Starting phenix.real_space_refine on Fri Mar 15 20:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/03_2024/3j9x_6310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/03_2024/3j9x_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_6310/03_2024/3j9x_6310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/03_2024/3j9x_6310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/03_2024/3j9x_6310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9x_6310/03_2024/3j9x_6310.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 25.69, per 1000 atoms: 0.36 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: 24.36 Conformation dependent library (CDL) restraints added in 7.6 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: 19.27 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: 26.27 Time building geometry restraints manager: 26.42 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: 36907 14.53 - 29.05: 3578 29.05 - 43.58: 1033 43.58 - 58.11: 816 58.11 - 72.63: 174 Dihedral angle restraints: 42508 sinusoidal: 21048 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 42505 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 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 4.850 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 154.200 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.880 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 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 : 14.920 72.632 28820 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 % Allowed : 0.00 % Favored : 99.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP W 17 PHE 0.019 0.006 PHE I 21 TYR 0.036 0.008 TYR N 76 ARG 0.006 0.001 ARG L 73 *********************** 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 : 5.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.4523 (tttt) cc_final: 0.3576 (mmpt) REVERT: H 96 LEU cc_start: 0.5845 (tp) cc_final: 0.5400 (tp) REVERT: H 111 PHE cc_start: 0.4888 (m-80) cc_final: 0.4596 (m-10) REVERT: K 45 PHE cc_start: 0.6982 (t80) cc_final: 0.6560 (t80) REVERT: Q 126 THR cc_start: 0.6234 (p) cc_final: 0.5918 (m) REVERT: W 124 ILE cc_start: 0.6451 (mm) cc_final: 0.6162 (mm) REVERT: Z 42 GLN cc_start: 0.6340 (mt0) cc_final: 0.5969 (mt0) REVERT: c 126 THR cc_start: 0.6254 (p) cc_final: 0.5236 (m) REVERT: d 10 TYR cc_start: 0.5228 (OUTLIER) cc_final: 0.4661 (p90) REVERT: h 111 PHE cc_start: 0.5979 (m-80) cc_final: 0.5613 (m-80) REVERT: k 124 ILE cc_start: 0.7776 (mm) cc_final: 0.7557 (mm) REVERT: k 126 THR cc_start: 0.7270 (p) cc_final: 0.7017 (p) REVERT: m 126 THR cc_start: 0.7037 (p) cc_final: 0.6780 (p) REVERT: n 47 THR cc_start: 0.6603 (m) cc_final: 0.6356 (m) REVERT: p 108 ILE cc_start: 0.6607 (mt) cc_final: 0.6309 (mt) REVERT: u 117 VAL cc_start: 0.7183 (t) cc_final: 0.6794 (t) REVERT: v 129 PRO cc_start: 0.3267 (Cg_exo) cc_final: 0.2985 (Cg_endo) REVERT: y 29 VAL cc_start: 0.6090 (t) cc_final: 0.5771 (t) REVERT: z 126 THR cc_start: 0.6119 (p) cc_final: 0.5849 (m) REVERT: 1 25 SER cc_start: 0.7015 (p) cc_final: 0.6576 (t) REVERT: 3 115 PRO cc_start: 0.8368 (Cg_exo) cc_final: 0.8098 (Cg_endo) REVERT: 6 89 ARG cc_start: 0.3903 (mtt-85) cc_final: 0.3264 (ttt180) outliers start: 29 outliers final: 19 residues processed: 2075 average time/residue: 0.6802 time to fit residues: 2369.5548 Evaluate side-chains 1008 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 988 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain Z residue 10 TYR Chi-restraints excluded: chain b residue 10 TYR Chi-restraints excluded: chain d residue 10 TYR Chi-restraints excluded: chain f residue 10 TYR Chi-restraints excluded: chain h residue 10 TYR Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain p residue 10 TYR Chi-restraints excluded: chain r residue 10 TYR Chi-restraints excluded: chain t residue 10 TYR Chi-restraints excluded: chain v residue 10 TYR Chi-restraints excluded: chain x residue 10 TYR Chi-restraints excluded: chain z residue 10 TYR Chi-restraints excluded: chain 2 residue 10 TYR Chi-restraints excluded: chain 4 residue 10 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 645 optimal weight: 5.9990 chunk 579 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 390 optimal weight: 30.0000 chunk 309 optimal weight: 8.9990 chunk 598 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 445 optimal weight: 7.9990 chunk 693 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN J 36 ASN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 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 N 36 ASN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN O 46 GLN ** P 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN Q 43 GLN Q 46 GLN Q 72 ASN 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 65 GLN ** V 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 36 ASN ** 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 g 116 GLN ** 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 ASN r 112 ASN ** s 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 114 ASN t 77 GLN ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN u 46 GLN ** u 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 116 GLN ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 123 ASN w 12 GLN ** w 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 116 GLN 4 12 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 46 GLN 4 114 ASN 4 123 ASN 5 116 GLN 6 18 GLN 6 77 GLN 6 112 ASN 6 123 ASN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3928 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= 0.325 Angle : 0.730 10.340 103348 Z= 0.424 Chirality : 0.045 0.305 11716 Planarity : 0.008 0.064 11020 Dihedral : 15.208 59.881 16506 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.81 % Allowed : 10.53 % Favored : 85.67 % 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: 1.06 (0.09), residues: 7308 helix: 0.93 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.18 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 17 PHE 0.028 0.002 PHE p 24 TYR 0.040 0.002 TYR D 10 ARG 0.007 0.001 ARG u 73 *********************** 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 1579 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1347 time to evaluate : 5.103 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: A 16 LYS cc_start: 0.4267 (tttt) cc_final: 0.3537 (mmpt) REVERT: A 75 ILE cc_start: 0.4155 (mt) cc_final: 0.3737 (mt) REVERT: A 103 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6499 (tt) REVERT: B 10 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4280 (p90) REVERT: C 33 ILE cc_start: 0.7968 (tt) cc_final: 0.7703 (tt) REVERT: G 14 TYR cc_start: 0.7222 (t80) cc_final: 0.6791 (t80) REVERT: M 96 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6508 (tt) REVERT: O 11 SER cc_start: 0.7518 (m) cc_final: 0.7192 (p) REVERT: Q 126 THR cc_start: 0.6622 (p) cc_final: 0.6294 (m) REVERT: S 18 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6856 (tp-100) REVERT: U 14 TYR cc_start: 0.6446 (t80) cc_final: 0.5899 (t80) REVERT: X 42 GLN cc_start: 0.6057 (mt0) cc_final: 0.5667 (mt0) REVERT: Y 90 ILE cc_start: 0.5523 (pt) cc_final: 0.5289 (pt) REVERT: Y 126 THR cc_start: 0.5781 (p) cc_final: 0.5355 (m) REVERT: b 42 GLN cc_start: 0.6664 (mt0) cc_final: 0.6426 (mt0) REVERT: c 107 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.5878 (t80) REVERT: d 42 GLN cc_start: 0.6957 (mp10) cc_final: 0.6621 (mp10) REVERT: e 107 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5956 (t80) REVERT: g 66 TYR cc_start: 0.7128 (m-10) cc_final: 0.6656 (m-80) REVERT: i 124 ILE cc_start: 0.8466 (mm) cc_final: 0.8249 (mm) REVERT: v 75 ILE cc_start: 0.7086 (mt) cc_final: 0.6625 (mt) REVERT: z 12 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6622 (mm-40) REVERT: z 126 THR cc_start: 0.6134 (p) cc_final: 0.5804 (m) REVERT: 3 18 GLN cc_start: 0.7973 (tp40) cc_final: 0.7687 (tp40) REVERT: 4 126 THR cc_start: 0.7422 (OUTLIER) cc_final: 0.6978 (m) REVERT: 6 100 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7752 (tt) outliers start: 232 outliers final: 115 residues processed: 1480 average time/residue: 0.6220 time to fit residues: 1606.5666 Evaluate side-chains 1139 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1016 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 123 ASN Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 18 GLN Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 10 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain b residue 10 TYR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 87 LEU Chi-restraints excluded: chain c residue 107 TYR Chi-restraints excluded: chain e residue 107 TYR Chi-restraints excluded: chain f residue 10 TYR Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain h residue 10 TYR Chi-restraints excluded: chain h residue 43 GLN Chi-restraints excluded: chain i residue 33 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 53 THR Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain m residue 35 SER Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 77 GLN Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 117 VAL Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain o residue 125 ILE Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 117 VAL Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 112 ASN Chi-restraints excluded: chain u residue 121 VAL Chi-restraints excluded: chain v residue 92 SER Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 124 ILE Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 10 TYR Chi-restraints excluded: chain x residue 112 ASN Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain y residue 69 THR Chi-restraints excluded: chain z residue 43 GLN Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 126 THR Chi-restraints excluded: chain 2 residue 42 GLN Chi-restraints excluded: chain 2 residue 43 GLN Chi-restraints excluded: chain 2 residue 103 LEU Chi-restraints excluded: chain 2 residue 123 ASN Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 3 residue 124 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 126 THR Chi-restraints excluded: chain 5 residue 11 SER Chi-restraints excluded: chain 6 residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 385 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 577 optimal weight: 0.0060 chunk 472 optimal weight: 20.0000 chunk 191 optimal weight: 0.9990 chunk 695 optimal weight: 6.9990 chunk 750 optimal weight: 30.0000 chunk 619 optimal weight: 6.9990 chunk 689 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 557 optimal weight: 8.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 22 ASN B 43 GLN B 114 ASN C 22 ASN C 43 GLN D 43 GLN E 12 GLN E 42 GLN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 GLN I 18 GLN I 116 GLN J 36 ASN J 42 GLN K 12 GLN K 18 GLN K 42 GLN L 42 GLN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN L 116 GLN M 12 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** S 43 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 42 GLN X 46 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 ASN b 43 GLN ** c 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN g 26 ASN h 36 ASN h 43 GLN j 46 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 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 18 GLN m 65 GLN n 42 GLN n 43 GLN ** o 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 44 ASN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 GLN t 123 ASN ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN ** v 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 18 GLN w 116 GLN ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 43 GLN y 12 GLN y 18 GLN ** y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN ** z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 123 ASN 3 12 GLN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 65 GLN 6 77 GLN 6 123 ASN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 73658 Z= 0.237 Angle : 0.643 9.816 103348 Z= 0.372 Chirality : 0.041 0.295 11716 Planarity : 0.006 0.061 11020 Dihedral : 14.165 59.708 16490 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.48 % Allowed : 12.48 % Favored : 84.04 % 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: 1.75 (0.09), residues: 7308 helix: 1.41 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.13 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 17 PHE 0.024 0.002 PHE r 79 TYR 0.041 0.002 TYR U 14 ARG 0.009 0.000 ARG Z 13 *********************** 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 1450 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1238 time to evaluate : 5.180 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: A 75 ILE cc_start: 0.4050 (mt) cc_final: 0.3639 (mt) REVERT: B 10 TYR cc_start: 0.5125 (OUTLIER) cc_final: 0.4179 (p90) REVERT: E 66 TYR cc_start: 0.6096 (m-10) cc_final: 0.5681 (m-80) REVERT: E 107 TYR cc_start: 0.6292 (OUTLIER) cc_final: 0.5575 (t80) REVERT: M 114 ASN cc_start: 0.5748 (t0) cc_final: 0.5271 (m-40) REVERT: N 42 GLN cc_start: 0.6042 (mp10) cc_final: 0.5364 (mp10) REVERT: Q 20 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7357 (tppt) REVERT: Q 51 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7508 (mmtm) REVERT: Q 126 THR cc_start: 0.6585 (p) cc_final: 0.6077 (m) REVERT: g 18 GLN cc_start: 0.6908 (tp40) cc_final: 0.6408 (mm110) REVERT: g 66 TYR cc_start: 0.7104 (m-10) cc_final: 0.6764 (m-80) REVERT: h 87 LEU cc_start: 0.6009 (tp) cc_final: 0.5776 (tp) REVERT: m 116 GLN cc_start: 0.6281 (mm110) cc_final: 0.6045 (mm110) REVERT: p 107 TYR cc_start: 0.6093 (OUTLIER) cc_final: 0.5782 (t80) REVERT: q 87 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.5484 (tp) REVERT: x 107 TYR cc_start: 0.4539 (OUTLIER) cc_final: 0.4151 (t80) REVERT: z 126 THR cc_start: 0.6278 (p) cc_final: 0.5782 (m) outliers start: 212 outliers final: 99 residues processed: 1344 average time/residue: 0.6226 time to fit residues: 1468.1640 Evaluate side-chains 1084 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 978 time to evaluate : 5.