ILE w 124 " ideal model delta sigma weight residual 1.545 1.497 0.048 1.05e-02 9.07e+03 2.11e+01 ... (remaining 73653 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.65: 5044 105.65 - 112.72: 39128 112.72 - 119.79: 22017 119.79 - 126.86: 34928 126.86 - 133.94: 2231 Bond angle restraints: 103348 Sorted by residual: angle pdb=" C GLY W 70 " pdb=" N PRO W 71 " pdb=" CA PRO W 71 " ideal model delta sigma weight residual 119.56 127.77 -8.21 1.02e+00 9.61e-01 6.47e+01 angle pdb=" C GLY 3 70 " pdb=" N PRO 3 71 " pdb=" CA PRO 3 71 " ideal model delta sigma weight residual 119.56 127.73 -8.17 1.02e+00 9.61e-01 6.41e+01 angle pdb=" C GLY 5 70 " pdb=" N PRO 5 71 " pdb=" CA PRO 5 71 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C GLY y 70 " pdb=" N PRO y 71 " pdb=" CA PRO y 71 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C GLY G 70 " pdb=" N PRO G 71 " pdb=" CA PRO G 71 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 ... (remaining 103343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.53: 36763 14.53 - 29.05: 3200 29.05 - 43.58: 579 43.58 - 58.11: 400 58.11 - 72.63: 174 Dihedral angle restraints: 41116 sinusoidal: 19656 harmonic: 21460 Sorted by residual: dihedral pdb=" N TYR J 10 " pdb=" CA TYR J 10 " pdb=" CB TYR J 10 " pdb=" CG TYR J 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.49 -49.49 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" N TYR z 10 " pdb=" CA TYR z 10 " pdb=" CB TYR z 10 " pdb=" CG TYR z 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.45 -49.45 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" N TYR D 10 " pdb=" CA TYR D 10 " pdb=" CB TYR D 10 " pdb=" CG TYR D 10 " ideal model delta sinusoidal sigma weight residual 60.00 109.44 -49.44 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 41113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5397 0.048 - 0.097: 3729 0.097 - 0.145: 1753 0.145 - 0.194: 634 0.194 - 0.242: 203 Chirality restraints: 11716 Sorted by residual: chirality pdb=" CA ASN H 48 " pdb=" N ASN H 48 " pdb=" C ASN H 48 " pdb=" CB ASN H 48 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN T 48 " pdb=" N ASN T 48 " pdb=" C ASN T 48 " pdb=" CB ASN T 48 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASN R 48 " pdb=" N ASN R 48 " pdb=" C ASN R 48 " pdb=" CB ASN R 48 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 11713 not shown) Planarity restraints: 11020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 38 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO I 39 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO I 39 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO I 39 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 3 38 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO 3 39 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO 3 39 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO 3 39 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER U 38 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO U 39 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO U 39 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO U 39 " 0.056 5.00e-02 4.00e+02 ... (remaining 11017 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 28852 2.87 - 3.38: 74518 3.38 - 3.89: 139080 3.89 - 4.39: 167330 4.39 - 4.90: 251685 Nonbonded interactions: 661465 Sorted by model distance: nonbonded pdb=" OG1 THR 1 126 " pdb=" O SER 1 128 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR i 126 " pdb=" O SER i 128 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR m 126 " pdb=" O SER m 128 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR w 126 " pdb=" O SER w 128 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR U 126 " pdb=" O SER U 128 " model vdw 2.369 2.440 ... (remaining 661460 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '7' selection = chain '8' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 696 5.49 5 S 58 5.16 5 C 42804 2.51 5 N 12354 2.21 5 O 14790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.420 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: 0.070 Extract box with map and model: 8.850 Check model and map are aligned: 0.810 Convert atoms to be neutral: 0.500 Process input model: 155.470 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.740 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 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 : 0.014 0.058 73658 Z= 0.908 Angle : 1.239 9.697 103348 Z= 0.844 Chirality : 0.080 0.242 11716 Planarity : 0.017 0.109 11020 Dihedral : 13.094 72.632 27428 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 1.59 % Allowed : 2.78 % Favored : 95.63 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.08), residues: 7308 helix: -0.23 (0.06), residues: 6206 sheet: None (None), residues: 0 loop : -0.69 (0.16), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2087 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 2058 time to evaluate : 5.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 2075 average time/residue: 0.6676 time to fit residues: 2325.8021 Evaluate side-chains 993 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 974 time to evaluate : 6.344 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.7806 time to fit residues: 30.6047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 645 optimal weight: 6.9990 chunk 579 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 309 optimal weight: 6.9990 chunk 598 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 445 optimal weight: 7.9990 chunk 693 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 114 ASN E 46 GLN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN I 46 GLN J 36 ASN K 116 GLN L 36 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 46 GLN ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 18 GLN M 46 GLN M 116 GLN N 36 ASN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN O 46 GLN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN Q 43 GLN Q 46 GLN Q 72 ASN R 46 GLN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 GLN S 114 ASN S 116 GLN ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN U 116 GLN V 18 GLN V 65 GLN ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 116 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 ASN Y 