Starting phenix.real_space_refine (version: dev) on Wed Dec 14 10:24:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/12_2022/3j9x_6310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/12_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_6310/12_2022/3j9x_6310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/12_2022/3j9x_6310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/12_2022/3j9x_6310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/12_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-4807/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: 28.90, 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: 26.91 Conformation dependent library (CDL) restraints added in 6.8 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: 18.88 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: 27.42 Time building geometry restraints manager: 29.11 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 7.230 Check model and map are aligned: 0.800 Convert atoms to be neutral: 0.470 Process input model: 161.320 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.770 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.950 ------------------------------------------------------------------------------- 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 : 5.298 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 outliers start: 29 outliers final: 19 residues processed: 2075 average time/residue: 0.6709 time to fit residues: 2330.6338 Evaluate side-chains 1004 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 985 time to evaluate : 5.229 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.7407 time to fit residues: 29.1242 ------------------------------------------------------------------------------- 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: 10.0000 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 36 ASN I 46 GLN L 36 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 Q 116 GLN 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 46 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 h 36 ASN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 43 GLN i 116 GLN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 18 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 p 42 GLN q 43 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 46 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 116 GLN u 123 ASN ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 123 ASN w 12 GLN ** w 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 46 GLN 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 46 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 6 112 ASN 6 123 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 73658 Z= 0.324 Angle : 0.718 9.972 103348 Z= 0.419 Chirality : 0.045 0.427 11716 Planarity : 0.008 0.062 11020 Dihedral : 12.932 59.867 15074 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 3.51 % 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: 1.09 (0.09), residues: 7308 helix: 0.94 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.18 (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 1554 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1340 time to evaluate : 5.310 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 outliers start: 214 outliers final: 112 residues processed: 1465 average time/residue: 0.6296 time to fit residues: 1600.8472 Evaluate side-chains 1129 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1017 time to evaluate : 5.308 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 0.5248 time to fit residues: 116.0450 ------------------------------------------------------------------------------- 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: 10.0000 chunk 215 optimal weight: 5.9990 chunk 577 optimal weight: 10.0000 chunk 472 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 695 optimal weight: 20.0000 chunk 750 optimal weight: 30.0000 chunk 619 optimal weight: 30.0000 chunk 689 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 557 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 114 ASN C 22 ASN C 43 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN I 18 GLN I 46 GLN I 116 GLN J 36 ASN J 42 GLN K 18 GLN K 42 GLN K 116 GLN L 42 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN L 116 GLN M 12 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN O 116 GLN Q 12 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 ASN S 18 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 ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 GLN ** X 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN b 43 GLN ** b 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 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** d 46 GLN f 46 GLN g 26 ASN h 36 ASN h 43 GLN j 46 GLN j 77 GLN ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 46 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 65 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 ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 GLN t 123 ASN u 123 ASN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 46 GLN ** 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** ** 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: 0.6624 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 73658 Z= 0.273 Angle : 0.665 10.668 103348 Z= 0.383 Chirality : 0.042 0.371 11716 Planarity : 0.006 0.061 11020 Dihedral : 12.203 59.890 15074 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 2.61 % 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: 1.63 (0.09), residues: 7308 helix: 1.34 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.23 (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 1402 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1243 time to evaluate : 5.281 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: 159 outliers final: 71 residues processed: 1318 average time/residue: 0.6676 time to fit residues: 1545.2953 Evaluate side-chains 1053 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 982 time to evaluate : 5.251 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.5614 time to fit residues: 80.6009 ------------------------------------------------------------------------------- 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: 7.9990 chunk 522 optimal weight: 40.0000 chunk 360 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 331 optimal weight: 30.0000 chunk 466 optimal weight: 4.9990 chunk 697 optimal weight: 30.0000 chunk 738 optimal weight: 30.0000 chunk 364 optimal weight: 10.0000 chunk 661 optimal weight: 7.9990 chunk 199 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 43 GLN ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN J 36 ASN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 GLN M 12 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN O 12 GLN P 36 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN R 42 GLN S 65 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 GLN Y 18 GLN Y 36 ASN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN Z 46 GLN ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 65 GLN a 98 ASN c 43 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** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 18 GLN f 42 GLN 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 k 43 GLN ** l 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN ** o 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 ASN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 GLN ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 36 ASN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 18 GLN z 43 GLN ** 1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 ASN ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 114 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 73658 Z= 0.291 Angle : 0.686 10.925 103348 Z= 0.389 Chirality : 0.042 0.307 11716 Planarity : 0.006 0.060 11020 Dihedral : 12.131 59.908 15074 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.17 % 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: 1.62 (0.09), residues: 7308 helix: 1.36 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.50 (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 1308 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1176 time to evaluate : 5.