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 119 ASP Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 51 LYS Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain V residue 10 TYR Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 112 ASN Chi-restraints excluded: chain X residue 10 TYR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 10 TYR Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain b residue 10 TYR Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain m residue 65 GLN Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain u residue 87 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 69 THR Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain x residue 10 TYR Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 69 THR Chi-restraints excluded: chain y residue 126 THR Chi-restraints excluded: chain z residue 43 GLN Chi-restraints excluded: chain z residue 62 VAL Chi-restraints excluded: chain z residue 122 VAL Chi-restraints excluded: chain z residue 124 ILE Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 126 THR Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 124 ILE Chi-restraints excluded: chain 2 residue 126 THR Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 5 residue 65 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 686 optimal weight: 6.9990 chunk 522 optimal weight: 5.9990 chunk 360 optimal weight: 30.0000 chunk 76 optimal weight: 8.9990 chunk 331 optimal weight: 30.0000 chunk 466 optimal weight: 9.9990 chunk 697 optimal weight: 30.0000 chunk 738 optimal weight: 30.0000 chunk 364 optimal weight: 7.9990 chunk 661 optimal weight: 5.9990 chunk 199 optimal weight: 30.0000 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 22 ASN C 22 ASN C 43 GLN D 18 GLN D 22 ASN ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN J 36 ASN J 42 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 18 GLN N 18 GLN N 22 ASN N 42 GLN ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN ** O 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN ** W 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 GLN a 65 GLN a 98 ASN a 112 ASN ** b 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 12 GLN ** c 18 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 46 GLN h 36 ASN ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 43 GLN k 43 GLN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 GLN ** l 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 65 GLN ** q 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 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 ** x 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 18 GLN y 46 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 123 ASN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 123 ASN ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 123 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 73658 Z= 0.286 Angle : 0.681 11.724 103348 Z= 0.388 Chirality : 0.042 0.309 11716 Planarity : 0.006 0.060 11020 Dihedral : 14.215 59.918 16484 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.43 % Allowed : 14.22 % Favored : 82.35 % 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: 1.75 (0.09), residues: 7308 helix: 1.43 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.32 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP n 17 PHE 0.035 0.002 PHE D 45 TYR 0.028 0.002 TYR O 10 ARG 0.014 0.001 ARG Q 13 *********************** 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 1344 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1135 time to evaluate : 5.115 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: B 108 ILE cc_start: 0.6005 (tt) cc_final: 0.5786 (tt) REVERT: D 117 VAL cc_start: 0.6825 (t) cc_final: 0.6553 (t) REVERT: E 66 TYR cc_start: 0.6471 (m-10) cc_final: 0.6194 (m-80) REVERT: E 96 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6729 (tt) REVERT: E 107 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.5491 (t80) REVERT: G 66 TYR cc_start: 0.7102 (m-10) cc_final: 0.6897 (m-80) REVERT: H 87 LEU cc_start: 0.6087 (tp) cc_final: 0.5834 (tt) REVERT: I 96 LEU cc_start: 0.6998 (tp) cc_final: 0.6771 (tp) REVERT: J 43 GLN cc_start: 0.6638 (pp30) cc_final: 0.6362 (pp30) REVERT: O 87 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7038 (tp) REVERT: S 126 THR cc_start: 0.5895 (p) cc_final: 0.5463 (m) REVERT: Z 65 GLN cc_start: 0.6108 (pt0) cc_final: 0.5838 (pt0) REVERT: c 99 MET cc_start: 0.7079 (tmm) cc_final: 0.6847 (tmm) REVERT: g 114 ASN cc_start: 0.5386 (t0) cc_final: 0.5109 (m-40) REVERT: l 96 LEU cc_start: 0.5932 (tp) cc_final: 0.5704 (tt) REVERT: m 114 ASN cc_start: 0.5763 (t0) cc_final: 0.5533 (m110) REVERT: p 107 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.6046 (t80) REVERT: q 87 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6087 (tp) REVERT: u 123 ASN cc_start: 0.5117 (t0) cc_final: 0.4872 (t0) REVERT: w 14 TYR cc_start: 0.7453 (t80) cc_final: 0.7252 (t80) REVERT: x 107 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4881 (t80) REVERT: z 126 THR cc_start: 0.6771 (p) cc_final: 0.6268 (m) REVERT: 4 43 GLN cc_start: 0.5751 (pp30) cc_final: 0.5492 (pp30) outliers start: 209 outliers final: 106 residues processed: 1250 average time/residue: 0.6277 time to fit residues: 1382.8034 Evaluate side-chains 1054 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 942 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 116 GLN Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 107 TYR Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 92 SER Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 66 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 65 GLN Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 66 TYR Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 66 TYR Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 33 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 42 GLN Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 125 