Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 09:39:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/10_2023/8ixd_35791_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/10_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_35791/10_2023/8ixd_35791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/10_2023/8ixd_35791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/10_2023/8ixd_35791_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixd_35791/10_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: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 31.65, 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: 25.86 Conformation dependent library (CDL) restraints added in 9.2 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: 10.38 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: 33.18 Time building geometry restraints manager: 28.31 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: 49684 26.11 - 52.23: 1301 52.23 - 78.34: 207 78.34 - 104.45: 36 104.45 - 130.56: 18 Dihedral angle restraints: 51246 sinusoidal: 20538 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 51243 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 28.220 Check model and map are aligned: 0.980 Set scattering table: 0.610 Process input model: 170.120 Find NCS groups from input model: 4.650 Set up NCS constraints: 0.830 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: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.840 ------------------------------------------------------------------------------- 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 : 12.663 130.563 31536 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 *********************** 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 : 6.919 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: 0.7983 time to fit residues: 4506.6841 Evaluate side-chains 2877 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 2801 time to evaluate : 7.003 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.6460 time to fit residues: 101.7785 ------------------------------------------------------------------------------- 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 105 HIS 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 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 ** U 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 416 ASN V 160 ASN V 255 ASN V 263 ASN ** V 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 52 ASN ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN R 165 ASN 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** Total number of N/Q/H flips: 99 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 85860 Z= 0.191 Angle : 0.598 8.971 116442 Z= 0.304 Chirality : 0.044 0.190 12825 Planarity : 0.004 0.078 15075 Dihedral : 7.809 142.699 11700 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.40 % Allowed : 3.08 % Favored : 96.51 % 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: -2.19 (0.07), residues: 10530 helix: -1.11 (0.07), residues: 4077 sheet: -1.65 (0.12), residues: 1674 loop : -1.54 (0.08), residues: 4779 *********************** 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 3165 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 3128 time to evaluate : 6.942 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 outliers start: 37 outliers final: 10 residues processed: 3147 average time/residue: 0.8375 time to fit residues: 4460.5047 Evaluate side-chains 2867 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2857 time to evaluate : 6.859 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6741 time to fit residues: 22.2148 ------------------------------------------------------------------------------- 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: 7.9990 chunk 294 optimal weight: 1.9990 chunk 789 optimal weight: 9.9990 chunk 645 optimal weight: 0.9990 chunk 261 optimal weight: 0.0010 chunk 949 optimal weight: 5.9990 chunk 1026 optimal weight: 9.9990 chunk 845 optimal weight: 5.9990 chunk 941 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 761 optimal weight: 5.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 28 HIS I 378 GLN ** Q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN ** Q 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN Q 247 ASN Q 280 GLN Q 292 GLN Y 63 ASN 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 306 ASN A 307 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 ASN J 105 HIS J 165 ASN J 195 ASN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 GLN ** 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 139 GLN B 348 GLN K 14 ASN K 48 ASN K 105 HIS K 131 GLN K 165 ASN K 335 ASN ** K 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN T 86 GLN T 263 ASN 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 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 320 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 190 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 GLN ** O 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 ASN O 48 ASN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN G 306 ASN G 315 HIS G 378 GLN P 14 ASN P 105 HIS P 165 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 11 GLN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN R 48 ASN ** R 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 329 GLN R 423 GLN R 424 GLN R 426 GLN Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 85860 Z= 0.284 Angle : 0.697 9.401 116442 Z= 0.363 Chirality : 0.047 0.252 12825 Planarity : 0.005 0.069 15075 Dihedral : 8.470 156.819 11700 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.22 % Allowed : 3.79 % Favored : 95.99 % 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: -1.61 (0.08), residues: 10530 helix: -0.69 (0.07), residues: 4158 sheet: -1.35 (0.11), residues: 1719 loop : -1.15 (0.09), residues: 4653 *********************** 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 3201 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 3181 time to evaluate : 6.952 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 outliers start: 20 outliers final: 8 residues processed: 3189 average time/residue: 0.8013 time to fit residues: 4295.6083 Evaluate side-chains 2922 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2914 time to evaluate : 6.983 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5792 time to fit residues: 18.7065 ------------------------------------------------------------------------------- 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: 0.9990 chunk 714 optimal weight: 0.9990 chunk 492 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 453 optimal weight: 0.0970 chunk 637 optimal weight: 1.9990 chunk 953 optimal weight: 9.9990 chunk 1009 optimal weight: 4.9990 chunk 497 optimal weight: 1.9990 chunk 903 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 