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 61 residues processed: 1232 average time/residue: 0.6291 time to fit residues: 1352.7191 Evaluate side-chains 1030 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 969 time to evaluate : 5.261 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5350 time to fit residues: 66.6532 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 5.9990 chunk 549 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 510 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 377 optimal weight: 8.9990 chunk 662 optimal weight: 8.9990 chunk 186 optimal weight: 40.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN A 112 ASN ** B 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 18 GLN C 22 ASN C 43 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** 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 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** ** 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 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** K 114 ASN L 114 ASN M 12 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN Q 12 GLN ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN S 77 GLN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 GLN W 12 GLN ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 ASN Z 46 GLN ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN ** 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** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN f 43 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 GLN ** 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** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 GLN ** k 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 36 ASN ** 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** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 46 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 46 GLN ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.8045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 73658 Z= 0.324 Angle : 0.707 12.632 103348 Z= 0.395 Chirality : 0.043 0.390 11716 Planarity : 0.006 0.059 11020 Dihedral : 12.164 59.997 15074 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.32 % 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: 1.49 (0.09), residues: 7308 helix: 1.32 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.93 (0.19), 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 1210 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1069 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 67 residues processed: 1146 average time/residue: 0.6306 time to fit residues: 1262.0304 Evaluate side-chains 992 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 925 time to evaluate : 5.327 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.5526 time to fit residues: 74.4766 ------------------------------------------------------------------------------- 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: 30.0000 chunk 665 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 433 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 739 optimal weight: 30.0000 chunk 613 optimal weight: 10.0000 chunk 342 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 388 optimal weight: 0.6980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 43 GLN B 42 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 77 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 42 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 77 GLN ** 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** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 GLN J 22 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 42 GLN ** U 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 GLN ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 43 GLN ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 GLN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 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** ** d 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 GLN ** 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** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 65 GLN ** l 18 GLN ** 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 42 GLN n 43 GLN n 46 GLN p 114 ASN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 GLN ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN v 18 GLN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 42 GLN x 18 GLN x 43 GLN ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN 2 42 GLN 4 46 GLN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 73658 Z= 0.229 Angle : 0.648 15.980 103348 Z= 0.362 Chirality : 0.040 0.376 11716 Planarity : 0.005 0.057 11020 Dihedral : 11.937 59.807 15074 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.90 (0.09), residues: 7308 helix: 1.61 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.83 (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 1177 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1100 time to evaluate : 5.374 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: 77 outliers final: 41 residues processed: 1139 average time/residue: 0.6379 time to fit residues: 1268.9358 Evaluate side-chains 977 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 936 time to evaluate : 5.291 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5928 time to fit residues: 49.9624 ------------------------------------------------------------------------------- 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: 8.9990 chunk 421 optimal weight: 5.9990 chunk 539 optimal weight: 5.9990 chunk 418 optimal weight: 6.9990 chunk 622 optimal weight: 9.9990 chunk 412 optimal weight: 1.9990 chunk 736 optimal weight: 40.0000 chunk 460 optimal weight: 8.9990 chunk 448 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 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 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN H 22 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** 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** b 46 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 12 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** d 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 ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 42 GLN ** l 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 114 ASN n 46 GLN q 46 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 46 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** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 42 GLN x 18 GLN ** x 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 42 GLN y 46 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN ** z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN 2 46 GLN ** 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.8764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 73658 Z= 0.244 Angle : 0.667 17.031 103348 Z= 0.369 Chirality : 0.041 0.399 11716 Planarity : 0.005 0.057 11020 Dihedral : 11.983 59.999 15074 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.18 % 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: 1.91 (0.09), residues: 7308 helix: 1.63 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.95 (0.19), 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 1092 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1020 time to evaluate : 5.408 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: 72 outliers final: 36 residues processed: 1061 average time/residue: 0.6507 time to fit residues: 1211.9213 Evaluate side-chains 955 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 919 time to evaluate : 5.341 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5617 time to fit residues: 43.6221 ------------------------------------------------------------------------------- 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: 10.0000 chunk 294 optimal weight: 8.9990 chunk 439 optimal weight: 40.0000 chunk 221 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 468 optimal weight: 4.9990 chunk 501 optimal weight: 8.9990 chunk 364 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 578 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 22 ASN C 112 ASN C 116 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 26 ASN ** 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 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** 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 65 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 46 GLN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 