ILE Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 92 SER Chi-restraints excluded: chain p residue 97 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 65 GLN Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 87 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain w residue 121 VAL Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 122 VAL Chi-restraints excluded: chain z residue 124 ILE Chi-restraints excluded: chain 1 residue 28 THR Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 2 residue 28 THR Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 103 LEU Chi-restraints excluded: chain 3 residue 126 THR Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 68 ILE Chi-restraints excluded: chain 4 residue 92 SER Chi-restraints excluded: chain 5 residue 11 SER Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 65 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 615 optimal weight: 8.9990 chunk 419 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 549 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 630 optimal weight: 40.0000 chunk 510 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 377 optimal weight: 5.9990 chunk 662 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 43 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 18 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 22 ASN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 ASN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN M 46 GLN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Q 77 GLN ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN W 65 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 ASN ** a 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 18 GLN ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 GLN j 43 GLN k 65 GLN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 GLN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN ** r 12 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 116 GLN u 18 GLN ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 42 GLN w 42 GLN x 18 GLN ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 43 GLN 1 46 GLN ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 123 ASN 3 18 GLN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 116 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 73658 Z= 0.269 Angle : 0.663 12.901 103348 Z= 0.375 Chirality : 0.041 0.353 11716 Planarity : 0.005 0.059 11020 Dihedral : 14.155 59.933 16470 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.05 % Allowed : 15.94 % Favored : 81.00 % 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: 1.83 (0.09), residues: 7308 helix: 1.52 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.54 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 17 PHE 0.032 0.002 PHE t 79 TYR 0.035 0.002 TYR B 76 ARG 0.005 0.000 ARG Q 13 *********************** 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 1277 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1091 time to evaluate : 5.172 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: B 99 MET cc_start: 0.6645 (mmm) cc_final: 0.6204 (tpp) REVERT: B 108 ILE cc_start: 0.6143 (tt) cc_final: 0.5927 (tt) REVERT: D 89 ARG cc_start: 0.5583 (mtt180) cc_final: 0.5291 (tpp-160) REVERT: D 117 VAL cc_start: 0.7284 (t) cc_final: 0.7006 (t) REVERT: E 66 TYR cc_start: 0.6721 (m-10) cc_final: 0.6426 (m-80) REVERT: E 107 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5694 (t80) REVERT: G 66 TYR cc_start: 0.7316 (m-10) cc_final: 0.6959 (m-80) REVERT: I 96 LEU cc_start: 0.7240 (tp) cc_final: 0.6993 (tp) REVERT: L 47 THR cc_start: 0.7842 (m) cc_final: 0.7602 (m) REVERT: T 46 GLN cc_start: 0.5460 (mt0) cc_final: 0.4951 (tm-30) REVERT: f 124 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6959 (mt) REVERT: p 107 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5807 (t80) REVERT: q 53 THR cc_start: 0.7500 (m) cc_final: 0.5388 (p) REVERT: q 57 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: r 107 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.6092 (t80) REVERT: s 57 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: s 132 TYR cc_start: 0.4270 (m-10) cc_final: 0.3933 (m-80) REVERT: t 107 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5871 (t80) REVERT: v 129 PRO cc_start: 0.3799 (Cg_exo) cc_final: 0.3500 (Cg_endo) REVERT: x 79 PHE cc_start: 0.7905 (t80) cc_final: 0.7689 (t80) REVERT: x 107 TYR cc_start: 0.5676 (OUTLIER) cc_final: 0.5334 (t80) REVERT: z 126 THR cc_start: 0.6884 (p) cc_final: 0.6358 (m) REVERT: 4 43 GLN cc_start: 0.6154 (pp30) cc_final: 0.5901 (pp30) outliers start: 186 outliers final: 106 residues processed: 1197 average time/residue: 0.6180 time to fit residues: 1300.0310 Evaluate side-chains 1054 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 940 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain Q residue 112 ASN Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain S residue 51 LYS Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 66 TYR Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 66 TYR Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 GLN Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 126 THR Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 81 LEU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 87 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 42 GLN Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 112 ASN Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 97 VAL Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 123 ASN Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 68 ILE Chi-restraints excluded: chain 4 residue 92 SER Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 248 optimal weight: 5.9990 chunk 665 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 739 optimal weight: 30.0000 chunk 613 optimal weight: 8.9990 chunk 342 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 388 optimal weight: 0.2980 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 43 GLN A 112 ASN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 43 GLN C 65 GLN ** D 18 GLN ** 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 ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 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 43 GLN L 114 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 GLN ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN Q 12 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 GLN W 43 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 GLN a 114 ASN b 46 GLN ** c 18 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** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 65 GLN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 