Starting phenix.real_space_refine on Thu Dec 14 15:17:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/12_2023/8ixd_35791_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/12_2023/8ixd_35791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/12_2023/8ixd_35791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/12_2023/8ixd_35791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/12_2023/8ixd_35791_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/12_2023/8ixd_35791_updated.pdb" } resolution = 4.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.006 sd= 0.060 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 81 5.49 5 S 558 5.16 5 C 52623 2.51 5 N 14382 2.21 5 O 16452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 213": "OE1" <-> "OE2" Residue "I TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 303": "OE1" <-> "OE2" Residue "I TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 46": "NH1" <-> "NH2" Residue "Q TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 205": "OE1" <-> "OE2" Residue "Q PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 288": "OE1" <-> "OE2" Residue "Q ARG 320": "NH1" <-> "NH2" Residue "Q ARG 359": "NH1" <-> "NH2" Residue "Q PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 391": "NH1" <-> "NH2" Residue "Y TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 244": "OE1" <-> "OE2" Residue "Y PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 46": "NH1" <-> "NH2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 288": "OE1" <-> "OE2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J ARG 359": "NH1" <-> "NH2" Residue "J PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 391": "NH1" <-> "NH2" Residue "S TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 244": "OE1" <-> "OE2" Residue "S PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 70": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 288": "OE1" <-> "OE2" Residue "K ARG 320": "NH1" <-> "NH2" Residue "K ARG 359": "NH1" <-> "NH2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 391": "NH1" <-> "NH2" Residue "T TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 244": "OE1" <-> "OE2" Residue "T PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 205": "OE1" <-> "OE2" Residue "L PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 288": "OE1" <-> "OE2" Residue "L ARG 320": "NH1" <-> "NH2" Residue "L ARG 359": "NH1" <-> "NH2" Residue "L PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "U TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 244": "OE1" <-> "OE2" Residue "U PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 205": "OE1" <-> "OE2" Residue "M PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "M ARG 359": "NH1" <-> "NH2" Residue "M PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 391": "NH1" <-> "NH2" Residue "V TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 244": "OE1" <-> "OE2" Residue "V PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 303": "OE1" <-> "OE2" Residue "E TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 288": "OE1" <-> "OE2" Residue "N ARG 320": "NH1" <-> "NH2" Residue "N ARG 359": "NH1" <-> "NH2" Residue "N PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 391": "NH1" <-> "NH2" Residue "W TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 244": "OE1" <-> "OE2" Residue "W PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "F TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 205": "OE1" <-> "OE2" Residue "O PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 288": "OE1" <-> "OE2" Residue "O ARG 320": "NH1" <-> "NH2" Residue "O ARG 359": "NH1" <-> "NH2" Residue "O PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 391": "NH1" <-> "NH2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 244": "OE1" <-> "OE2" Residue "X PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 213": "OE1" <-> "OE2" Residue "G TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 303": "OE1" <-> "OE2" Residue "G TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 46": "NH1" <-> "NH2" Residue "P TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 288": "OE1" <-> "OE2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 359": "NH1" <-> "NH2" Residue "P PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 391": "NH1" <-> "NH2" Residue "Z TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 244": "OE1" <-> "OE2" Residue "Z PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 70": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 303": "OE1" <-> "OE2" Residue "H TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 205": "OE1" <-> "OE2" Residue "R PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 288": "OE1" <-> "OE2" Residue "R ARG 320": "NH1" <-> "NH2" Residue "R ARG 359": "NH1" <-> "NH2" Residue "R PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 391": "NH1" <-> "NH2" Residue "a TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 244": "OE1" <-> "OE2" Residue "a PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 84096 Number of models: 1 Model: "" Number of chains: 45 Chain: "I" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "Q" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "Y" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "A" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "J" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "S" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "K" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "T" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "C" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "L" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "U" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "D" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "M" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "V" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "E" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "N" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "W" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "F" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "O" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "X" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "P" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "Z" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "H" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 407} Chain breaks: 1 Chain: "R" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3354 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "a" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2544 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'G2P': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.89, per 1000 atoms: 0.38 Number of scatterers: 84096 At special positions: 0 Unit cell: (196.382, 151.57, 293.914, 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 558 16.00 P 81 15.00 O 16452 8.00 N 14382 7.00 C 52623 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 27.92 Conformation dependent library (CDL) restraints added in 11.6 seconds 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 414 helices and 90 sheets defined 39.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.63 Creating SS restraints... Processing helix chain 'I' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.758A pdb=" N ASP I 126 " --> pdb=" O ASP I 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN I 134 " --> pdb=" O LYS I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 189 through 203 removed outlier: 3.743A pdb=" N HIS I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR I 199 " --> pdb=" O LEU I 195 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU I 202 " --> pdb=" O HIS I 198 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS I 203 " --> pdb=" O THR I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG I 221 " --> pdb=" O ASP I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 244 removed outlier: 3.870A pdb=" N LEU I 236 " --> pdb=" O ASN I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 249 No H-bonds generated for 'chain 'I' and resid 246 through 249' Processing helix chain 'I' and resid 258 through 263 removed outlier: 3.566A pdb=" N PHE I 261 " --> pdb=" O LEU I 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR I 263 " --> pdb=" O GLU I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 289 removed outlier: 3.742A pdb=" N TYR I 288 " --> pdb=" O ALA I 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS I 289 " --> pdb=" O GLU I 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 284 through 289' Processing helix chain 'I' and resid 294 through 301 Processing helix chain 'I' and resid 304 through 306 No H-bonds generated for 'chain 'I' and resid 304 through 306' Processing helix chain 'I' and resid 331 through 343 removed outlier: 3.676A pdb=" N ALA I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU I 403 " --> pdb=" O HIS I 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET I 404 " --> pdb=" O LYS I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 417 Processing helix chain 'I' and resid 421 through 441 Processing helix chain 'Q' and resid 11 through 28 Processing helix chain 'Q' and resid 42 through 45 No H-bonds generated for 'chain 'Q' and resid 42 through 45' Processing helix chain 'Q' and resid 55 through 57 No H-bonds generated for 'chain 'Q' and resid 55 through 57' Processing helix chain 'Q' and resid 71 through 77 Processing helix chain 'Q' and resid 101 through 106 Processing helix chain 'Q' and resid 110 through 126 removed outlier: 4.202A pdb=" N ASP Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP Q 118 " --> pdb=" O ASP Q 114 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL Q 119 " --> pdb=" O SER Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE Q 152 " --> pdb=" O GLY Q 148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER Q 153 " --> pdb=" O THR Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 195 removed outlier: 3.756A pdb=" N HIS Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU Q 194 " --> pdb=" O HIS Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 213 Processing helix chain 'Q' and resid 222 through 236 removed outlier: 3.617A pdb=" N LEU Q 228 " --> pdb=" O ASP Q 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Q 232 " --> pdb=" O LEU Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 257 Processing helix chain 'Q' and resid 286 through 293 removed outlier: 3.669A pdb=" N GLN Q 291 " --> pdb=" O PRO Q 287 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN Q 292 " --> pdb=" O GLU Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 305 through 307 No H-bonds generated for 'chain 'Q' and resid 305 through 307' Processing helix chain 'Q' and resid 323 through 335 removed outlier: 3.728A pdb=" N LEU Q 331 " --> pdb=" O ASP Q 327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN Q 334 " --> pdb=" O MET Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 340 No H-bonds generated for 'chain 'Q' and resid 338 through 340' Processing helix chain 'Q' and resid 372 through 389 removed outlier: 3.685A pdb=" N LYS Q 379 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG Q 380 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU Q 383 " --> pdb=" O ARG Q 380 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR Q 386 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA Q 387 " --> pdb=" O GLN Q 384 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET Q 388 " --> pdb=" O PHE Q 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE Q 389 " --> pdb=" O THR Q 386 " (cutoff:3.500A) Processing helix chain 'Q' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU Q 401 " --> pdb=" O TRP Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 424 Processing helix chain 'Y' and resid 20 through 23 No H-bonds generated for 'chain 'Y' and resid 20 through 23' Processing helix chain 'Y' and resid 58 through 64 Processing helix chain 'Y' and resid 68 through 75 Processing helix chain 'Y' and resid 92 through 95 No H-bonds generated for 'chain 'Y' and resid 92 through 95' Processing helix chain 'Y' and resid 107 through 121 Processing helix chain 'Y' and resid 176 through 188 Processing helix chain 'Y' and resid 238 through 241 No H-bonds generated for 'chain 'Y' and resid 238 through 241' Processing helix chain 'Y' and resid 245 through 270 removed outlier: 3.911A pdb=" N ILE Y 254 " --> pdb=" O ALA Y 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN Y 255 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU Y 258 " --> pdb=" O ASN Y 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER Y 259 " --> pdb=" O LYS Y 256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL Y 264 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE Y 265 " --> pdb=" O GLY Y 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU Y 268 " --> pdb=" O ILE Y 265 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU Y 270 " --> pdb=" O ALA Y 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 279 No H-bonds generated for 'chain 'Y' and resid 277 through 279' Processing helix chain 'Y' and resid 281 through 285 Processing helix chain 'Y' and resid 287 through 291 Processing helix chain 'Y' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU Y 309 " --> pdb=" O SER Y 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER Y 310 " --> pdb=" O TYR Y 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU Y 311 " --> pdb=" O ASN Y 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR Y 312 " --> pdb=" O GLU Y 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS Y 313 " --> pdb=" O SER Y 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU Y 317 " --> pdb=" O SER Y 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE Y 318 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG Y 321 " --> pdb=" O PHE Y 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.759A pdb=" N ASP A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.744A pdb=" N HIS A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.870A pdb=" N LEU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.566A pdb=" N PHE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.742A pdb=" N TYR A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 331 through 343 removed outlier: 3.676A pdb=" N ALA A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU A 403 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 421 through 441 Processing helix chain 'J' and resid 11 through 28 Processing helix chain 'J' and resid 42 through 45 No H-bonds generated for 'chain 'J' and resid 42 through 45' Processing helix chain 'J' and resid 55 through 57 No H-bonds generated for 'chain 'J' and resid 55 through 57' Processing helix chain 'J' and resid 71 through 77 Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 110 through 126 removed outlier: 4.202A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N SER J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP J 118 " --> pdb=" O ASP J 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER J 153 " --> pdb=" O THR J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 195 removed outlier: 3.756A pdb=" N HIS J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 213 Processing helix chain 'J' and resid 222 through 236 removed outlier: 3.617A pdb=" N LEU J 228 " --> pdb=" O ASP J 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR J 232 " --> pdb=" O LEU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 257 Processing helix chain 'J' and resid 286 through 293 removed outlier: 3.668A pdb=" N GLN J 291 " --> pdb=" O PRO J 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN J 292 " --> pdb=" O GLU J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 305 through 307 No H-bonds generated for 'chain 'J' and resid 305 through 307' Processing helix chain 'J' and resid 323 through 335 removed outlier: 3.728A pdb=" N LEU J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN J 334 " --> pdb=" O MET J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 340 No H-bonds generated for 'chain 'J' and resid 338 through 340' Processing helix chain 'J' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS J 379 " --> pdb=" O GLU J 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG J 380 " --> pdb=" O LEU J 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU J 383 " --> pdb=" O ARG J 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 386 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA J 387 " --> pdb=" O GLN J 384 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET J 388 " --> pdb=" O PHE J 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE J 389 " --> pdb=" O THR J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU J 401 " --> pdb=" O TRP J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 424 Processing helix chain 'S' and resid 20 through 23 No H-bonds generated for 'chain 'S' and resid 20 through 23' Processing helix chain 'S' and resid 58 through 64 Processing helix chain 'S' and resid 68 through 75 Processing helix chain 'S' and resid 92 through 95 No H-bonds generated for 'chain 'S' and resid 92 through 95' Processing helix chain 'S' and resid 107 through 121 removed outlier: 3.500A pdb=" N SER S 121 " --> pdb=" O ASN S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 188 Processing helix chain 'S' and resid 238 through 241 No H-bonds generated for 'chain 'S' and resid 238 through 241' Processing helix chain 'S' and resid 245 through 270 removed outlier: 3.911A pdb=" N ILE S 254 " --> pdb=" O ALA S 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN S 255 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU S 258 " --> pdb=" O ASN S 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER S 259 " --> pdb=" O LYS S 256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL S 264 " --> pdb=" O LEU S 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE S 265 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU S 268 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU S 270 " --> pdb=" O ALA S 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 279 No H-bonds generated for 'chain 'S' and resid 277 through 279' Processing helix chain 'S' and resid 281 through 285 Processing helix chain 'S' and resid 287 through 291 Processing helix chain 'S' and resid 306 through 323 removed outlier: 3.703A pdb=" N GLU S 309 " --> pdb=" O SER S 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER S 310 " --> pdb=" O TYR S 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU S 311 " --> pdb=" O ASN S 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR S 312 " --> pdb=" O GLU S 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS S 313 " --> pdb=" O SER S 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU S 317 " --> pdb=" O SER S 314 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE S 318 " --> pdb=" O THR S 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG S 321 " --> pdb=" O PHE S 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.758A pdb=" N ASP B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.744A pdb=" N HIS B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU B 202 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 removed outlier: 3.871A pdb=" N LEU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.565A pdb=" N PHE B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 263 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.742A pdb=" N TYR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 289' Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 331 through 343 removed outlier: 3.677A pdb=" N ALA B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU B 403 " --> pdb=" O HIS B 399 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'K' and resid 11 through 28 Processing helix chain 'K' and resid 42 through 45 No H-bonds generated for 'chain 'K' and resid 42 through 45' Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 71 through 77 Processing helix chain 'K' and resid 101 through 106 Processing helix chain 'K' and resid 110 through 126 removed outlier: 4.201A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP K 118 " --> pdb=" O ASP K 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE K 152 " --> pdb=" O GLY K 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER K 153 " --> pdb=" O THR K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 195 removed outlier: 3.756A pdb=" N HIS K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN K 191 " --> pdb=" O LEU K 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU K 194 " --> pdb=" O HIS K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 213 Processing helix chain 'K' and resid 222 through 236 removed outlier: 3.617A pdb=" N LEU K 228 " --> pdb=" O ASP K 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR K 232 " --> pdb=" O LEU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 257 Processing helix chain 'K' and resid 286 through 293 removed outlier: 3.668A pdb=" N GLN K 291 " --> pdb=" O PRO K 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN K 292 " --> pdb=" O GLU K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 323 through 335 removed outlier: 3.728A pdb=" N LEU K 331 " --> pdb=" O ASP K 327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN K 334 " --> pdb=" O MET K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 340 No H-bonds generated for 'chain 'K' and resid 338 through 340' Processing helix chain 'K' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS K 379 " --> pdb=" O GLU K 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG K 380 " --> pdb=" O LEU K 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU K 383 " --> pdb=" O ARG K 380 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR K 386 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 387 " --> pdb=" O GLN K 384 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET K 388 " --> pdb=" O PHE K 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE K 389 " --> pdb=" O THR K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU K 401 " --> pdb=" O TRP K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'T' and resid 20 through 23 No H-bonds generated for 'chain 'T' and resid 20 through 23' Processing helix chain 'T' and resid 58 through 64 Processing helix chain 'T' and resid 68 through 75 Processing helix chain 'T' and resid 92 through 95 No H-bonds generated for 'chain 'T' and resid 92 through 95' Processing helix chain 'T' and resid 107 through 121 Processing helix chain 'T' and resid 176 through 188 Processing helix chain 'T' and resid 238 through 241 No H-bonds generated for 'chain 'T' and resid 238 through 241' Processing helix chain 'T' and resid 245 through 270 removed outlier: 3.911A pdb=" N ILE T 254 " --> pdb=" O ALA T 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN T 255 " --> pdb=" O LYS T 252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU T 258 " --> pdb=" O ASN T 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER T 259 " --> pdb=" O LYS T 256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL T 264 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE T 265 " --> pdb=" O GLY T 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU T 268 " --> pdb=" O ILE T 265 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU T 270 " --> pdb=" O ALA T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 277 through 279 No H-bonds generated for 'chain 'T' and resid 277 through 279' Processing helix chain 'T' and resid 281 through 285 Processing helix chain 'T' and resid 287 through 291 Processing helix chain 'T' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU T 309 " --> pdb=" O SER T 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER T 310 " --> pdb=" O TYR T 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU T 311 " --> pdb=" O ASN T 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR T 312 " --> pdb=" O GLU T 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS T 313 " --> pdb=" O SER T 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU T 317 " --> pdb=" O SER T 314 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE T 318 " --> pdb=" O THR T 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG T 321 " --> pdb=" O PHE T 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.758A pdb=" N ASP C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.745A pdb=" N HIS C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU C 202 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS C 203 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 3.563A pdb=" N ARG C 221 " --> pdb=" O ASP C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.871A pdb=" N LEU C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 249 No H-bonds generated for 'chain 'C' and resid 246 through 249' Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.565A pdb=" N PHE C 261 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 263 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.742A pdb=" N TYR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 289' Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.677A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.663A pdb=" N LEU C 403 " --> pdb=" O HIS C 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 421 through 441 Processing helix chain 'L' and resid 11 through 28 Processing helix chain 'L' and resid 42 through 45 No H-bonds generated for 'chain 'L' and resid 42 through 45' Processing helix chain 'L' and resid 55 through 57 No H-bonds generated for 'chain 'L' and resid 55 through 57' Processing helix chain 'L' and resid 71 through 77 Processing helix chain 'L' and resid 101 through 106 Processing helix chain 'L' and resid 110 through 126 removed outlier: 4.202A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP L 118 " --> pdb=" O ASP L 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 119 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 158 removed outlier: 3.956A pdb=" N ILE L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER L 153 " --> pdb=" O THR L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 195 removed outlier: 3.757A pdb=" N HIS L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 213 Processing helix chain 'L' and resid 222 through 236 removed outlier: 3.617A pdb=" N LEU L 228 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 257 Processing helix chain 'L' and resid 286 through 293 removed outlier: 3.669A pdb=" N GLN L 291 " --> pdb=" O PRO L 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN L 292 " --> pdb=" O GLU L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 307 No H-bonds generated for 'chain 'L' and resid 305 through 307' Processing helix chain 'L' and resid 323 through 335 removed outlier: 3.727A pdb=" N LEU L 331 " --> pdb=" O ASP L 327 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN L 334 " --> pdb=" O MET L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS L 379 " --> pdb=" O GLU L 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG L 380 " --> pdb=" O LEU L 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU L 383 " --> pdb=" O ARG L 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR L 386 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA L 387 " --> pdb=" O GLN L 384 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET L 388 " --> pdb=" O PHE L 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE L 389 " --> pdb=" O THR L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU L 401 " --> pdb=" O TRP L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 424 Processing helix chain 'U' and resid 20 through 23 No H-bonds generated for 'chain 'U' and resid 20 through 23' Processing helix chain 'U' and resid 58 through 64 Processing helix chain 'U' and resid 68 through 75 Processing helix chain 'U' and resid 92 through 95 No H-bonds generated for 'chain 'U' and resid 92 through 95' Processing helix chain 'U' and resid 107 through 121 removed outlier: 3.500A pdb=" N SER U 121 " --> pdb=" O ASN U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 188 Processing helix chain 'U' and resid 238 through 241 No H-bonds generated for 'chain 'U' and resid 238 through 241' Processing helix chain 'U' and resid 245 through 270 removed outlier: 3.910A pdb=" N ILE U 254 " --> pdb=" O ALA U 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN U 255 " --> pdb=" O LYS U 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU U 258 " --> pdb=" O ASN U 255 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER U 259 " --> pdb=" O LYS U 256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL U 264 " --> pdb=" O LEU U 261 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE U 265 " --> pdb=" O GLY U 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU U 268 " --> pdb=" O ILE U 265 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU U 270 " --> pdb=" O ALA U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 279 No H-bonds generated for 'chain 'U' and resid 277 through 279' Processing helix chain 'U' and resid 281 through 285 Processing helix chain 'U' and resid 287 through 291 Processing helix chain 'U' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU U 309 " --> pdb=" O SER U 306 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N SER U 310 " --> pdb=" O TYR U 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU U 311 " --> pdb=" O ASN U 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR U 312 " --> pdb=" O GLU U 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS U 313 " --> pdb=" O SER U 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU U 317 " --> pdb=" O SER U 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE U 318 " --> pdb=" O THR U 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG U 321 " --> pdb=" O PHE U 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.758A pdb=" N ASP D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.744A pdb=" N HIS D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS D 203 " --> pdb=" O THR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG D 221 " --> pdb=" O ASP D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.871A pdb=" N LEU D 236 " --> pdb=" O ASN D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 249 No H-bonds generated for 'chain 'D' and resid 246 through 249' Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.565A pdb=" N PHE D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 263 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.743A pdb=" N TYR D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 289' Processing helix chain 'D' and resid 294 through 301 Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 331 through 343 removed outlier: 3.677A pdb=" N ALA D 336 " --> pdb=" O LYS D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU D 403 " --> pdb=" O HIS D 399 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 421 through 441 Processing helix chain 'M' and resid 11 through 28 Processing helix chain 'M' and resid 42 through 45 No H-bonds generated for 'chain 'M' and resid 42 through 45' Processing helix chain 'M' and resid 55 through 57 No H-bonds generated for 'chain 'M' and resid 55 through 57' Processing helix chain 'M' and resid 71 through 77 Processing helix chain 'M' and resid 101 through 106 Processing helix chain 'M' and resid 110 through 126 removed outlier: 4.202A pdb=" N ASP M 114 " --> pdb=" O ALA M 110 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP M 118 " --> pdb=" O ASP M 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL M 119 " --> pdb=" O SER M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE M 152 " --> pdb=" O GLY M 148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER M 153 " --> pdb=" O THR M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 195 removed outlier: 3.756A pdb=" N HIS M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN M 191 " --> pdb=" O LEU M 187 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU M 194 " --> pdb=" O HIS M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 213 Processing helix chain 'M' and resid 222 through 236 removed outlier: 3.618A pdb=" N LEU M 228 " --> pdb=" O ASP M 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR M 232 " --> pdb=" O LEU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 257 Processing helix chain 'M' and resid 286 through 293 removed outlier: 3.668A pdb=" N GLN M 291 " --> pdb=" O PRO M 287 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 307 No H-bonds generated for 'chain 'M' and resid 305 through 307' Processing helix chain 'M' and resid 323 through 335 removed outlier: 3.727A pdb=" N LEU M 331 " --> pdb=" O ASP M 327 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN M 334 " --> pdb=" O MET M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 340 No H-bonds generated for 'chain 'M' and resid 338 through 340' Processing helix chain 'M' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS M 379 " --> pdb=" O GLU M 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG M 380 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU M 383 " --> pdb=" O ARG M 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR M 386 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA M 387 " --> pdb=" O GLN M 384 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET M 388 " --> pdb=" O PHE M 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE M 389 " --> pdb=" O THR M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU M 401 " --> pdb=" O TRP M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 424 Processing helix chain 'V' and resid 20 through 23 No H-bonds generated for 'chain 'V' and resid 20 through 23' Processing helix chain 'V' and resid 58 through 64 Processing helix chain 'V' and resid 68 through 75 Processing helix chain 'V' and resid 92 through 95 No H-bonds generated for 'chain 'V' and resid 92 through 95' Processing helix chain 'V' and resid 107 through 121 removed outlier: 3.500A pdb=" N SER V 121 " --> pdb=" O ASN V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 176 through 188 Processing helix chain 'V' and resid 238 through 241 No H-bonds generated for 'chain 'V' and resid 238 through 241' Processing helix chain 'V' and resid 245 through 270 removed outlier: 3.911A pdb=" N ILE V 254 " --> pdb=" O ALA V 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN V 255 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU V 258 " --> pdb=" O ASN V 255 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER V 259 " --> pdb=" O LYS V 256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL V 264 " --> pdb=" O LEU V 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE V 265 " --> pdb=" O GLY V 262 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU V 268 " --> pdb=" O ILE V 265 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU V 270 " --> pdb=" O ALA V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 277 through 279 No H-bonds generated for 'chain 'V' and resid 277 through 279' Processing helix chain 'V' and resid 281 through 285 Processing helix chain 'V' and resid 287 through 291 Processing helix chain 'V' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU V 309 " --> pdb=" O SER V 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER V 310 " --> pdb=" O TYR V 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU V 311 " --> pdb=" O ASN V 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR V 312 " --> pdb=" O GLU V 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS V 313 " --> pdb=" O SER V 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU V 317 " --> pdb=" O SER V 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE V 318 " --> pdb=" O THR V 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG V 321 " --> pdb=" O PHE V 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.758A pdb=" N ASP E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 189 through 203 removed outlier: 3.744A pdb=" N HIS E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR E 199 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU E 202 " --> pdb=" O HIS E 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS E 203 " --> pdb=" O THR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.870A pdb=" N LEU E 236 " --> pdb=" O ASN E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 249 No H-bonds generated for 'chain 'E' and resid 246 through 249' Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.566A pdb=" N PHE E 261 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 263 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.742A pdb=" N TYR E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 289' Processing helix chain 'E' and resid 294 through 301 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 331 through 343 removed outlier: 3.676A pdb=" N ALA E 336 " --> pdb=" O LYS E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU E 403 " --> pdb=" O HIS E 399 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 421 through 441 Processing helix chain 'N' and resid 11 through 28 Processing helix chain 'N' and resid 42 through 45 No H-bonds generated for 'chain 'N' and resid 42 through 45' Processing helix chain 'N' and resid 55 through 57 No H-bonds generated for 'chain 'N' and resid 55 through 57' Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 101 through 106 Processing helix chain 'N' and resid 110 through 126 removed outlier: 4.202A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP N 118 " --> pdb=" O ASP N 114 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL N 119 " --> pdb=" O SER N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE N 152 " --> pdb=" O GLY N 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER N 153 " --> pdb=" O THR N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 195 removed outlier: 3.756A pdb=" N HIS N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 213 Processing helix chain 'N' and resid 222 through 236 removed outlier: 3.617A pdb=" N LEU N 228 " --> pdb=" O ASP N 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 257 Processing helix chain 'N' and resid 286 through 293 removed outlier: 3.668A pdb=" N GLN N 291 " --> pdb=" O PRO N 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN N 292 " --> pdb=" O GLU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 307 No H-bonds generated for 'chain 'N' and resid 305 through 307' Processing helix chain 'N' and resid 323 through 335 removed outlier: 3.728A pdb=" N LEU N 331 " --> pdb=" O ASP N 327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN N 334 " --> pdb=" O MET N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 340 No H-bonds generated for 'chain 'N' and resid 338 through 340' Processing helix chain 'N' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS N 379 " --> pdb=" O GLU N 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG N 380 " --> pdb=" O LEU N 377 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU N 383 " --> pdb=" O ARG N 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR N 386 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA N 387 " --> pdb=" O GLN N 384 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET N 388 " --> pdb=" O PHE N 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE N 389 " --> pdb=" O THR N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU N 401 " --> pdb=" O TRP N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 424 Processing helix chain 'W' and resid 20 through 23 No H-bonds generated for 'chain 'W' and resid 20 through 23' Processing helix chain 'W' and resid 58 through 64 Processing helix chain 'W' and resid 68 through 75 Processing helix chain 'W' and resid 92 through 95 No H-bonds generated for 'chain 'W' and resid 92 through 95' Processing helix chain 'W' and resid 107 through 121 removed outlier: 3.500A pdb=" N SER W 121 " --> pdb=" O ASN W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 188 Processing helix chain 'W' and resid 238 through 241 No H-bonds generated for 'chain 'W' and resid 238 through 241' Processing helix chain 'W' and resid 245 through 270 removed outlier: 3.911A pdb=" N ILE W 254 " --> pdb=" O ALA W 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN W 255 " --> pdb=" O LYS W 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU W 258 " --> pdb=" O ASN W 255 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER W 259 " --> pdb=" O LYS W 256 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL W 264 " --> pdb=" O LEU W 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE W 265 " --> pdb=" O GLY W 262 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU W 268 " --> pdb=" O ILE W 265 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU W 270 " --> pdb=" O ALA W 267 " (cutoff:3.500A) Processing helix chain 'W' and resid 277 through 279 No H-bonds generated for 'chain 'W' and resid 277 through 279' Processing helix chain 'W' and resid 281 through 285 Processing helix chain 'W' and resid 287 through 291 Processing helix chain 'W' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU W 309 " --> pdb=" O SER W 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER W 310 " --> pdb=" O TYR W 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU W 311 " --> pdb=" O ASN W 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR W 312 " --> pdb=" O GLU W 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS W 313 " --> pdb=" O SER W 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU W 317 " --> pdb=" O SER W 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE W 318 " --> pdb=" O THR W 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG W 321 " --> pdb=" O PHE W 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 27 removed outlier: 3.719A pdb=" N ALA F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 22 " --> pdb=" O ASN F 18 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.758A pdb=" N ASP F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN F 134 " --> pdb=" O LYS F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.743A pdb=" N HIS F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU F 202 " --> pdb=" O HIS F 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS F 203 " --> pdb=" O THR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 244 removed outlier: 3.871A pdb=" N LEU F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 249 No H-bonds generated for 'chain 'F' and resid 246 through 249' Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.566A pdb=" N PHE F 261 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F 263 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.743A pdb=" N TYR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 289' Processing helix chain 'F' and resid 294 through 301 Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 331 through 343 removed outlier: 3.677A pdb=" N ALA F 336 " --> pdb=" O LYS F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU F 403 " --> pdb=" O HIS F 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 421 through 441 Processing helix chain 'O' and resid 11 through 28 Processing helix chain 'O' and resid 42 through 45 No H-bonds generated for 'chain 'O' and resid 42 through 45' Processing helix chain 'O' and resid 55 through 57 No H-bonds generated for 'chain 'O' and resid 55 through 57' Processing helix chain 'O' and resid 71 through 77 Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 110 through 126 removed outlier: 4.201A pdb=" N ASP O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER O 115 " --> pdb=" O GLU O 111 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP O 118 " --> pdb=" O ASP O 114 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL O 119 " --> pdb=" O SER O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE O 152 " --> pdb=" O GLY O 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER O 153 " --> pdb=" O THR O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 195 removed outlier: 3.757A pdb=" N HIS O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN O 191 " --> pdb=" O LEU O 187 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU O 194 " --> pdb=" O HIS O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 213 Processing helix chain 'O' and resid 222 through 236 removed outlier: 3.618A pdb=" N LEU O 228 " --> pdb=" O ASP O 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR O 232 " --> pdb=" O LEU O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 257 Processing helix chain 'O' and resid 286 through 293 removed outlier: 3.669A pdb=" N GLN O 291 " --> pdb=" O PRO O 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN O 292 " --> pdb=" O GLU O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 307 No H-bonds generated for 'chain 'O' and resid 305 through 307' Processing helix chain 'O' and resid 323 through 335 removed outlier: 3.728A pdb=" N LEU O 331 " --> pdb=" O ASP O 327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN O 334 " --> pdb=" O MET O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 340 No H-bonds generated for 'chain 'O' and resid 338 through 340' Processing helix chain 'O' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS O 379 " --> pdb=" O GLU O 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG O 380 " --> pdb=" O LEU O 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU O 383 " --> pdb=" O ARG O 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR O 386 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA O 387 " --> pdb=" O GLN O 384 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET O 388 " --> pdb=" O PHE O 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE O 389 " --> pdb=" O THR O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU O 401 " --> pdb=" O TRP O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 424 Processing helix chain 'X' and resid 20 through 23 No H-bonds generated for 'chain 'X' and resid 20 through 23' Processing helix chain 'X' and resid 58 through 64 Processing helix chain 'X' and resid 68 through 75 Processing helix chain 'X' and resid 92 through 95 No H-bonds generated for 'chain 'X' and resid 92 through 95' Processing helix chain 'X' and resid 107 through 121 removed outlier: 3.500A pdb=" N SER X 121 " --> pdb=" O ASN X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 188 Processing helix chain 'X' and resid 238 through 241 No H-bonds generated for 'chain 'X' and resid 238 through 241' Processing helix chain 'X' and resid 245 through 270 removed outlier: 3.911A pdb=" N ILE X 254 " --> pdb=" O ALA X 251 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN X 255 " --> pdb=" O LYS X 252 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU X 258 " --> pdb=" O ASN X 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER X 259 " --> pdb=" O LYS X 256 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL X 264 " --> pdb=" O LEU X 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE X 265 " --> pdb=" O GLY X 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU X 268 " --> pdb=" O ILE X 265 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU X 270 " --> pdb=" O ALA X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 277 through 279 No H-bonds generated for 'chain 'X' and resid 277 through 279' Processing helix chain 'X' and resid 281 through 285 Processing helix chain 'X' and resid 287 through 291 Processing helix chain 'X' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU X 309 " --> pdb=" O SER X 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER X 310 " --> pdb=" O TYR X 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU X 311 " --> pdb=" O ASN X 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR X 312 " --> pdb=" O GLU X 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS X 313 " --> pdb=" O SER X 310 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU X 317 " --> pdb=" O SER X 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE X 318 " --> pdb=" O THR X 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG X 321 " --> pdb=" O PHE X 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 22 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.759A pdb=" N ASP G 126 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 189 through 203 removed outlier: 3.744A pdb=" N HIS G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR G 199 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU G 202 " --> pdb=" O HIS G 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS G 203 " --> pdb=" O THR G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG G 221 " --> pdb=" O ASP G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.870A pdb=" N LEU G 236 " --> pdb=" O ASN G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 249 No H-bonds generated for 'chain 'G' and resid 246 through 249' Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.566A pdb=" N PHE G 261 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR G 263 " --> pdb=" O GLU G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.743A pdb=" N TYR G 288 " --> pdb=" O ALA G 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 284 through 289' Processing helix chain 'G' and resid 294 through 301 Processing helix chain 'G' and resid 304 through 306 No H-bonds generated for 'chain 'G' and resid 304 through 306' Processing helix chain 'G' and resid 331 through 343 removed outlier: 3.676A pdb=" N ALA G 336 " --> pdb=" O LYS