298 ASN Q 307 HIS Y 78 ASN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN J 37 HIS J 195 ASN ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 424 GLN S 160 ASN S 211 ASN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS ** K 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN K 370 ASN ** K 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS C 289 HIS C 315 HIS C 362 ASN ** L 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 289 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 HIS M 292 GLN ** V 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 320 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 HIS ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 184 ASN N 256 ASN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 117 ASN W 156 HIS W 160 ASN F 15 GLN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 203 HIS F 239 GLN F 255 ASN F 315 HIS O 28 HIS O 298 ASN ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 60 GLN ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN G 315 HIS P 190 HIS P 307 HIS P 329 GLN Z 160 ASN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 HIS H 378 GLN H 412 HIS R 14 ASN R 307 HIS R 423 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 85860 Z= 0.164 Angle : 0.583 8.731 116442 Z= 0.293 Chirality : 0.044 0.230 12825 Planarity : 0.004 0.070 15075 Dihedral : 8.065 155.221 11700 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.08 % Allowed : 2.26 % Favored : 97.66 % 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: -0.44 (0.08), residues: 4122 sheet: -1.01 (0.12), residues: 1719 loop : -1.08 (0.09), residues: 4689 *********************** 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 3115 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 3108 time to evaluate : 6.957 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 outliers start: 7 outliers final: 3 residues processed: 3110 average time/residue: 0.8114 time to fit residues: 4239.1914 Evaluate side-chains 2910 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2907 time to evaluate : 8.677 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.7139 time to fit residues: 13.8993 ------------------------------------------------------------------------------- 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: 7.9990 chunk 572 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 751 optimal weight: 10.0000 chunk 416 optimal weight: 0.7980 chunk 861 optimal weight: 0.7980 chunk 697 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 515 optimal weight: 0.3980 chunk 905 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 307 GLN Q 307 HIS ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 ASN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 287 GLN Y 320 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 165 ASN 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN ** K 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 198 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS C 315 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN D 289 HIS D 315 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 GLN ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 198 HIS ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 362 ASN N 11 GLN ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 ASN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 156 HIS ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 HIS F 255 ASN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** O 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 329 GLN ** X 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN P 298 ASN P 307 HIS ** P 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS H 289 HIS ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 375 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.5352 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= 0.192 Angle : 0.602 9.271 116442 Z= 0.305 Chirality : 0.045 0.248 12825 Planarity : 0.004 0.060 15075 Dihedral : 8.216 160.906 11700 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % 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: -1.20 (0.08), residues: 10530 helix: -0.41 (0.08), residues: 4095 sheet: -0.79 (0.12), residues: 1728 loop : -1.01 (0.09), residues: 4707 *********************** 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 3132 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3129 time to evaluate : 6.868 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: 3130 average time/residue: 0.8169 time to fit residues: 4294.3659 Evaluate side-chains 2910 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 2909 time to evaluate : 6.903 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6997 time to fit residues: 11.0746 ------------------------------------------------------------------------------- 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: 1.9990 chunk 592 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 1010 optimal weight: 9.9990 chunk 838 optimal weight: 0.6980 chunk 467 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 530 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 ASN Q 307 HIS Q 337 ASN Q 375 GLN ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 426 GLN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN J 11 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN B 307 GLN B 315 HIS K 335 ASN C 113 HIS C 315 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN L 335 ASN L 337 ASN L 384 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 HIS ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 63 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 416 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 HIS F 222 ASN F 239 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 134 GLN ** O 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN O 337 ASN ** X 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 ASN G 234 ASN G 306 ASN G 315 HIS P 99 ASN ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 307 HIS Z 263 ASN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN H 239 GLN H 289 HIS H 307 GLN ** R 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 HIS ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 414 ASN a 117 ASN a 160 ASN a 255 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 85860 Z= 0.275 Angle : 0.674 9.450 116442 Z= 0.349 Chirality : 0.047 0.260 12825 Planarity : 0.005 0.082 15075 Dihedral : 8.683 174.676 11700 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.07 % Allowed : 2.11 % Favored : 97.83 % 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: -1.30 (0.08), residues: 10530 helix: -0.58 (0.08), residues: 4185 sheet: -0.76 (0.12), residues: 1692 loop : -1.02 (0.09), residues: 4653 *********************** 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 3195 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 