114 ASN n 43 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** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 18 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 123 ASN 4 42 GLN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.7698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 73658 Z= 0.239 Angle : 0.651 16.460 103348 Z= 0.366 Chirality : 0.040 0.274 11716 Planarity : 0.005 0.057 11020 Dihedral : 14.137 59.913 16468 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.91 % Allowed : 17.16 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.09), residues: 7308 helix: 1.63 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.59 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 17 PHE 0.039 0.002 PHE 2 79 TYR 0.040 0.002 TYR B 76 ARG 0.005 0.000 ARG s 13 *********************** 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 1231 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1054 time to evaluate : 5.123 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: A 16 LYS cc_start: 0.4858 (ttmt) cc_final: 0.4532 (tptt) REVERT: B 99 MET cc_start: 0.6691 (mmm) cc_final: 0.6450 (tpp) REVERT: E 10 TYR cc_start: 0.6690 (t80) cc_final: 0.6386 (t80) REVERT: E 107 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.5643 (t80) REVERT: F 42 GLN cc_start: 0.6957 (tt0) cc_final: 0.6548 (tt0) REVERT: F 43 GLN cc_start: 0.6788 (tm-30) cc_final: 0.6497 (pp30) REVERT: G 66 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: G 119 ASP cc_start: 0.4647 (m-30) cc_final: 0.4386 (m-30) REVERT: O 45 PHE cc_start: 0.6878 (t80) cc_final: 0.6560 (t80) REVERT: f 124 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6913 (mt) REVERT: h 103 LEU cc_start: 0.8301 (mp) cc_final: 0.8073 (mt) REVERT: m 57 GLU cc_start: 0.6428 (mp0) cc_final: 0.6179 (mp0) REVERT: m 81 LEU cc_start: 0.6769 (mt) cc_final: 0.6374 (mt) REVERT: n 43 GLN cc_start: 0.5839 (tt0) cc_final: 0.5594 (tt0) REVERT: o 49 VAL cc_start: 0.8123 (m) cc_final: 0.7809 (p) REVERT: o 53 THR cc_start: 0.7378 (m) cc_final: 0.5678 (p) REVERT: o 57 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5986 (mp0) REVERT: p 107 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5730 (t80) REVERT: q 49 VAL cc_start: 0.7884 (t) cc_final: 0.7610 (t) REVERT: q 57 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: r 107 TYR cc_start: 0.6297 (OUTLIER) cc_final: 0.6038 (t80) REVERT: s 57 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: s 132 TYR cc_start: 0.4606 (m-10) cc_final: 0.4286 (m-80) REVERT: t 107 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.5813 (t80) REVERT: v 129 PRO cc_start: 0.3889 (Cg_exo) cc_final: 0.3643 (Cg_endo) REVERT: x 79 PHE cc_start: 0.7917 (t80) cc_final: 0.7578 (t80) REVERT: x 107 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.5254 (t80) REVERT: z 43 GLN cc_start: 0.6042 (mm-40) cc_final: 0.5827 (mm-40) REVERT: 4 43 GLN cc_start: 0.6025 (pp30) cc_final: 0.5755 (pp30) outliers start: 177 outliers final: 104 residues processed: 1162 average time/residue: 0.6134 time to fit residues: 1253.4741 Evaluate side-chains 1046 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 932 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 12 GLN Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 112 ASN Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain X residue 43 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 66 TYR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain f residue 124 ILE Chi-restraints excluded: chain g residue 9 SER Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 65 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain w residue 133 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 112 ASN Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 97 VAL Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU 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: 6.9990 chunk 421 optimal weight: 30.0000 chunk 539 optimal weight: 7.9990 chunk 418 optimal weight: 0.3980 chunk 622 optimal weight: 9.9990 chunk 412 optimal weight: 6.9990 chunk 736 optimal weight: 30.0000 chunk 460 optimal weight: 3.9990 chunk 448 optimal weight: 30.0000 chunk 339 optimal weight: 7.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- 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 42 GLN A 46 GLN ** B 42 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 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN ** E 26 ASN ** 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** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN Q 12 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 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 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 GLN W 43 GLN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 65 GLN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 18 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 ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 73658 Z= 0.238 Angle : 0.661 17.780 103348 Z= 0.367 Chirality : 0.041 0.353 11716 Planarity : 0.005 0.055 11020 Dihedral : 14.193 59.899 16468 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.66 % Allowed : 18.00 % Favored : 79.34 % 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: 1.97 (0.09), residues: 7308 helix: 1.64 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.73 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP n 17 PHE 0.030 0.002 PHE D 45 TYR 0.031 0.002 TYR G 10 ARG 0.004 0.000 ARG s 13 *********************** 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 1173 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1011 time to evaluate : 5.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.4757 (ttmt) cc_final: 0.4455 (tptt) REVERT: B 109 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.6309 (p) REVERT: E 107 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5644 (t80) REVERT: H 43 GLN cc_start: 0.6734 (pp30) cc_final: 0.6360 (pp30) REVERT: J 96 LEU cc_start: 0.5944 (tp) cc_final: 0.5734 (tt) REVERT: M 118 LEU cc_start: 0.7466 (mp) cc_final: 0.7172 (mp) REVERT: h 43 GLN cc_start: 0.7125 (pp30) cc_final: 0.6576 (pp30) REVERT: o 57 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: p 107 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5562 (t80) REVERT: q 49 VAL cc_start: 0.8026 (t) cc_final: 0.7776 (t) REVERT: q 57 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6244 (mp0) REVERT: q 87 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6751 (tp) REVERT: r 107 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.5985 (t80) REVERT: s 57 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: t 107 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5711 (t80) REVERT: v 107 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5125 (t80) REVERT: v 129 PRO cc_start: 0.3828 (Cg_exo) cc_final: 0.3511 (Cg_endo) REVERT: x 79 PHE cc_start: 0.7964 (t80) cc_final: 0.7655 (t80) REVERT: x 107 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5392 (t80) outliers start: 162 outliers final: 107 residues processed: 1103 average time/residue: 0.6089 time to fit residues: 1183.0235 Evaluate side-chains 1040 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 922 time to evaluate : 5.