G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 406 removed outlier: 3.663A pdb=" N LEU G 403 " --> pdb=" O HIS G 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET G 404 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 417 Processing helix chain 'G' and resid 421 through 441 Processing helix chain 'P' and resid 11 through 28 Processing helix chain 'P' and resid 42 through 45 No H-bonds generated for 'chain 'P' and resid 42 through 45' Processing helix chain 'P' and resid 55 through 57 No H-bonds generated for 'chain 'P' and resid 55 through 57' Processing helix chain 'P' and resid 71 through 77 Processing helix chain 'P' and resid 101 through 106 Processing helix chain 'P' and resid 110 through 126 removed outlier: 4.201A pdb=" N ASP P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP P 118 " --> pdb=" O ASP P 114 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL P 119 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER P 153 " --> pdb=" O THR P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 195 removed outlier: 3.757A pdb=" N HIS P 190 " --> pdb=" O THR P 186 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU P 194 " --> pdb=" O HIS P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 213 Processing helix chain 'P' and resid 222 through 236 removed outlier: 3.618A pdb=" N LEU P 228 " --> pdb=" O ASP P 224 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR P 232 " --> pdb=" O LEU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 257 Processing helix chain 'P' and resid 286 through 293 removed outlier: 3.669A pdb=" N GLN P 291 " --> pdb=" O PRO P 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN P 292 " --> pdb=" O GLU P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 305 through 307 No H-bonds generated for 'chain 'P' and resid 305 through 307' Processing helix chain 'P' and resid 323 through 335 removed outlier: 3.729A pdb=" N LEU P 331 " --> pdb=" O ASP P 327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN P 334 " --> pdb=" O MET P 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 340 No H-bonds generated for 'chain 'P' and resid 338 through 340' Processing helix chain 'P' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS P 379 " --> pdb=" O GLU P 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG P 380 " --> pdb=" O LEU P 377 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU P 383 " --> pdb=" O ARG P 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR P 386 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA P 387 " --> pdb=" O GLN P 384 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET P 388 " --> pdb=" O PHE P 385 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE P 389 " --> pdb=" O THR P 386 " (cutoff:3.500A) Processing helix chain 'P' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU P 401 " --> pdb=" O TRP P 397 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 424 Processing helix chain 'Z' and resid 20 through 23 No H-bonds generated for 'chain 'Z' and resid 20 through 23' Processing helix chain 'Z' and resid 58 through 64 Processing helix chain 'Z' and resid 68 through 75 Processing helix chain 'Z' and resid 92 through 95 No H-bonds generated for 'chain 'Z' and resid 92 through 95' Processing helix chain 'Z' and resid 107 through 121 Processing helix chain 'Z' and resid 176 through 188 Processing helix chain 'Z' and resid 238 through 241 No H-bonds generated for 'chain 'Z' and resid 238 through 241' Processing helix chain 'Z' and resid 245 through 270 removed outlier: 3.910A pdb=" N ILE Z 254 " --> pdb=" O ALA Z 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN Z 255 " --> pdb=" O LYS Z 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU Z 258 " --> pdb=" O ASN Z 255 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER Z 259 " --> pdb=" O LYS Z 256 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Z 264 " --> pdb=" O LEU Z 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE Z 265 " --> pdb=" O GLY Z 262 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Z 268 " --> pdb=" O ILE Z 265 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU Z 270 " --> pdb=" O ALA Z 267 " (cutoff:3.500A) Processing helix chain 'Z' and resid 277 through 279 No H-bonds generated for 'chain 'Z' and resid 277 through 279' Processing helix chain 'Z' and resid 281 through 285 Processing helix chain 'Z' and resid 287 through 291 Processing helix chain 'Z' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU Z 309 " --> pdb=" O SER Z 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER Z 310 " --> pdb=" O TYR Z 307 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU Z 311 " --> pdb=" O ASN Z 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR Z 312 " --> pdb=" O GLU Z 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS Z 313 " --> pdb=" O SER Z 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU Z 317 " --> pdb=" O SER Z 314 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE Z 318 " --> pdb=" O THR Z 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG Z 321 " --> pdb=" O PHE Z 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.718A pdb=" N ALA H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU H 22 " --> pdb=" O ASN H 18 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU H 23 " --> pdb=" O ALA H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.757A pdb=" N ASP H 126 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN H 134 " --> pdb=" O LYS H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 164 Processing helix chain 'H' and resid 189 through 203 removed outlier: 3.744A pdb=" N HIS H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR H 199 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU H 202 " --> pdb=" O HIS H 198 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS H 203 " --> pdb=" O THR H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 221 removed outlier: 3.564A pdb=" N ARG H 221 " --> pdb=" O ASP H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 244 removed outlier: 3.871A pdb=" N LEU H 236 " --> pdb=" O ASN H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 249 No H-bonds generated for 'chain 'H' and resid 246 through 249' Processing helix chain 'H' and resid 258 through 263 removed outlier: 3.566A pdb=" N PHE H 261 " --> pdb=" O LEU H 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR H 263 " --> pdb=" O GLU H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.743A pdb=" N TYR H 288 " --> pdb=" O ALA H 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 284 through 289' Processing helix chain 'H' and resid 294 through 301 Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 331 through 343 removed outlier: 3.675A pdb=" N ALA H 336 " --> pdb=" O LYS H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 406 removed outlier: 3.664A pdb=" N LEU H 403 " --> pdb=" O HIS H 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET H 404 " --> pdb=" O LYS H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 417 Processing helix chain 'H' and resid 421 through 441 Processing helix chain 'R' and resid 11 through 28 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 55 through 57 No H-bonds generated for 'chain 'R' and resid 55 through 57' Processing helix chain 'R' and resid 71 through 77 Processing helix chain 'R' and resid 101 through 106 Processing helix chain 'R' and resid 110 through 126 removed outlier: 4.202A pdb=" N ASP R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP R 118 " --> pdb=" O ASP R 114 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL R 119 " --> pdb=" O SER R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 158 removed outlier: 3.955A pdb=" N ILE R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 195 removed outlier: 3.756A pdb=" N HIS R 190 " --> pdb=" O THR R 186 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU R 194 " --> pdb=" O HIS R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 213 Processing helix chain 'R' and resid 222 through 236 removed outlier: 3.617A pdb=" N LEU R 228 " --> pdb=" O ASP R 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 257 Processing helix chain 'R' and resid 286 through 293 removed outlier: 3.668A pdb=" N GLN R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN R 292 " --> pdb=" O GLU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 307 No H-bonds generated for 'chain 'R' and resid 305 through 307' Processing helix chain 'R' and resid 323 through 335 removed outlier: 3.728A pdb=" N LEU R 331 " --> pdb=" O ASP R 327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN R 334 " --> pdb=" O MET R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 340 No H-bonds generated for 'chain 'R' and resid 338 through 340' Processing helix chain 'R' and resid 372 through 389 removed outlier: 3.684A pdb=" N LYS R 379 " --> pdb=" O GLU R 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG R 380 " --> pdb=" O LEU R 377 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU R 383 " --> pdb=" O ARG R 380 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR R 386 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA R 387 " --> pdb=" O GLN R 384 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET R 388 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE R 389 " --> pdb=" O THR R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 401 removed outlier: 4.355A pdb=" N GLU R 401 " --> pdb=" O TRP R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 424 Processing helix chain 'a' and resid 20 through 23 No H-bonds generated for 'chain 'a' and resid 20 through 23' Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 68 through 75 Processing helix chain 'a' and resid 92 through 95 No H-bonds generated for 'chain 'a' and resid 92 through 95' Processing helix chain 'a' and resid 107 through 121 removed outlier: 3.501A pdb=" N SER a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 188 Processing helix chain 'a' and resid 238 through 241 No H-bonds generated for 'chain 'a' and resid 238 through 241' Processing helix chain 'a' and resid 245 through 270 removed outlier: 3.910A pdb=" N ILE a 254 " --> pdb=" O ALA a 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN a 255 " --> pdb=" O LYS a 252 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU a 258 " --> pdb=" O ASN a 255 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER a 259 " --> pdb=" O LYS a 256 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL a 264 " --> pdb=" O LEU a 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE a 265 " --> pdb=" O GLY a 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU a 268 " --> pdb=" O ILE a 265 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU a 270 " --> pdb=" O ALA a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 277 through 279 No H-bonds generated for 'chain 'a' and resid 277 through 279' Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 287 through 291 Processing helix chain 'a' and resid 306 through 323 removed outlier: 3.704A pdb=" N GLU a 309 " --> pdb=" O SER a 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER a 310 " --> pdb=" O TYR a 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU a 311 " --> pdb=" O ASN a 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR a 312 " --> pdb=" O GLU a 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS a 313 " --> pdb=" O SER a 310 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU a 317 " --> pdb=" O SER a 314 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE a 318 " --> pdb=" O THR a 315 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG a 321 " --> pdb=" O PHE a 318 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER I 6 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL I 74 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS I 8 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE I 5 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 142 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 7 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER I 171 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL I 143 " --> pdb=" O SER I 171 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU I 173 " --> pdb=" O VAL I 143 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS I 145 " --> pdb=" O LEU I 173 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE I 175 " --> pdb=" O HIS I 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS I 206 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER I 176 " --> pdb=" O CYS I 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE I 208 " --> pdb=" O SER I 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR I 178 " --> pdb=" O PHE I 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL I 210 " --> pdb=" O TYR I 178 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 59 through 61 removed outlier: 3.708A pdb=" N VAL I 68 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU I 324 " --> pdb=" O CYS I 382 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 384 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'Q' and resid 63 through 66 removed outlier: 8.889A pdb=" N ILE Q 64 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS Q 6 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL Q 66 " --> pdb=" O HIS Q 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN Q 8 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE Q 133 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE Q 7 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS Q 137 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE Q 163 " --> pdb=" O PHE Q 133 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU Q 135 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN Q 165 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS Q 137 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE Q 167 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR Q 200 " --> pdb=" O SER Q 168 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET Q 170 " --> pdb=" O TYR Q 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE Q 202 " --> pdb=" O MET Q 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'Q' and resid 51 through 53 removed outlier: 3.565A pdb=" N VAL Q 60 " --> pdb=" O ASN Q 52 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Q' and resid 269 through 271 Processing sheet with id= G, first strand: chain 'Y' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG Y 50 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS Y 10 " --> pdb=" O THR Y 296 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN Y 78 " --> pdb=" O ARG Y 295 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR Y 297 " --> pdb=" O ASN Y 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR Y 80 " --> pdb=" O THR Y 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL Y 299 " --> pdb=" O THR Y 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE Y 82 " --> pdb=" O VAL Y 299 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS Y 301 " --> pdb=" O PHE Y 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR Y 84 " --> pdb=" O CYS Y 301 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY Y 79 " --> pdb=" O LYS Y 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR Y 228 " --> pdb=" O GLY Y 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA Y 83 " --> pdb=" O VAL Y 230 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS Y 213 " --> pdb=" O HIS Y 129 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'Y' and resid 32 through 34 removed outlier: 3.629A pdb=" N THR Y 38 " --> pdb=" O GLN Y 34 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Y' and resid 207 through 210 Processing sheet with id= J, first strand: chain 'Y' and resid 155 through 157 Processing sheet with id= K, first strand: chain 'A' and resid 71 through 74 removed outlier: 7.230A pdb=" N SER A 6 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL A 74 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS A 8 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 5 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 142 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 7 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER A 171 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 143 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 173 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS A 145 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE A 175 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS A 206 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER A 176 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE A 208 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR A 178 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 210 " --> pdb=" O TYR A 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL A 68 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU A 324 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 384 " --> pdb=" O CYS A 322 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE J 64 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS J 6 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL J 66 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN J 8 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL J 5 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE J 133 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE J 7 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU J 135 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA J 9 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS J 137 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE J 163 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU J 135 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN J 165 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS J 137 " --> pdb=" O ASN J 165 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE J 167 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR J 200 " --> pdb=" O SER J 168 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET J 170 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE J 202 " --> pdb=" O MET J 170 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 51 through 53 removed outlier: 3.565A pdb=" N VAL J 60 " --> pdb=" O ASN J 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 269 through 271 Processing sheet with id= Q, first strand: chain 'S' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG S 50 " --> pdb=" O VAL S 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS S 10 " --> pdb=" O THR S 296 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN S 78 " --> pdb=" O ARG S 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR S 297 " --> pdb=" O ASN S 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR S 80 " --> pdb=" O THR S 297 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL S 299 " --> pdb=" O THR S 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE S 82 " --> pdb=" O VAL S 299 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N CYS S 301 " --> pdb=" O PHE S 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR S 84 " --> pdb=" O CYS S 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY S 79 " --> pdb=" O LYS S 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR S 228 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA S 83 " --> pdb=" O VAL S 230 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS S 213 " --> pdb=" O HIS S 129 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'S' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 207 through 210 Processing sheet with id= T, first strand: chain 'S' and resid 155 through 157 Processing sheet with id= U, first strand: chain 'B' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER B 6 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL B 74 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS B 8 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 5 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 142 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 7 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER B 171 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 143 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 173 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS B 145 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE B 175 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS B 206 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER B 176 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE B 208 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR B 178 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B 210 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL B 68 " --> pdb=" O SER B 60 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU B 324 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 384 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE K 64 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS K 6 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL K 66 " --> pdb=" O HIS K 6 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN K 8 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL K 5 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE K 133 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE K 7 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU K 135 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA K 9 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS K 137 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE K 163 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU K 135 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN K 165 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS K 137 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE K 167 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR K 200 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET K 170 " --> pdb=" O TYR K 200 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE K 202 " --> pdb=" O MET K 170 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 51 through 53 removed outlier: 3.566A pdb=" N VAL K 60 " --> pdb=" O ASN K 52 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 269 through 271 Processing sheet with id= AA, first strand: chain 'T' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG T 50 " --> pdb=" O VAL T 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS T 10 " --> pdb=" O THR T 296 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN T 78 " --> pdb=" O ARG T 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR T 297 " --> pdb=" O ASN T 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR T 80 " --> pdb=" O THR T 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL T 299 " --> pdb=" O THR T 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE T 82 " --> pdb=" O VAL T 299 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS T 301 " --> pdb=" O PHE T 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR T 84 " --> pdb=" O CYS T 301 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY T 79 " --> pdb=" O LYS T 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR T 228 " --> pdb=" O GLY T 79 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA T 83 " --> pdb=" O VAL T 230 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS T 213 " --> pdb=" O HIS T 129 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'T' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'T' and resid 207 through 210 Processing sheet with id= AD, first strand: chain 'T' and resid 155 through 157 Processing sheet with id= AE, first strand: chain 'C' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER C 6 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL C 74 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS C 8 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 5 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 142 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 7 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 171 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 143 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C 173 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS C 145 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE C 175 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS C 206 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER C 176 " --> pdb=" O CYS C 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE C 208 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR C 178 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 210 " --> pdb=" O TYR C 178 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL C 68 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU C 324 " --> pdb=" O CYS C 382 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 384 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 63 through 66 removed outlier: 8.891A pdb=" N ILE L 64 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS L 6 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL L 66 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN L 8 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL L 5 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE L 133 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE L 7 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU L 135 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA L 9 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS L 137 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE L 163 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU L 135 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN L 165 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS L 137 " --> pdb=" O ASN L 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE L 167 " --> pdb=" O HIS L 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR L 200 " --> pdb=" O SER L 168 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET L 170 " --> pdb=" O TYR L 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE L 202 " --> pdb=" O MET L 170 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 51 through 53 removed outlier: 3.564A pdb=" N VAL L 60 " --> pdb=" O ASN L 52 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 269 through 271 Processing sheet with id= AK, first strand: chain 'U' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG U 50 " --> pdb=" O VAL U 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS U 10 " --> pdb=" O THR U 296 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN U 78 " --> pdb=" O ARG U 295 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR U 297 " --> pdb=" O ASN U 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR U 80 " --> pdb=" O THR U 297 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL U 299 " --> pdb=" O THR U 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE U 82 " --> pdb=" O VAL U 299 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N CYS U 301 " --> pdb=" O PHE U 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR U 84 " --> pdb=" O CYS U 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY U 79 " --> pdb=" O LYS U 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR U 228 " --> pdb=" O GLY U 79 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA U 83 " --> pdb=" O VAL U 230 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS U 213 " --> pdb=" O HIS U 129 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'U' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR U 38 " --> pdb=" O GLN U 34 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'U' and resid 207 through 210 Processing sheet with id= AN, first strand: chain 'U' and resid 155 through 157 Processing sheet with id= AO, first strand: chain 'D' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER D 6 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL D 74 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS D 8 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE D 5 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 142 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 7 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER D 171 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 143 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU D 173 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS D 145 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE D 175 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS D 206 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER D 176 " --> pdb=" O CYS D 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE D 208 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR D 178 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL D 210 " --> pdb=" O TYR D 178 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL D 68 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 277 through 279 removed outlier: 3.676A pdb=" N LEU D 324 " --> pdb=" O CYS D 382 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 384 " --> pdb=" O CYS D 322 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE M 64 " --> pdb=" O ILE M 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS M 6 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL M 66 " --> pdb=" O HIS M 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN M 8 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL M 5 " --> pdb=" O GLN M 131 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE M 133 " --> pdb=" O VAL M 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE M 7 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU M 135 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA M 9 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS M 137 " --> pdb=" O ALA M 9 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE M 163 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N LEU M 135 " --> pdb=" O ILE M 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN M 165 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS M 137 " --> pdb=" O ASN M 165 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE M 167 " --> pdb=" O HIS M 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR M 200 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET M 170 " --> pdb=" O TYR M 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE M 202 " --> pdb=" O MET M 170 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'M' and resid 51 through 53 removed outlier: 3.566A pdb=" N VAL M 60 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 269 through 271 Processing sheet with id= AU, first strand: chain 'V' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG V 50 " --> pdb=" O VAL V 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS V 10 " --> pdb=" O THR V 296 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN V 78 " --> pdb=" O ARG V 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR V 297 " --> pdb=" O ASN V 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR V 80 " --> pdb=" O THR V 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL V 299 " --> pdb=" O THR V 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE V 82 " --> pdb=" O VAL V 299 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N CYS V 301 " --> pdb=" O PHE V 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR V 84 " --> pdb=" O CYS V 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY V 79 " --> pdb=" O LYS V 226 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR V 228 " --> pdb=" O GLY V 79 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA V 83 " --> pdb=" O VAL V 230 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS V 213 " --> pdb=" O HIS V 129 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'V' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR V 38 " --> pdb=" O GLN V 34 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'V' and resid 207 through 210 Processing sheet with id= AX, first strand: chain 'V' and resid 155 through 157 Processing sheet with id= AY, first strand: chain 'E' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER E 6 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL E 74 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS E 8 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE E 5 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 142 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 7 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER E 171 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL E 143 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU E 173 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS E 145 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE E 175 " --> pdb=" O HIS E 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS E 206 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER E 176 " --> pdb=" O CYS E 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE E 208 " --> pdb=" O SER E 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR E 178 