116 GLN ** Z 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN a 116 GLN ** b 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 GLN c 116 GLN ** d 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 114 ASN ** e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 112 ASN e 116 GLN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 43 GLN f 46 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 116 GLN h 36 ASN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 43 GLN ** i 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 GLN ** j 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 42 GLN ** k 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 42 GLN m 77 GLN ** n 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN n 77 GLN o 42 GLN o 43 GLN ** o 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 114 ASN p 36 ASN q 43 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 ASN r 112 ASN ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 114 ASN t 77 GLN ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 116 GLN ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 123 ASN w 12 GLN ** w 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 18 GLN ** x 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 GLN x 123 ASN y 18 GLN ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 65 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 116 GLN z 123 ASN 1 18 GLN 1 42 GLN ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 116 GLN 2 42 GLN 2 43 GLN 2 46 GLN 2 123 ASN 3 116 GLN 4 12 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 46 GLN 4 114 ASN 4 123 ASN 5 116 GLN 6 18 GLN 6 77 GLN 6 112 ASN 6 123 ASN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 73658 Z= 0.328 Angle : 0.742 11.635 103348 Z= 0.427 Chirality : 0.045 0.451 11716 Planarity : 0.009 0.118 11020 Dihedral : 12.942 59.844 15074 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 7308 helix: 0.93 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.25 (0.20), residues: 986 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1357 time to evaluate : 6.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 108 residues processed: 1475 average time/residue: 0.6593 time to fit residues: 1710.8930 Evaluate side-chains 1133 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1025 time to evaluate : 5.357 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.5506 time to fit residues: 118.4587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 385 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 577 optimal weight: 7.9990 chunk 472 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 695 optimal weight: 0.9980 chunk 750 optimal weight: 30.0000 chunk 619 optimal weight: 6.9990 chunk 689 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 557 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 114 ASN C 22 ASN D 43 GLN D 88 ASN E 12 GLN E 42 GLN F 18 GLN F 22 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN I 18 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 116 GLN J 36 ASN J 42 GLN K 12 GLN K 18 GLN L 42 GLN L 46 GLN M 12 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN Q 12 GLN Q 43 GLN Q 77 GLN Q 116 GLN S 43 GLN S 77 GLN ** T 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 GLN V 77 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN b 43 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 GLN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN g 26 ASN h 43 GLN j 77 GLN ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 43 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN m 65 GLN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 GLN n 43 GLN ** o 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 GLN r 44 ASN s 18 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 GLN ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 18 GLN w 116 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 43 GLN y 12 GLN y 18 GLN ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 65 GLN 6 123 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 73658 Z= 0.266 Angle : 0.670 12.269 103348 Z= 0.387 Chirality : 0.041 0.314 11716 Planarity : 0.007 0.094 11020 Dihedral : 12.141 59.732 15074 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 7308 helix: 1.34 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.36 (0.20), residues: 986 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1459 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1292 time to evaluate : 5.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 167 outliers final: 72 residues processed: 1371 average time/residue: 0.6307 time to fit residues: 1512.7690 Evaluate side-chains 1045 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 973 time to evaluate : 5.391 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.5641 time to fit residues: 81.8746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 686 optimal weight: 8.9990 chunk 522 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 331 optimal weight: 30.0000 chunk 466 optimal weight: 9.9990 chunk 697 optimal weight: 30.0000 chunk 738 optimal weight: 30.0000 chunk 364 optimal weight: 20.0000 chunk 661 optimal weight: 0.0980 chunk 199 optimal weight: 30.0000 overall best weight: 7.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 43 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN D 18 GLN D 22 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN J 42 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 116 GLN N 18 GLN N 22 ASN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN P 36 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 ASN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 ASN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 65 GLN a 98 ASN a 112 ASN c 12 GLN ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN ** h 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 GLN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN t 43 GLN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 46 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 18 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 114 ASN ** z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 ASN 2 43 GLN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 GLN 4 36 ASN 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 116 GLN 6 123 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.121 73658 Z= 0.319 Angle : 0.711 14.371 103348 Z= 0.402 Chirality : 0.042 0.421 11716 Planarity : 0.007 0.093 11020 Dihedral : 12.148 59.902 15074 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.75 % Favored : 98.23 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.09), residues: 7308 helix: 1.28 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.60 (0.19), residues: 986 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1188 time to evaluate : 5.