3189 time to evaluate : 6.914 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 outliers start: 6 outliers final: 4 residues processed: 3191 average time/residue: 0.8311 time to fit residues: 4464.5832 Evaluate side-chains 2990 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2986 time to evaluate : 7.044 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6368 time to fit residues: 14.5735 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 5.9990 chunk 575 optimal weight: 6.9990 chunk 737 optimal weight: 9.9990 chunk 571 optimal weight: 7.9990 chunk 850 optimal weight: 0.8980 chunk 564 optimal weight: 9.9990 chunk 1006 optimal weight: 3.9990 chunk 629 optimal weight: 0.4980 chunk 613 optimal weight: 2.9990 chunk 464 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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** ** I 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 245 GLN Q 307 HIS ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 426 GLN Y 63 ASN Y 160 ASN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 GLN A 15 GLN A 264 ASN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 134 GLN ** J 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 347 ASN ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 ASN S 211 ASN B 291 GLN B 307 GLN B 412 HIS ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 ASN ** K 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN ** M 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 GLN ** 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 198 HIS E 362 ASN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 416 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 HIS F 239 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 60 GLN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 HIS G 315 HIS ** G 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 190 HIS P 384 GLN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN ** H 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 57 ASN ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN a 160 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 85860 Z= 0.274 Angle : 0.691 10.578 116442 Z= 0.356 Chirality : 0.048 0.301 12825 Planarity : 0.005 0.088 15075 Dihedral : 8.894 179.183 11700 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.09 % Allowed : 1.56 % Favored : 98.35 % 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: -1.39 (0.08), residues: 10530 helix: -0.65 (0.08), residues: 4059 sheet: -0.82 (0.12), residues: 1719 loop : -1.07 (0.09), residues: 4752 *********************** 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 3224 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3216 time to evaluate : 6.994 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 outliers start: 8 outliers final: 3 residues processed: 3217 average time/residue: 0.8208 time to fit residues: 4433.1464 Evaluate side-chains 3006 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3003 time to evaluate : 7.078 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6257 time to fit residues: 13.3349 ------------------------------------------------------------------------------- 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: 10.0000 chunk 401 optimal weight: 0.1980 chunk 600 optimal weight: 0.0980 chunk 303 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 639 optimal weight: 0.0000 chunk 685 optimal weight: 4.9990 chunk 497 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 790 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 GLN Q 245 GLN Q 292 GLN Q 307 HIS ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 160 ASN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 GLN A 15 GLN ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 HIS ** J 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** S 117 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 280 GLN ** K 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN T 198 ASN C 289 HIS C 348 GLN L 335 ASN M 190 HIS M 264 HIS ** M 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN E 239 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN ** N 14 ASN ** 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 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 ASN F 139 GLN F 203 HIS F 262 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 264 HIS O 298 ASN ** O 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 HIS ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 306 ASN P 134 GLN P 137 HIS P 334 GLN ** P 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 370 ASN Z 63 ASN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN H 232 ASN H 255 ASN H 289 HIS H 412 HIS R 37 HIS ** R 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN ** R 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN ** a 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 85860 Z= 0.168 Angle : 0.624 11.151 116442 Z= 0.313 Chirality : 0.045 0.206 12825 Planarity : 0.004 0.069 15075 Dihedral : 8.588 172.306 11700 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.05 % Allowed : 0.82 % Favored : 99.13 % 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: -1.23 (0.08), residues: 10530 helix: -0.53 (0.08), residues: 4221 sheet: -0.64 (0.12), residues: 1737 loop : -1.01 (0.09), residues: 4572 *********************** 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 3172 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 3167 time to evaluate : 6.939 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 outliers start: 5 outliers final: 4 residues processed: 3169 average time/residue: 0.8092 time to fit residues: 4318.0813 Evaluate side-chains 2969 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2965 time to evaluate : 6.971 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6462 time to fit residues: 14.5711 ------------------------------------------------------------------------------- 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: 0.0470 chunk 964 optimal weight: 10.0000 chunk 879 optimal weight: 1.9990 chunk 937 optimal weight: 5.9990 chunk 963 optimal weight: 0.0040 chunk 564 optimal weight: 0.2980 chunk 408 optimal weight: 0.9990 chunk 736 optimal weight: 0.3980 chunk 287 optimal weight: 7.9990 chunk 847 optimal weight: 0.0980 chunk 886 optimal weight: 1.9990 overall best weight: 0.1690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 GLN Q 292 GLN Q 307 HIS ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 320 GLN A 107 ASN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN J 11 GLN J 131 GLN ** J 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 GLN ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** S 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 ASN B 192 ASN B 203 HIS ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 GLN ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 