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL E 210 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL E 68 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'E' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU E 324 " --> pdb=" O CYS E 382 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 384 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'N' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE N 64 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS N 6 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL N 66 " --> pdb=" O HIS N 6 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN N 8 " --> pdb=" O VAL N 66 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL N 5 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE N 133 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE N 7 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU N 135 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA N 9 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS N 137 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE N 163 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU N 135 " --> pdb=" O ILE N 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN N 165 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS N 137 " --> pdb=" O ASN N 165 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE N 167 " --> pdb=" O HIS N 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR N 200 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET N 170 " --> pdb=" O TYR N 200 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE N 202 " --> pdb=" O MET N 170 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'N' and resid 51 through 53 removed outlier: 3.565A pdb=" N VAL N 60 " --> pdb=" O ASN N 52 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 269 through 271 Processing sheet with id= BE, first strand: chain 'W' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG W 50 " --> pdb=" O VAL W 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS W 10 " --> pdb=" O THR W 296 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN W 78 " --> pdb=" O ARG W 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR W 297 " --> pdb=" O ASN W 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR W 80 " --> pdb=" O THR W 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL W 299 " --> pdb=" O THR W 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE W 82 " --> pdb=" O VAL W 299 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS W 301 " --> pdb=" O PHE W 82 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR W 84 " --> pdb=" O CYS W 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY W 79 " --> pdb=" O LYS W 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR W 228 " --> pdb=" O GLY W 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA W 83 " --> pdb=" O VAL W 230 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS W 213 " --> pdb=" O HIS W 129 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'W' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR W 38 " --> pdb=" O GLN W 34 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'W' and resid 207 through 210 Processing sheet with id= BH, first strand: chain 'W' and resid 155 through 157 Processing sheet with id= BI, first strand: chain 'F' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER F 6 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL F 74 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N HIS F 8 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 5 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 142 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 7 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER F 171 " --> pdb=" O PHE F 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL F 143 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 173 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS F 145 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE F 175 " --> pdb=" O HIS F 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS F 206 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER F 176 " --> pdb=" O CYS F 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE F 208 " --> pdb=" O SER F 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR F 178 " --> pdb=" O PHE F 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL F 210 " --> pdb=" O TYR F 178 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL F 68 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'F' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU F 324 " --> pdb=" O CYS F 382 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 384 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'O' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE O 64 " --> pdb=" O ILE O 4 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N HIS O 6 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL O 66 " --> pdb=" O HIS O 6 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN O 8 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL O 5 " --> pdb=" O GLN O 131 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE O 133 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE O 7 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU O 135 " --> pdb=" O ILE O 7 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA O 9 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS O 137 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE O 163 " --> pdb=" O PHE O 133 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU O 135 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN O 165 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N HIS O 137 " --> pdb=" O ASN O 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE O 167 " --> pdb=" O HIS O 137 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR O 200 " --> pdb=" O SER O 168 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET O 170 " --> pdb=" O TYR O 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE O 202 " --> pdb=" O MET O 170 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'O' and resid 51 through 53 removed outlier: 3.566A pdb=" N VAL O 60 " --> pdb=" O ASN O 52 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'O' and resid 269 through 271 Processing sheet with id= BO, first strand: chain 'X' and resid 50 through 52 removed outlier: 4.016A pdb=" N ARG X 50 " --> pdb=" O VAL X 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS X 10 " --> pdb=" O THR X 296 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN X 78 " --> pdb=" O ARG X 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR X 297 " --> pdb=" O ASN X 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR X 80 " --> pdb=" O THR X 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL X 299 " --> pdb=" O THR X 80 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE X 82 " --> pdb=" O VAL X 299 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS X 301 " --> pdb=" O PHE X 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR X 84 " --> pdb=" O CYS X 301 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY X 79 " --> pdb=" O LYS X 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR X 228 " --> pdb=" O GLY X 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA X 83 " --> pdb=" O VAL X 230 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS X 213 " --> pdb=" O HIS X 129 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'X' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR X 38 " --> pdb=" O GLN X 34 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'X' and resid 207 through 210 Processing sheet with id= BR, first strand: chain 'X' and resid 155 through 157 Processing sheet with id= BS, first strand: chain 'G' and resid 71 through 74 removed outlier: 7.231A pdb=" N SER G 6 " --> pdb=" O VAL G 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL G 74 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS G 8 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE G 5 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU G 142 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE G 7 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER G 171 " --> pdb=" O PHE G 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL G 143 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU G 173 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS G 145 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE G 175 " --> pdb=" O HIS G 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS G 206 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER G 176 " --> pdb=" O CYS G 206 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE G 208 " --> pdb=" O SER G 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR G 178 " --> pdb=" O PHE G 208 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL G 210 " --> pdb=" O TYR G 178 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL G 68 " --> pdb=" O SER G 60 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'G' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU G 324 " --> pdb=" O CYS G 382 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU G 384 " --> pdb=" O CYS G 322 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'P' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE P 64 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS P 6 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL P 66 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN P 8 " --> pdb=" O VAL P 66 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL P 5 " --> pdb=" O GLN P 131 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE P 133 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE P 7 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU P 135 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA P 9 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS P 137 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE P 163 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU P 135 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN P 165 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS P 137 " --> pdb=" O ASN P 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE P 167 " --> pdb=" O HIS P 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR P 200 " --> pdb=" O SER P 168 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET P 170 " --> pdb=" O TYR P 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE P 202 " --> pdb=" O MET P 170 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'P' and resid 51 through 53 removed outlier: 3.565A pdb=" N VAL P 60 " --> pdb=" O ASN P 52 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'P' and resid 269 through 271 Processing sheet with id= BY, first strand: chain 'Z' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG Z 50 " --> pdb=" O VAL Z 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS Z 10 " --> pdb=" O THR Z 296 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN Z 78 " --> pdb=" O ARG Z 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR Z 297 " --> pdb=" O ASN Z 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR Z 80 " --> pdb=" O THR Z 297 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL Z 299 " --> pdb=" O THR Z 80 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE Z 82 " --> pdb=" O VAL Z 299 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS Z 301 " --> pdb=" O PHE Z 82 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR Z 84 " --> pdb=" O CYS Z 301 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY Z 79 " --> pdb=" O LYS Z 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR Z 228 " --> pdb=" O GLY Z 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA Z 83 " --> pdb=" O VAL Z 230 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS Z 213 " --> pdb=" O HIS Z 129 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'Z' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR Z 38 " --> pdb=" O GLN Z 34 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'Z' and resid 207 through 210 Processing sheet with id= CB, first strand: chain 'Z' and resid 155 through 157 Processing sheet with id= CC, first strand: chain 'H' and resid 71 through 74 removed outlier: 7.232A pdb=" N SER H 6 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL H 74 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS H 8 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE H 5 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU H 142 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE H 7 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER H 171 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL H 143 " --> pdb=" O SER H 171 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU H 173 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS H 145 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N PHE H 175 " --> pdb=" O HIS H 145 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS H 206 " --> pdb=" O GLU H 174 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N SER H 176 " --> pdb=" O CYS H 206 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE H 208 " --> pdb=" O SER H 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR H 178 " --> pdb=" O PHE H 208 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL H 210 " --> pdb=" O TYR H 178 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.707A pdb=" N VAL H 68 " --> pdb=" O SER H 60 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'H' and resid 277 through 279 removed outlier: 3.675A pdb=" N LEU H 324 " --> pdb=" O CYS H 382 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 384 " --> pdb=" O CYS H 322 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'R' and resid 63 through 66 removed outlier: 8.890A pdb=" N ILE R 64 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N HIS R 6 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL R 66 " --> pdb=" O HIS R 6 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN R 8 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL R 5 " --> pdb=" O GLN R 131 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE R 133 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE R 7 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU R 135 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA R 9 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS R 137 " --> pdb=" O ALA R 9 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE R 163 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU R 135 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN R 165 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N HIS R 137 " --> pdb=" O ASN R 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE R 167 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR R 200 " --> pdb=" O SER R 168 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET R 170 " --> pdb=" O TYR R 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE R 202 " --> pdb=" O MET R 170 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'R' and resid 51 through 53 removed outlier: 3.565A pdb=" N VAL R 60 " --> pdb=" O ASN R 52 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'R' and resid 269 through 271 Processing sheet with id= CI, first strand: chain 'a' and resid 50 through 52 removed outlier: 4.015A pdb=" N ARG a 50 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS a 10 " --> pdb=" O THR a 296 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN a 78 " --> pdb=" O ARG a 295 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR a 297 " --> pdb=" O ASN a 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR a 80 " --> pdb=" O THR a 297 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL a 299 " --> pdb=" O THR a 80 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE a 82 " --> pdb=" O VAL a 299 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS a 301 " --> pdb=" O PHE a 82 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR a 84 " --> pdb=" O CYS a 301 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY a 79 " --> pdb=" O LYS a 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR a 228 " --> pdb=" O GLY a 79 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA a 83 " --> pdb=" O VAL a 230 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS a 213 " --> pdb=" O HIS a 129 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'a' and resid 32 through 34 removed outlier: 3.630A pdb=" N THR a 38 " --> pdb=" O GLN a 34 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'a' and resid 207 through 210 Processing sheet with id= CL, first strand: chain 'a' and resid 155 through 157 2730 hydrogen bonds defined for protein. 