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 66 TYR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 112 ASN Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 92 SER Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain U residue 75 ILE Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 66 TYR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain W residue 43 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 66 TYR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 116 GLN Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain l residue 117 VAL Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 GLN Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain n residue 119 ASP Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain p residue 119 ASP Chi-restraints excluded: chain q residue 43 GLN Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain s residue 134 SER Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 112 ASN Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain z residue 92 SER Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 123 ASN Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 455 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 439 optimal weight: 8.9990 chunk 221 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 468 optimal weight: 5.9990 chunk 501 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 578 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 43 GLN B 42 GLN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN C 65 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 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 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN G 18 GLN G 26 ASN G 46 GLN ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN S 65 GLN S 77 GLN V 65 GLN W 12 GLN W 43 GLN ** Y 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 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** ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 GLN p 114 ASN ** r 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 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 ** y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.8643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 73658 Z= 0.244 Angle : 0.673 18.315 103348 Z= 0.373 Chirality : 0.041 0.412 11716 Planarity : 0.005 0.057 11020 Dihedral : 14.277 62.930 16468 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.78 % Allowed : 18.65 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.09), residues: 7308 helix: 1.64 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -0.88 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP p 17 PHE 0.034 0.002 PHE D 45 TYR 0.038 0.002 TYR F 10 ARG 0.004 0.000 ARG s 13 *********************** 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 1166 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 997 time to evaluate : 5.133 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: A 16 LYS cc_start: 0.4885 (ttmt) cc_final: 0.4391 (tptt) REVERT: D 99 MET cc_start: 0.6790 (mmm) cc_final: 0.6156 (tpp) REVERT: E 107 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.5650 (t80) REVERT: H 43 GLN cc_start: 0.6790 (pp30) cc_final: 0.6353 (pp30) REVERT: J 96 LEU cc_start: 0.6334 (tp) cc_final: 0.5990 (tt) REVERT: J 108 ILE cc_start: 0.6726 (pt) cc_final: 0.6399 (mt) REVERT: K 45 PHE cc_start: 0.7038 (t80) cc_final: 0.6684 (t80) REVERT: O 28 THR cc_start: 0.8002 (p) cc_final: 0.7689 (p) REVERT: U 10 TYR cc_start: 0.7293 (t80) cc_final: 0.7076 (t80) REVERT: h 43 GLN cc_start: 0.7042 (pp30) cc_final: 0.6620 (pp30) REVERT: o 57 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: p 107 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5607 (t80) REVERT: q 57 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: q 87 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6827 (tp) REVERT: r 107 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.6012 (t80) REVERT: s 57 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: t 107 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.5736 (t80) REVERT: v 107 TYR cc_start: 0.5712 (OUTLIER) cc_final: 0.5268 (t80) REVERT: x 79 PHE cc_start: 0.7946 (t80) cc_final: 0.7636 (t80) REVERT: x 107 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.5352 (t80) REVERT: 3 103 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7593 (mt) outliers start: 169 outliers final: 104 residues processed: 1096 average time/residue: 0.6235 time to fit residues: 1200.8341 Evaluate side-chains 1024 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 909 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 112 ASN Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain W residue 43 GLN Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Y residue 124 ILE Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 66 TYR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain f residue 116 GLN Chi-restraints excluded: chain f residue 117 VAL Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 65 GLN Chi-restraints excluded: chain h residue 116 GLN Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 65 GLN Chi-restraints excluded: chain k residue 124 ILE Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 107 TYR Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 87 LEU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 107 TYR Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain s residue 134 SER Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 112 ASN Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain z residue 123 ASN Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 28 THR Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 669 optimal weight: 7.9990 chunk 705 optimal weight: 30.0000 chunk 643 optimal weight: 5.9990 chunk 686 optimal weight: 6.9990 chunk 413 optimal weight: 30.0000 chunk 298 optimal weight: 0.0170 chunk 538 optimal weight: 30.0000 chunk 210 optimal weight: 30.0000 chunk 620 optimal weight: 6.9990 chunk 649 optimal weight: 7.9990 chunk 683 optimal weight: 7.