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 65 residues processed: 1261 average time/residue: 0.6204 time to fit residues: 1367.7450 Evaluate side-chains 1019 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 954 time to evaluate : 5.413 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.5284 time to fit residues: 70.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 615 optimal weight: 20.0000 chunk 419 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 549 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 630 optimal weight: 6.9990 chunk 510 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 377 optimal weight: 7.9990 chunk 662 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 43 GLN D 22 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN S 18 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 GLN ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 ASN ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN c 43 GLN ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 18 GLN e 77 GLN ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** f 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 GLN h 36 ASN ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 GLN ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 65 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 114 ASN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 18 GLN y 42 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 46 GLN ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 12 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.7166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 73658 Z= 0.264 Angle : 0.671 13.935 103348 Z= 0.378 Chirality : 0.040 0.291 11716 Planarity : 0.007 0.104 11020 Dihedral : 11.848 58.983 15074 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.09), residues: 7308 helix: 1.53 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.68 (0.20), residues: 986 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1102 time to evaluate : 7.663 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 outliers start: 120 outliers final: 53 residues processed: 1164 average time/residue: 0.6439 time to fit residues: 1320.5904 Evaluate side-chains 998 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 945 time to evaluate : 6.100 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.5869 time to fit residues: 64.0535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 248 optimal weight: 6.9990 chunk 665 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 433 optimal weight: 30.0000 chunk 182 optimal weight: 10.0000 chunk 739 optimal weight: 30.0000 chunk 613 optimal weight: 9.9990 chunk 342 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 244 optimal weight: 0.4980 chunk 388 optimal weight: 20.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN D 18 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN a 114 ASN c 43 GLN c 46 GLN ** c 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 GLN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 46 GLN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 18 GLN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 42 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 114 ASN 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.143 73658 Z= 0.275 Angle : 0.679 16.463 103348 Z= 0.382 Chirality : 0.041 0.359 11716 Planarity : 0.007 0.112 11020 Dihedral : 11.835 59.393 15074 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.09), residues: 7308 helix: 1.59 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.80 (0.19), residues: 986 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1066 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 36 residues processed: 1118 average time/residue: 0.6247 time to fit residues: 1225.4558 Evaluate side-chains 975 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 939 time to evaluate : 5.327 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5479 time to fit residues: 43.0059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 712 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 421 optimal weight: 5.9990 chunk 539 optimal weight: 8.9990 chunk 418 optimal weight: 0.9990 chunk 622 optimal weight: 20.0000 chunk 412 optimal weight: 4.9990 chunk 736 optimal weight: 30.0000 chunk 460 optimal weight: 3.9990 chunk 448 optimal weight: 0.2980 chunk 339 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 112 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN N 22 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 12 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 GLN ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 GLN c 43 GLN ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 ASN j 43 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN n 46 GLN q 46 GLN r 42 GLN s 42 GLN ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN 2 46 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.204 73658 Z= 0.251 Angle : 0.672 20.521 103348 Z= 0.376 Chirality : 0.040 0.324 11716 Planarity : 0.007 0.117 11020 Dihedral : 11.784 59.732 15074 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.09), residues: 7308 helix: 1.66 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.75 (0.20), residues: 986 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1043 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 32 residues processed: 1083 average time/residue: 0.6307 time to fit residues: 1194.2792 Evaluate side-chains 958 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 926 time to evaluate : 5.365 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5886 time to fit residues: 40.4791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 455 optimal weight: 20.0000 chunk 294 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 468 optimal weight: 8.9990 chunk 501 optimal weight: 9.9990 chunk 364 optimal weight: 0.0070 chunk 68 optimal weight: 8.9990 chunk 578 optimal weight: 6.