7191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 34.69 Time building geometry restraints manager: 30.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 28296 1.36 - 1.49: 21547 1.49 - 1.63: 35099 1.63 - 1.76: 27 1.76 - 1.90: 891 Bond restraints: 85860 Sorted by residual: bond pdb=" C1' G2P P 502 " pdb=" C2' G2P P 502 " ideal model delta sigma weight residual 1.537 1.268 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C1' G2P K 502 " pdb=" C2' G2P K 502 " ideal model delta sigma weight residual 1.537 1.269 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C1' G2P O 502 " pdb=" C2' G2P O 502 " ideal model delta sigma weight residual 1.537 1.269 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1' G2P M 502 " pdb=" C2' G2P M 502 " ideal model delta sigma weight residual 1.537 1.269 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1' G2P R 502 " pdb=" C2' G2P R 502 " ideal model delta sigma weight residual 1.537 1.269 0.268 2.00e-02 2.50e+03 1.79e+02 ... (remaining 85855 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.54: 3362 107.54 - 114.72: 48820 114.72 - 121.90: 44463 121.90 - 129.08: 18987 129.08 - 136.26: 810 Bond angle restraints: 116442 Sorted by residual: angle pdb=" PB ATP Z 401 " pdb=" O3B ATP Z 401 " pdb=" PG ATP Z 401 " ideal model delta sigma weight residual 139.87 120.69 19.18 1.00e+00 1.00e+00 3.68e+02 angle pdb=" PB ATP W 401 " pdb=" O3B ATP W 401 " pdb=" PG ATP W 401 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP U 401 " pdb=" O3B ATP U 401 " pdb=" PG ATP U 401 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP Y 401 " pdb=" O3B ATP Y 401 " pdb=" PG ATP Y 401 " ideal model delta sigma weight residual 139.87 120.72 19.15 1.00e+00 1.00e+00 3.67e+02 angle pdb=" PB ATP V 401 " pdb=" O3B ATP V 401 " pdb=" PG ATP V 401 " ideal model delta sigma weight residual 139.87 120.72 19.15 1.00e+00 1.00e+00 3.67e+02 ... (remaining 116437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.11: 49936 26.11 - 52.23: 1436 52.23 - 78.34: 324 78.34 - 104.45: 63 104.45 - 130.56: 18 Dihedral angle restraints: 51777 sinusoidal: 21069 harmonic: 30708 Sorted by residual: dihedral pdb=" C8 GTP R 501 " pdb=" C1' GTP R 501 " pdb=" N9 GTP R 501 " pdb=" O4' GTP R 501 " ideal model delta sinusoidal sigma weight residual 104.59 -25.97 130.56 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C8 GTP M 501 " pdb=" C1' GTP M 501 " pdb=" N9 GTP M 501 " pdb=" O4' GTP M 501 " ideal model delta sinusoidal sigma weight residual 104.59 -25.92 130.52 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C8 GTP K 501 " pdb=" C1' GTP K 501 " pdb=" N9 GTP K 501 " pdb=" O4' GTP K 501 " ideal model delta sinusoidal sigma weight residual 104.59 -25.91 130.50 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 51774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 10205 0.050 - 0.100: 2057 0.100 - 0.149: 498 0.149 - 0.199: 56 0.199 - 0.249: 9 Chirality restraints: 12825 Sorted by residual: chirality pdb=" C3' G2P Q 502 " pdb=" C2' G2P Q 502 " pdb=" C4' G2P Q 502 " pdb=" O3' G2P Q 502 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' G2P L 502 " pdb=" C2' G2P L 502 " pdb=" C4' G2P L 502 " pdb=" O3' G2P L 502 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C3' G2P J 502 " pdb=" C2' G2P J 502 " pdb=" C4' G2P J 502 " pdb=" O3' G2P J 502 " both_signs ideal model delta sigma weight residual False -2.71 -2.46 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 12822 not shown) Planarity restraints: 15075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 108 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO T 109 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO T 109 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO T 109 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Z 108 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO Z 109 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO Z 109 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO Z 109 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE U 108 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO U 109 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO U 109 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO U 109 " -0.026 5.00e-02 4.00e+02 ... (remaining 15072 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 2043 2.68 - 3.24: 84490 3.24 - 3.79: 131820 3.79 - 4.35: 189887 4.35 - 4.90: 300850 Nonbonded interactions: 709090 Sorted by model distance: nonbonded pdb=" OG1 THR F 185 " pdb=" O3' GTP O 501 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR C 185 " pdb=" O3' GTP L 501 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR E 185 " pdb=" O3' GTP N 501 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR G 185 " pdb=" O3' GTP P 501 " model vdw 2.131 2.440 nonbonded pdb=" OG1 THR H 185 " pdb=" O3' GTP R 501 " model vdw 2.131 2.440 ... (remaining 709085 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 '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' } ncs_group { reference = 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' } ncs_group { reference = 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' } 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: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 28.690 Check model and map are aligned: 1.230 Set scattering table: 0.620 Process input model: 176.770 Find NCS groups from input model: 4.700 Set up NCS constraints: 0.910 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 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 : 0.008 0.269 85860 Z= 0.500 Angle : 0.882 19.184 116442 Z= 0.506 Chirality : 0.045 0.249 12825 Planarity : 0.003 0.046 15075 Dihedral : 13.701 130.563 32067 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.46 % Allowed : 5.09 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -3.93 (0.06), residues: 10530 helix: -3.08 (0.05), residues: 4041 sheet: -2.15 (0.11), residues: 1755 loop : -2.18 (0.08), residues: 4734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 344 HIS 0.006 0.001 HIS G 113 PHE 0.015 0.001 PHE E 55 TYR 0.011 0.001 TYR R 50 ARG 0.003 0.001 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3412 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 3187 time to evaluate : 6.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 225 outliers final: 76 residues processed: 3336 average time/residue: 0.8577 time to fit residues: 4889.1874 Evaluate side-chains 2877 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 2801 time to evaluate : 6.898 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.6956 time to fit residues: 108.8215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 881 optimal weight: 7.9990 chunk 791 optimal weight: 6.9990 chunk 439 optimal weight: 8.9990 chunk 270 optimal weight: 0.9990 chunk 533 optimal weight: 0.1980 chunk 422 optimal weight: 2.9990 chunk 818 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 497 optimal weight: 2.9990 chunk 609 optimal weight: 0.1980 chunk 948 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 203 HIS ** I 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 GLN I 264 ASN I 348 GLN ** Q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN Q 52 ASN Q 105 HIS Q 165 ASN Q 190 HIS Q 280 GLN Q 298 ASN ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 416 ASN Q 423 GLN Y 8 ASN Y 160 ASN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 139 GLN A 198 HIS A 262 GLN J 165 ASN J 184 ASN ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 416 ASN J 426 GLN ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 255 ASN S 308 ASN B 28 HIS ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 262 GLN B 315 HIS B 348 GLN K 14 ASN K 52 ASN K 105 HIS K 165 ASN K 195 ASN ** K 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN K 375 GLN C 255 ASN C 262 GLN C 289 HIS L 48 ASN L 52 ASN ** L 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 ASN D 134 GLN D 203 HIS D 255 ASN D 262 GLN D 315 HIS ** D 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN M 52 ASN M 131 GLN M 165 ASN M 190 HIS M 227 HIS M 292 GLN ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 416 ASN V 160 ASN V 255 ASN V 263 ASN V 320 GLN ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN E 203 HIS E 262 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN N 165 ASN ** N 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 GLN W 255 ASN F 11 GLN F 255 ASN F 262 GLN ** O 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 ASN O 89 ASN O 105 HIS O 131 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 165 ASN O 195 ASN O 279 GLN O 329 GLN ** G 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 HIS ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN G 289 HIS ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN P 52 ASN P 131 GLN P 165 ASN P 184 ASN P 227 HIS P 292 GLN ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 ASN Z 255 ASN Z 320 GLN H 134 GLN H 139 GLN ** H 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 GLN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN R 52 ASN ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN R 256 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 416 ASN ** R 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 ASN Total number of N/Q/H flips: 100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 85860 Z= 0.192 Angle : 0.601 8.626 116442 Z= 0.305 Chirality : 0.044 0.185 12825 Planarity : 0.004 0.078 15075 Dihedral : 9.833 143.088 12231 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.42 % Allowed : 3.14 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -2.21 (0.07), residues: 10530 helix: -1.16 (0.07), residues: 4122 sheet: -1.65 (0.12), residues: 1683 loop : -1.54 (0.08), residues: 4725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP Q 21 HIS 0.010 0.001 HIS G 289 PHE 0.027 0.002 PHE K 367 TYR 0.029 0.001 TYR N 159 ARG 0.008 0.001 ARG M 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3173 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 3135 time to evaluate : 6.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 13 residues processed: 3154 average time/residue: 0.8441 time to fit residues: 4512.7794 Evaluate side-chains 2876 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 2863 time to evaluate : 6.888 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.7155 time to fit residues: 27.0219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 526 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 789 optimal weight: 0.0970 chunk 645 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 949 optimal weight: 3.9990 chunk 1026 optimal weight: 6.9990 chunk 845 optimal weight: 3.9990 chunk 941 optimal weight: 8.9990 chunk 323 optimal weight: 6.9990 chunk 761 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 28 HIS I 107 ASN Q 14 ASN ** Q 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN Q 184 ASN Q 247 ASN Q 280 GLN Q 292 GLN Y 160 ASN Y 263 ASN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 165 ASN J 195 ASN ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 GLN ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 160 ASN B 11 GLN B 28 HIS B 348 GLN K 14 ASN K 48 ASN K 131 GLN K 165 ASN K 335 ASN ** K 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN T 86 GLN T 160 ASN T 263 ASN C 28 HIS C 255 ASN C 289 HIS C 315 HIS ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 HIS L 131 GLN L 329 GLN ** U 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 289 HIS D 315 HIS ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 ASN M 48 ASN M 105 HIS ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 165 ASN M 190 HIS M 292 GLN M 307 HIS ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 160 ASN ** V 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 320 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS ** E 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN N 131 GLN N 184 ASN ** N 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 424 GLN W 160 ASN W 308 ASN F 113 HIS F 139 GLN F 239 GLN F 315 HIS F 348 GLN O 14 ASN ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS G 378 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN P 105 HIS P 165 ASN P 184 ASN P 292 GLN P 307 HIS P 329 GLN P 416 ASN Z 160 ASN Z 320 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN ** H 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN R 14 ASN R 15 GLN ** R 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 329 GLN R 424 GLN R 426 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 85860 Z= 0.245 Angle : 0.651 9.363 116442 Z= 0.335 Chirality : 0.046 0.270 12825 Planarity : 0.004 0.068 15075 Dihedral : 9.489 153.364 12231 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.19 % Allowed : 3.40 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.51 (0.08), residues: 10530 helix: -0.60 (0.07), residues: 4140 sheet: -1.21 (0.12), residues: 1647 loop : -1.16 (0.09), residues: 4743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Q 397 HIS 0.009 0.001 HIS L 264 PHE 0.032 0.002 PHE K 317 TYR 0.027 0.002 TYR N 159 ARG 0.009 0.001 ARG M 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3159 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 3142 time to evaluate : 7.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 3149 average time/residue: 0.8391 time to fit residues: 4454.7478 Evaluate side-chains 2902 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2897 time to evaluate : 6.989 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6124 time to fit residues: 15.7522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 938 optimal weight: 2.9990 chunk 714 optimal weight: 0.9990 chunk 492 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 453 optimal weight: 2.9990 chunk 637 optimal weight: 5.9990 chunk 953 optimal weight: 6.9990 chunk 1009 optimal weight: 0.1980 chunk 497 optimal weight: 10.0000 chunk 903 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Q 307 HIS Y 78 ASN Y 93 HIS ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS J 195 ASN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 GLN J 426 GLN S 160 ASN S 211 ASN B 315 HIS K 335 ASN K 370 ASN ** K 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 315 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN D 289 HIS D 315 HIS D 378 GLN M 190 HIS M 292 GLN ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS E 289 HIS E 362 ASN ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 HIS ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 HIS N 131 GLN N 184 ASN N 256 ASN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 ASN W 156 HIS W 160 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 239 GLN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN O 131 GLN ** O 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN X 60 GLN ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 190 HIS P 227 HIS P 307 HIS Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 378 GLN H 412 HIS R 37 HIS R 190 HIS R 256 ASN R 307 HIS a 255 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 85860 Z= 0.169 Angle : 0.584 8.835 116442 Z= 0.293 Chirality : 0.044 0.224 12825 Planarity : 0.004 0.082 15075 Dihedral : 9.224 153.118 12231 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.32 (0.08), residues: 10530 helix: -0.47 (0.08), residues: 4185 sheet: -0.97 (0.12), residues: 1728 loop : -1.07 (0.09), residues: 4617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Q 397 HIS 0.016 0.001 HIS O 105 PHE 0.024 0.001 PHE K 317 TYR 0.028 0.001 TYR I 24 ARG 0.011 0.000 ARG J 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3132 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 3125 time to evaluate : 6.