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** D 43 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** E 114 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN O 65 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 ASN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 ASN ** Y 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 GLN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 GLN b 77 GLN ** 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** 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** g 46 GLN ** h 18 GLN ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 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** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 43 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** ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 42 GLN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.8997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 73658 Z= 0.242 Angle : 0.683 18.587 103348 Z= 0.376 Chirality : 0.041 0.359 11716 Planarity : 0.005 0.056 11020 Dihedral : 14.319 65.537 16468 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.36 % Allowed : 19.34 % Favored : 78.29 % 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: 1.65 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.00 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP p 17 PHE 0.033 0.002 PHE o 45 TYR 0.035 0.002 TYR d 10 ARG 0.005 0.000 ARG o 13 *********************** 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 1090 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 946 time to evaluate : 5.124 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: A 16 LYS cc_start: 0.4941 (ttmt) cc_final: 0.4486 (tptt) REVERT: B 96 LEU cc_start: 0.6132 (tp) cc_final: 0.5593 (tt) REVERT: B 99 MET cc_start: 0.6089 (tpp) cc_final: 0.5878 (tpp) REVERT: D 99 MET cc_start: 0.6789 (mmm) cc_final: 0.6213 (tpp) REVERT: E 107 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.5769 (t80) REVERT: H 43 GLN cc_start: 0.6854 (pp30) cc_final: 0.6344 (pp30) REVERT: J 96 LEU cc_start: 0.6241 (tp) cc_final: 0.5963 (tt) REVERT: J 108 ILE cc_start: 0.6851 (pt) cc_final: 0.6489 (mt) REVERT: L 66 TYR cc_start: 0.6205 (OUTLIER) cc_final: 0.5854 (t80) REVERT: L 126 THR cc_start: 0.7824 (p) cc_final: 0.7595 (t) REVERT: U 10 TYR cc_start: 0.7374 (t80) cc_final: 0.6951 (t80) REVERT: h 43 GLN cc_start: 0.7014 (pp30) cc_final: 0.6570 (pp30) REVERT: h 103 LEU cc_start: 0.8288 (mp) cc_final: 0.7933 (mt) REVERT: o 57 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5784 (mp0) REVERT: p 107 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5400 (t80) REVERT: q 57 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: q 99 MET cc_start: 0.6679 (mmm) cc_final: 0.6310 (tpp) REVERT: s 57 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: t 107 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5755 (t80) REVERT: v 107 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.5117 (t80) REVERT: x 79 PHE cc_start: 0.7930 (t80) cc_final: 0.7662 (t80) REVERT: x 107 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.5379 (t80) REVERT: 3 103 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7671 (mt) REVERT: 4 89 ARG cc_start: 0.4692 (OUTLIER) cc_final: 0.4261 (tpp-160) outliers start: 144 outliers final: 96 residues processed: 1035 average time/residue: 0.6164 time to fit residues: 1121.1980 Evaluate side-chains 980 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 873 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 66 TYR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 112 ASN Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 96 LEU Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 66 TYR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 65 GLN Chi-restraints excluded: chain k residue 65 GLN Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain s residue 134 SER Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 96 LEU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain x residue 97 VAL Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 89 ARG Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 450 optimal weight: 6.9990 chunk 725 optimal weight: 30.0000 chunk 442 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 504 optimal weight: 7.9990 chunk 761 optimal weight: 30.0000 chunk 700 optimal weight: 30.0000 chunk 606 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 468 optimal weight: 5.9990 chunk 371 optimal weight: 0.0060 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN C 22 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN ** V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 GLN a 116 GLN ** b 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 77 GLN ** 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** ** 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** f 116 GLN ** 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 ASN ** i 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 77 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** ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 42 GLN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 46 GLN ** 6 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.9197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 73658 Z= 0.232 Angle : 0.689 18.700 103348 Z= 0.377 Chirality : 0.041 0.367 11716 Planarity : 0.005 0.056 11020 Dihedral : 14.346 66.596 16468 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.79 % Allowed : 20.13 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.09), residues: 7308 helix: 1.66 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP p 17 PHE 0.033 0.001 PHE D 45 TYR 0.034 0.002 TYR O 10 ARG 0.009 0.000 ARG M 13 ********************** 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 1042 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 933 time to evaluate : 5.132 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: A 16 LYS cc_start: 0.4951 (ttmt) cc_final: 0.4502 (tptt) REVERT: B 96 LEU cc_start: 0.6101 (tp) cc_final: 0.5546 (tt) REVERT: C 18 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6595 (tp40) REVERT: D 43 GLN cc_start: 0.6497 (pp30) cc_final: 0.6001 (pp30) REVERT: D 96 LEU cc_start: 0.6058 (mt) cc_final: 0.5692 (tt) REVERT: D 99 MET cc_start: 0.6823 (mmm) cc_final: 0.6263 (tpp) REVERT: E 107 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.5752 (t80) REVERT: H 43 GLN cc_start: 0.6808 (pp30) cc_final: 0.5998 (pp30) REVERT: J 96 LEU cc_start: 0.6363 (tp) cc_final: 0.6096 (tt) REVERT: J 108 ILE cc_start: 0.6797 (pt) cc_final: 0.6525 (mt) REVERT: L 66 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.6030 (t80) REVERT: M 12 GLN cc_start: 0.6621 (mt0) cc_final: 0.6418 (mt0) REVERT: U 10 TYR cc_start: 0.7350 (t80) cc_final: 0.7014 (t80) REVERT: W 43 GLN cc_start: 0.5590 (mm-40) cc_final: 0.5217 (mm-40) REVERT: d 96 LEU cc_start: 0.6582 (tp) cc_final: 0.6100 (tt) REVERT: h 43 GLN cc_start: 0.6911 (pp30) cc_final: 0.6503 (pp30) REVERT: h 103 LEU cc_start: 0.8237 (mp) cc_final: 0.7942 (mt) REVERT: k 65 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: n 124 ILE cc_start: 0.7971 (mm) cc_final: 0.7756 (mm) REVERT: o 57 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5778 (mp0) REVERT: p 107 TYR cc_start: 0.6153 (OUTLIER) cc_final: 0.5384 (t80) REVERT: q 57 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: q 99 MET cc_start: 0.6706 (mmm) cc_final: 0.6321 (mmt) REVERT: s 57 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: t 107 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.5789 (t80) REVERT: v 107 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.5252 (t80) REVERT: x 79 PHE cc_start: 0.7955 (t80) cc_final: 0.7712 (t80) REVERT: x 107 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.5394 (t80) REVERT: 3 103 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7736 (mt) REVERT: 4 89 ARG cc_start: 0.4767 (OUTLIER) cc_final: 0.4192 (tpp-160) outliers start: 109 outliers final: 91 residues processed: 1001 average time/residue: 0.6132 time to fit residues: 1082.2403 Evaluate side-chains 979 residues out of total 6090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 875 time to evaluate : 5.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 107 TYR Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 66 TYR Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 42 GLN Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 55 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 107 TYR Chi-restraints excluded: chain P residue 119 ASP Chi-restraints excluded: chain Q residue 11 SER Chi-restraints excluded: chain Q residue 112 ASN Chi-restraints excluded: chain R residue 119 ASP Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain V residue 55 VAL Chi-restraints excluded: chain V residue 66 TYR Chi-restraints excluded: chain V residue 96 LEU Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain d residue 43 GLN Chi-restraints excluded: chain d residue 46 GLN Chi-restraints excluded: chain d residue 66 TYR Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain e residue 34 LEU Chi-restraints excluded: chain g residue 87 LEU Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 124 ILE Chi-restraints excluded: chain j residue 10 TYR Chi-restraints excluded: chain j residue 65 GLN Chi-restraints excluded: chain k residue 65 GLN Chi-restraints excluded: chain l residue 34 LEU Chi-restraints excluded: chain l residue 119 ASP Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain n residue 42 GLN Chi-restraints excluded: chain n residue 66 TYR Chi-restraints excluded: chain n residue 107 TYR Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain p residue 40 VAL Chi-restraints excluded: chain p residue 107 TYR Chi-restraints excluded: chain q residue 57 GLU Chi-restraints excluded: chain q residue 133 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain s residue 7 SER Chi-restraints excluded: chain s residue 57 GLU Chi-restraints excluded: chain s residue 87 LEU Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 133 VAL Chi-restraints excluded: chain s residue 134 SER Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 107 TYR Chi-restraints excluded: chain t residue 124 ILE Chi-restraints excluded: chain u residue 57 GLU Chi-restraints excluded: chain u residue 133 VAL Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain v residue 97 VAL Chi-restraints excluded: chain v residue 107 TYR Chi-restraints excluded: chain v residue 123 ASN Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 112 ASN Chi-restraints excluded: chain x residue 107 TYR Chi-restraints excluded: chain x residue 124 ILE Chi-restraints excluded: chain y residue 28 THR Chi-restraints excluded: chain z residue 55 VAL Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 112 ASN Chi-restraints excluded: chain 1 residue 134 SER Chi-restraints excluded: chain 3 residue 87 LEU Chi-restraints excluded: chain 3 residue 103 LEU Chi-restraints excluded: chain 3 residue 112 ASN Chi-restraints excluded: chain 4 residue 42 GLN Chi-restraints excluded: chain 4 residue 89 ARG Chi-restraints excluded: chain 4 residue 103 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 6 residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 764 random chunks: chunk 481 optimal weight: 9.9990 chunk 645 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 558 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 607 optimal weight: 30.0000 chunk 254 optimal weight: 6.9990 chunk 623 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 43 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** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 GLN W 65 GLN ** X 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 GLN ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 ASN a 12 GLN a 116 GLN b 77 GLN ** 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** ** 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 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 116 GLN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 77 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** ** z 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 123 ASN 4 123 ASN ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.077077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.072468 restraints weight = 291546.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.073791 restraints weight = 142348.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.074601 restraints weight = 79983.969| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.9480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 73658 Z= 0.254 Angle : 0.700 18.492 103348 Z= 0.382 Chirality : 0.042 0.395 11716 Planarity : 0.005 0.057 11020 Dihedral : 14.393 67.748 16468 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.04 % Allowed : 20.21 % Favored : 77.75 % 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: 1.89 (0.09), residues: 7308 helix: 1.64 (0.06), residues: 6322 sheet: None (None), residues: 0 loop : -1.19 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 17 PHE 0.035 0.002 PHE o 45 TYR 0.034 0.002 TYR O 10 ARG 0.006 0.000 ARG M 13 =============================================================================== Job complete usr+sys time: 18342.53 seconds wall clock time: 323 minutes 20.88 seconds (19400.88 seconds total)