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 22 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 GLN Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 GLN ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 77 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 GLN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 GLN n 46 GLN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN x 43 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 46 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN 1 42 GLN ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.8405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.314 73658 Z= 0.277 Angle : 0.694 21.225 103348 Z= 0.390 Chirality : 0.041 0.368 11716 Planarity : 0.007 0.149 11020 Dihedral : 11.859 59.924 15074 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.09), residues: 7308 helix: 1.60 (0.06), residues: 6380 sheet: None (None), residues: 0 loop : -0.43 (0.20), residues: 928 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1022 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 20 residues processed: 1047 average time/residue: 0.6334 time to fit residues: 1161.0362 Evaluate side-chains 942 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 922 time to evaluate : 5.405 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5815 time to fit residues: 27.5907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 669 optimal weight: 50.0000 chunk 705 optimal weight: 30.0000 chunk 643 optimal weight: 20.0000 chunk 686 optimal weight: 2.9990 chunk 413 optimal weight: 10.0000 chunk 298 optimal weight: 0.3980 chunk 538 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 620 optimal weight: 40.0000 chunk 649 optimal weight: 7.9990 chunk 683 optimal weight: 30.0000 overall best weight: 6.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 22 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 GLN ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 114 ASN i 36 ASN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 12 GLN x 12 GLN ** x 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN z 77 GLN ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 46 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.8432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.563 73658 Z= 0.348 Angle : 0.777 73.891 103348 Z= 0.422 Chirality : 0.042 0.435 11716 Planarity : 0.008 0.174 11020 Dihedral : 11.881 59.939 15074 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.09), residues: 7308 helix: 1.57 (0.06), residues: 6380 sheet: None (None), residues: 0 loop : -0.48 (0.20), residues: 928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 928 time to evaluate : 5.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 948 average time/residue: 0.6394 time to fit residues: 1065.1029 Evaluate side-chains 933 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 908 time to evaluate : 5.333 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.6295 time to fit residues: 34.2283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 450 optimal weight: 7.9990 chunk 725 optimal weight: 30.0000 chunk 442 optimal weight: 20.0000 chunk 344 optimal weight: 5.9990 chunk 504 optimal weight: 10.0000 chunk 761 optimal weight: 30.0000 chunk 700 optimal weight: 20.0000 chunk 606 optimal weight: 20.0000 chunk 62 optimal weight: 0.0040 chunk 468 optimal weight: 10.0000 chunk 371 optimal weight: 1.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 22 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN N 22 ASN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** x 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.915 73658 Z= 0.400 Angle : 0.816 73.566 103348 Z= 0.451 Chirality : 0.042 0.431 11716 Planarity : 0.008 0.202 11020 Dihedral : 11.882 59.940 15074 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.09), residues: 7308 helix: 1.57 (0.06), residues: 6380 sheet: None (None), residues: 0 loop : -0.48 (0.20), residues: 928 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 915 time to evaluate : 6.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 918 average time/residue: 0.6343 time to fit residues: 1022.1308 Evaluate side-chains 911 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 907 time to evaluate : 5.409 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5277 time to fit residues: 10.8045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 481 optimal weight: 30.0000 chunk 645 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 558 optimal weight: 0.0270 chunk 89 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 607 optimal weight: 7.9990 chunk 254 optimal weight: 20.0000 chunk 623 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 36 ASN ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 42 GLN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** x 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 ASN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 4 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 46 GLN 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.078883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.074305 restraints weight = 289559.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.075593 restraints weight = 141827.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.076418 restraints weight = 80855.499| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.8922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.451 73658 Z= 0.314 Angle : 0.745 30.741 103348 Z= 0.412 Chirality : 0.042 0.411 11716 Planarity : 0.007 0.132 11020 Dihedral : 11.977 64.015 15074 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.10), residues: 7308 helix: 1.56 (0.06), residues: 6380 sheet: None (None), residues: 0 loop : -0.67 (0.20), residues: 928 =============================================================================== Job complete usr+sys time: 18138.58 seconds wall clock time: 319 minutes 22.20 seconds (19162.20 seconds total)