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 3126 average time/residue: 0.8843 time to fit residues: 4681.1304 Evaluate side-chains 2932 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2930 time to evaluate : 6.956 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7181 time to fit residues: 12.4329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 840 optimal weight: 0.9990 chunk 572 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 751 optimal weight: 8.9990 chunk 416 optimal weight: 2.9990 chunk 861 optimal weight: 0.9990 chunk 697 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 515 optimal weight: 5.9990 chunk 905 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 298 ASN Q 307 HIS ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 63 ASN Y 78 ASN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 GLN A 11 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN T 198 ASN C 113 HIS C 289 HIS C 315 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 ASN L 384 GLN U 263 ASN ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 HIS D 315 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 320 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS E 307 GLN N 11 GLN ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 347 ASN W 156 HIS ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN F 239 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 227 HIS ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 298 ASN P 307 HIS P 384 GLN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS ** R 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 375 GLN ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 85860 Z= 0.220 Angle : 0.625 8.620 116442 Z= 0.319 Chirality : 0.045 0.241 12825 Planarity : 0.004 0.063 15075 Dihedral : 9.429 161.478 12231 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.24 (0.08), residues: 10530 helix: -0.48 (0.08), residues: 4167 sheet: -0.78 (0.12), residues: 1737 loop : -1.02 (0.09), residues: 4626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP Q 397 HIS 0.012 0.001 HIS H 289 PHE 0.027 0.002 PHE I 147 TYR 0.021 0.001 TYR G 230 ARG 0.009 0.000 ARG J 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3145 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3140 time to evaluate : 7.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 3140 average time/residue: 0.8427 time to fit residues: 4464.1330 Evaluate side-chains 2933 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2931 time to evaluate : 6.972 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.7119 time to fit residues: 12.9421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 339 optimal weight: 0.6980 chunk 908 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 592 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 chunk 1010 optimal weight: 6.9990 chunk 838 optimal weight: 1.9990 chunk 467 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 334 optimal weight: 9.9990 chunk 530 optimal weight: 0.0070 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 307 GLN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 HIS Q 375 GLN Q 416 ASN Q 426 GLN ** Y 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN J 131 GLN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 211 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN C 315 HIS C 348 GLN L 292 GLN L 384 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 198 ASN D 28 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 HIS ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS E 203 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 347 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 HIS F 239 GLN F 255 ASN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 298 ASN ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 ASN G 232 ASN P 99 ASN ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 ASN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 GLN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 307 GLN R 57 ASN R 190 HIS ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 414 ASN a 117 ASN a 160 ASN ** a 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 85860 Z= 0.189 Angle : 0.611 9.225 116442 Z= 0.308 Chirality : 0.045 0.265 12825 Planarity : 0.004 0.085 15075 Dihedral : 9.420 165.319 12231 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.09 % Allowed : 1.62 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.14 (0.08), residues: 10530 helix: -0.43 (0.08), residues: 4131 sheet: -0.62 (0.12), residues: 1746 loop : -0.97 (0.09), residues: 4653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP Q 397 HIS 0.014 0.001 HIS M 137 PHE 0.028 0.001 PHE M 389 TYR 0.031 0.001 TYR I 24 ARG 0.021 0.000 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3127 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3119 time to evaluate : 7.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 3121 average time/residue: 0.8480 time to fit residues: 4463.9732 Evaluate side-chains 2889 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2886 time to evaluate : 6.932 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7041 time to fit residues: 13.7471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 973 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 575 optimal weight: 0.8980 chunk 737 optimal weight: 0.9980 chunk 571 optimal weight: 10.0000 chunk 850 optimal weight: 1.9990 chunk 564 optimal weight: 9.9990 chunk 1006 optimal weight: 8.9990 chunk 629 optimal weight: 1.9990 chunk 613 optimal weight: 1.9990 chunk 464 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Q 307 HIS ** Q 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 426 GLN Y 160 ASN Y 320 GLN A 264 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 190 HIS ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 414 ASN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 ASN B 192 ASN B 232 ASN B 315 HIS ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN C 348 GLN L 335 ASN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 347 ASN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS E 255 ASN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 222 ASN F 239 GLN F 262 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 134 GLN O 227 HIS O 298 ASN ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 GLN Z 320 GLN H 239 GLN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS ** H 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 85860 Z= 0.184 Angle : 0.613 8.824 116442 Z= 0.309 Chirality : 0.045 0.293 12825 Planarity : 0.004 0.077 15075 Dihedral : 9.515 167.904 12231 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.08 % Allowed : 1.19 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.03 (0.08), residues: 10530 helix: -0.37 (0.08), residues: 4059 sheet: -0.56 (0.12), residues: 1809 loop : -0.87 (0.09), residues: 4662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 397 HIS 0.012 0.001 HIS H 289 PHE 0.028 0.001 PHE R 270 TYR 0.023 0.001 TYR G 278 ARG 0.008 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3125 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 3118 time to evaluate : 6.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 3119 average time/residue: 0.8567 time to fit residues: 4505.1226 Evaluate side-chains 2907 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2903 time to evaluate : 6.889 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6877 time to fit residues: 15.0421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 622 optimal weight: 7.9990 chunk 401 optimal weight: 3.9990 chunk 600 optimal weight: 0.3980 chunk 303 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 639 optimal weight: 0.5980 chunk 685 optimal weight: 6.9990 chunk 497 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 790 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 ASN Q 292 GLN Q 298 ASN Q 307 HIS ** Q 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 60 GLN Y 320 GLN A 264 ASN J 11 GLN J 131 GLN J 134 GLN ** J 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 416 ASN S 117 ASN B 192 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 198 ASN C 232 ASN L 370 ASN ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS E 203 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 GLN ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 416 ASN N 424 GLN W 263 ASN F 139 GLN F 239 GLN F 262 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN O 28 HIS O 134 GLN O 298 ASN O 337 ASN ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 334 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 ASN H 289 HIS R 134 GLN ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 85860 Z= 0.207 Angle : 0.640 9.934 116442 Z= 0.324 Chirality : 0.046 0.289 12825 Planarity : 0.004 0.068 15075 Dihedral : 9.620 171.437 12231 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.04 % Allowed : 0.87 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.02 (0.08), residues: 10530 helix: -0.40 (0.08), residues: 4086 sheet: -0.52 (0.12), residues: 1809 loop : -0.83 (0.09), residues: 4635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP Q 397 HIS 0.017 0.001 HIS F 289 PHE 0.029 0.001 PHE R 270 TYR 0.027 0.001 TYR W 120 ARG 0.013 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3131 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 3127 time to evaluate : 6.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 3129 average time/residue: 0.8884 time to fit residues: 4706.5802 Evaluate side-chains 2953 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2953 time to evaluate : 6.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 915 optimal weight: 9.9990 chunk 964 optimal weight: 0.7980 chunk 879 optimal weight: 1.9990 chunk 937 optimal weight: 5.9990 chunk 963 optimal weight: 2.9990 chunk 564 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 chunk 736 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 847 optimal weight: 7.9990 chunk 886 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Q 307 HIS ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 GLN ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 426 GLN Y 320 GLN A 15 GLN A 264 ASN J 11 GLN J 131 GLN ** J 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 416 ASN S 117 ASN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN T 86 GLN C 291 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN L 334 GLN U 93 HIS D 234 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 HIS ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 GLN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS E 239 GLN ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN E 412 HIS ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 416 ASN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 222 ASN F 239 GLN F 262 GLN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 134 GLN O 298 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN G 198 HIS G 289 HIS G 291 GLN P 137 HIS ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 85860 Z= 0.318 Angle : 0.748 10.189 116442 Z= 0.388 Chirality : 0.049 0.314 12825 Planarity : 0.005 0.104 15075 Dihedral : 10.212 179.767 12231 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.03 % Allowed : 0.69 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.42 (0.08), residues: 10530 helix: -0.75 (0.08), residues: 4212 sheet: -0.59 (0.13), residues: 1701 loop : -1.10 (0.09), residues: 4617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP Q 397 HIS 0.012 0.002 HIS M 137 PHE 0.034 0.002 PHE N 367 TYR 0.042 0.002 TYR N 159 ARG 0.013 0.001 ARG D 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3218 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3215 time to evaluate : 6.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3215 average time/residue: 0.8583 time to fit residues: 4647.7748 Evaluate side-chains 3007 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 3006 time to evaluate : 6.960 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7308 time to fit residues: 11.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 934 optimal weight: 5.9990 chunk 615 optimal weight: 7.9990 chunk 991 optimal weight: 9.9990 chunk 605 optimal weight: 0.0170 chunk 470 optimal weight: 0.9990 chunk 689 optimal weight: 2.9990 chunk 1040 optimal weight: 6.9990 chunk 957 optimal weight: 0.9990 chunk 828 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 639 optimal weight: 0.4980 overall best weight: 1.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 GLN Q 245 GLN Q 307 HIS ** Q 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 384 GLN Q 424 GLN ** Q 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN A 56 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 272 HIS ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN J 131 GLN ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 ASN ** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 HIS B 291 GLN B 307 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN C 291 GLN L 334 GLN L 335 ASN D 234 ASN ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 HIS M 292 GLN ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS E 203 HIS E 239 GLN E 264 ASN E 289 HIS E 362 ASN E 412 HIS N 14 ASN N 57 ASN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 337 ASN W 117 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 134 GLN O 298 ASN X 60 GLN P 227 HIS P 334 GLN Z 63 ASN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN H 232 ASN H 239 GLN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 412 HIS R 105 HIS ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 85860 Z= 0.189 Angle : 0.662 9.430 116442 Z= 0.334 Chirality : 0.046 0.376 12825 Planarity : 0.004 0.095 15075 Dihedral : 9.935 172.867 12231 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.18 (0.08), residues: 10530 helix: -0.60 (0.08), residues: 4176 sheet: -0.48 (0.13), residues: 1692 loop : -0.91 (0.09), residues: 4662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP G 394 HIS 0.013 0.001 HIS M 137 PHE 0.032 0.002 PHE H 155 TYR 0.033 0.002 TYR N 159 ARG 0.015 0.001 ARG L 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21060 Ramachandran restraints generated. 10530 Oldfield, 0 Emsley, 10530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3170 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3170 time to evaluate : 7.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3170 average time/residue: 0.8545 time to fit residues: 4572.6408 Evaluate side-chains 2959 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2959 time to evaluate : 6.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.8772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1044 random chunks: chunk 507 optimal weight: 3.9990 chunk 657 optimal weight: 6.9990 chunk 882 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 763 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 829 optimal weight: 0.2980 chunk 347 optimal weight: 4.9990 chunk 851 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 HIS Q 347 ASN Q 416 ASN Q 426 GLN Y 160 ASN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 134 GLN ** J 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 416 ASN S 117 ASN B 222 ASN B 289 HIS B 307 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN T 58 GLN C 203 HIS C 291 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 GLN D 67 HIS ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 HIS M 292 GLN M 298 ASN ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 424 GLN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 203 HIS E 264 ASN E 362 ASN N 131 GLN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 416 ASN ** W 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 117 ASN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 222 ASN F 239 GLN ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 134 GLN O 348 ASN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 334 GLN ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN H 289 HIS R 28 HIS ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.166264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.133713 restraints weight = 141337.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.138439 restraints weight = 79136.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.141682 restraints weight = 49305.570| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 85860 Z= 0.217 Angle : 0.681 9.439 116442 Z= 0.346 Chirality : 0.047 0.367 12825 Planarity : 0.005 0.166 15075 Dihedral : 9.981 173.718 12231 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.21 (0.08), residues: 10530 helix: -0.59 (0.08), residues: 4113 sheet: -0.45 (0.13), residues: 1746 loop : -1.00 (0.09), residues: 4671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP R 397 HIS 0.015 0.001 HIS R 396 PHE 0.037 0.002 PHE R 266 TYR 0.031 0.002 TYR F 230 ARG 0.021 0.001 ARG G 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51939.14 seconds wall clock time: 907 minutes 26.78 seconds (54446.78 seconds total)