HIS ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS E 239 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 362 ASN N 14 ASN ** N 99 ASN ** 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 416 ASN W 117 ASN F 139 GLN F 222 ASN F 239 GLN F 255 ASN F 262 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN O 370 ASN G 192 ASN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 GLN P 134 GLN ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 298 ASN ** P 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 424 GLN Z 320 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN H 239 GLN H 255 ASN H 289 HIS H 412 HIS R 37 HIS ** R 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 117 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 85860 Z= 0.157 Angle : 0.611 12.950 116442 Z= 0.305 Chirality : 0.044 0.208 12825 Planarity : 0.004 0.081 15075 Dihedral : 8.372 168.501 11700 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.08 % Allowed : 0.48 % Favored : 99.44 % 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: -0.47 (0.08), residues: 4140 sheet: -0.31 (0.13), residues: 1701 loop : -0.86 (0.09), residues: 4689 *********************** 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 3139 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 3132 time to evaluate : 6.918 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: 3 residues processed: 3132 average time/residue: 0.8115 time to fit residues: 4280.0406 Evaluate side-chains 2908 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2905 time to evaluate : 6.855 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6398 time to fit residues: 13.3331 ------------------------------------------------------------------------------- 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: 2.9990 chunk 615 optimal weight: 0.9980 chunk 991 optimal weight: 5.9990 chunk 605 optimal weight: 0.9990 chunk 470 optimal weight: 1.9990 chunk 689 optimal weight: 1.9990 chunk 1040 optimal weight: 0.6980 chunk 957 optimal weight: 0.9980 chunk 828 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 639 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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** I 289 HIS ** I 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 131 GLN Q 134 GLN Q 292 GLN ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 ASN B 239 GLN ** K 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 ASN ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 58 GLN ** L 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 HIS M 227 HIS ** M 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 320 GLN E 239 GLN E 362 ASN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 117 ASN F 113 HIS F 139 GLN F 145 HIS F 222 ASN F 255 ASN F 262 GLN F 289 HIS ** F 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS ** O 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 198 ASN G 192 ASN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 134 GLN ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN H 239 GLN H 255 ASN H 289 HIS ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 HIS a 117 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.6687 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= 0.168 Angle : 0.624 11.777 116442 Z= 0.311 Chirality : 0.044 0.361 12825 Planarity : 0.004 0.091 15075 Dihedral : 8.253 170.310 11700 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.04 % Allowed : 0.24 % Favored : 99.72 % 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: -0.95 (0.08), residues: 10530 helix: -0.45 (0.08), residues: 4149 sheet: -0.13 (0.13), residues: 1683 loop : -0.85 (0.09), residues: 4698 ********************** 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 3093 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 3089 time to evaluate : 6.959 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 outliers start: 4 outliers final: 2 residues processed: 3089 average time/residue: 0.8256 time to fit residues: 4284.8544 Evaluate side-chains 2884 residues out of total 9153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2882 time to evaluate : 6.924 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6907 time to fit residues: 12.2669 ------------------------------------------------------------------------------- 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: 6.9990 chunk 657 optimal weight: 0.0770 chunk 882 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 763 optimal weight: 0.0570 chunk 122 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 829 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 851 optimal weight: 7.9990 chunk 105 optimal weight: 0.0370 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 11 GLN ** I 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 GLN Q 292 GLN Q 307 HIS ** Q 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 375 GLN Q 416 ASN ** Q 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 426 GLN ** Y 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 306 ASN J 131 GLN ** J 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 ASN B 203 HIS ** K 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 335 ASN L 337 ASN ** L 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN D 378 GLN D 386 ASN ** M 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 HIS ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS E 239 GLN E 362 ASN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 337 ASN N 426 GLN ** W 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 117 ASN F 139 GLN F 222 ASN F 289 HIS F 348 GLN ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 378 GLN P 89 ASN ** P 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 184 ASN P 227 HIS ** P 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN H 239 GLN H 289 HIS H 348 GLN R 37 HIS ** R 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 HIS a 117 ASN a 255 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.171407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.137720 restraints weight = 140127.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.142603 restraints weight = 79783.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.145937 restraints weight = 50149.755| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 85860 Z= 0.160 Angle : 0.616 12.076 116442 Z= 0.306 Chirality : 0.044 0.332 12825 Planarity : 0.004 0.097 15075 Dihedral : 8.121 168.374 11700 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.05 % Allowed : 0.31 % Favored : 99.64 % 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: -0.93 (0.08), residues: 10530 helix: -0.45 (0.08), residues: 4131 sheet: -0.02 (0.13), residues: 1683 loop : -0.86 (0.09), residues: 4716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49447.13 seconds wall clock time: 854 minutes 7.91 seconds (51247.91 seconds total)