42 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 12 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 42 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 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 ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 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** n 42 GLN n 43 GLN n 46 GLN ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 GLN ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 46 GLN v 18 GLN ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 12 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 4 46 GLN ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.9174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 73658 Z= 0.249 Angle : 0.678 18.206 103348 Z= 0.372 Chirality : 0.042 0.425 11716 Planarity : 0.005 0.057 11020 Dihedral : 12.029 64.396 15074 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.67 % 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: 1.93 (0.09), residues: 7308 helix: 1.66 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.06 (0.19), residues: 986 *********************** 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 1031 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 990 time to evaluate : 5.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 1009 average time/residue: 0.6246 time to fit residues: 1103.9218 Evaluate side-chains 925 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 906 time to evaluate : 5.288 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5932 time to fit residues: 26.6857 ------------------------------------------------------------------------------- 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: 30.0000 chunk 705 optimal weight: 30.0000 chunk 643 optimal weight: 10.0000 chunk 686 optimal weight: 7.9990 chunk 413 optimal weight: 7.9990 chunk 298 optimal weight: 30.0000 chunk 538 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 620 optimal weight: 40.0000 chunk 649 optimal weight: 7.9990 chunk 683 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 ASN ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 ASN ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** 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** R 123 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 GLN W 12 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 GLN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 12 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 42 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 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** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 GLN ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 GLN n 46 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 GLN ** s 18 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** ** u 46 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** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 43 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.9627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 73658 Z= 0.265 Angle : 0.696 17.134 103348 Z= 0.381 Chirality : 0.042 0.342 11716 Planarity : 0.005 0.058 11020 Dihedral : 12.150 67.858 15074 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.76 % 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: 1.80 (0.09), residues: 7308 helix: 1.60 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.28 (0.19), residues: 986 *********************** 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 1010 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 964 time to evaluate : 5.363 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: 46 outliers final: 22 residues processed: 985 average time/residue: 0.6316 time to fit residues: 1087.6785 Evaluate side-chains 924 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 902 time to evaluate : 5.322 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5620 time to fit residues: 29.2006 ------------------------------------------------------------------------------- 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: 30.0000 chunk 725 optimal weight: 30.0000 chunk 442 optimal weight: 0.0970 chunk 344 optimal weight: 30.0000 chunk 504 optimal weight: 7.9990 chunk 761 optimal weight: 30.0000 chunk 700 optimal weight: 30.0000 chunk 606 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 468 optimal weight: 0.9980 chunk 371 optimal weight: 7.9990 overall best weight: 3.6184 ------------------------------------------------------------------------------- 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** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 ASN ** 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** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN I 65 GLN J 18 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** 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** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 GLN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 GLN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 12 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 42 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 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** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 GLN ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 114 ASN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 GLN m 43 GLN q 42 GLN ** q 43 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** ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.9834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 73658 Z= 0.223 Angle : 0.700 18.621 103348 Z= 0.377 Chirality : 0.041 0.361 11716 Planarity : 0.005 0.058 11020 Dihedral : 12.090 69.470 15074 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.34 % 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: 1.92 (0.09), residues: 7308 helix: 1.67 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.23 (0.18), residues: 986 ********************** 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 1023 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1002 time to evaluate : 5.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 1007 average time/residue: 0.6355 time to fit residues: 1109.6280 Evaluate side-chains 920 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 911 time to evaluate : 5.294 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.6606 time to fit residues: 16.6212 ------------------------------------------------------------------------------- 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: 20.0000 chunk 645 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 558 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 607 optimal weight: 30.0000 chunk 254 optimal weight: 10.0000 chunk 623 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 ASN ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN J 18 GLN J 22 ASN ** 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** W 101 ASN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 GLN ** c 12 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 42 GLN ** f 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 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** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 GLN ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 36 ASN ** y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 18 GLN 5 18 GLN 5 22 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.076660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.072090 restraints weight = 290000.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.073425 restraints weight = 140716.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.074184 restraints weight = 78223.250| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 1.0090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 73658 Z= 0.274 Angle : 0.715 18.127 103348 Z= 0.388 Chirality : 0.043 0.338 11716 Planarity : 0.005 0.058 11020 Dihedral : 12.204 69.256 15074 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: 1.81 (0.09), residues: 7308 helix: 1.62 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.42 (0.18), residues: 986 =============================================================================== Job complete usr+sys time: 18076.96 seconds wall clock time: 318 minutes 15.33 seconds (19095.33 seconds total)