Starting phenix.real_space_refine (version: dev) on Tue Dec 13 23:34:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/12_2022/7eep_31079.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/12_2022/7eep_31079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/12_2022/7eep_31079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/12_2022/7eep_31079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/12_2022/7eep_31079.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/12_2022/7eep_31079.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 173": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ARG 576": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 285": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 505": "NH1" <-> "NH2" Residue "D ARG 533": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 285": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E ARG 366": "NH1" <-> "NH2" Residue "E ARG 413": "NH1" <-> "NH2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 505": "NH1" <-> "NH2" Residue "E ARG 533": "NH1" <-> "NH2" Residue "E ARG 534": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 223": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 233": "NH1" <-> "NH2" Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 259": "NH1" <-> "NH2" Residue "F ARG 270": "NH1" <-> "NH2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 285": "NH1" <-> "NH2" Residue "F ARG 297": "NH1" <-> "NH2" Residue "F ARG 366": "NH1" <-> "NH2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "F ARG 505": "NH1" <-> "NH2" Residue "F ARG 533": "NH1" <-> "NH2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 233": "NH1" <-> "NH2" Residue "G PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 270": "NH1" <-> "NH2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 297": "NH1" <-> "NH2" Residue "G ARG 366": "NH1" <-> "NH2" Residue "G ARG 413": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 505": "NH1" <-> "NH2" Residue "G ARG 533": "NH1" <-> "NH2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ARG 536": "NH1" <-> "NH2" Residue "G ARG 576": "NH1" <-> "NH2" Residue "H ARG 21": "NH1" <-> "NH2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H ARG 223": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H ARG 270": "NH1" <-> "NH2" Residue "H TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 285": "NH1" <-> "NH2" Residue "H ARG 297": "NH1" <-> "NH2" Residue "H ARG 366": "NH1" <-> "NH2" Residue "H ARG 413": "NH1" <-> "NH2" Residue "H ARG 418": "NH1" <-> "NH2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H ARG 505": "NH1" <-> "NH2" Residue "H ARG 533": "NH1" <-> "NH2" Residue "H ARG 534": "NH1" <-> "NH2" Residue "H ARG 536": "NH1" <-> "NH2" Residue "H ARG 576": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 146": "NH1" <-> "NH2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I ARG 157": "NH1" <-> "NH2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 173": "NH1" <-> "NH2" Residue "I ARG 223": "NH1" <-> "NH2" Residue "I ARG 224": "NH1" <-> "NH2" Residue "I ARG 233": "NH1" <-> "NH2" Residue "I PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 259": "NH1" <-> "NH2" Residue "I ARG 270": "NH1" <-> "NH2" Residue "I TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 285": "NH1" <-> "NH2" Residue "I ARG 297": "NH1" <-> "NH2" Residue "I ARG 366": "NH1" <-> "NH2" Residue "I ARG 413": "NH1" <-> "NH2" Residue "I ARG 418": "NH1" <-> "NH2" Residue "I ARG 420": "NH1" <-> "NH2" Residue "I ARG 505": "NH1" <-> "NH2" Residue "I ARG 533": "NH1" <-> "NH2" Residue "I ARG 534": "NH1" <-> "NH2" Residue "I ARG 536": "NH1" <-> "NH2" Residue "I ARG 576": "NH1" <-> "NH2" Residue "J ARG 21": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J ARG 155": "NH1" <-> "NH2" Residue "J ARG 157": "NH1" <-> "NH2" Residue "J PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "J ARG 223": "NH1" <-> "NH2" Residue "J ARG 224": "NH1" <-> "NH2" Residue "J ARG 233": "NH1" <-> "NH2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 259": "NH1" <-> "NH2" Residue "J ARG 270": "NH1" <-> "NH2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 285": "NH1" <-> "NH2" Residue "J ARG 297": "NH1" <-> "NH2" Residue "J ARG 366": "NH1" <-> "NH2" Residue "J ARG 413": "NH1" <-> "NH2" Residue "J ARG 418": "NH1" <-> "NH2" Residue "J ARG 420": "NH1" <-> "NH2" Residue "J ARG 505": "NH1" <-> "NH2" Residue "J ARG 533": "NH1" <-> "NH2" Residue "J ARG 534": "NH1" <-> "NH2" Residue "J ARG 536": "NH1" <-> "NH2" Residue "J ARG 576": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 35": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ARG 103": "NH1" <-> "NH2" Residue "K ARG 117": "NH1" <-> "NH2" Residue "K ARG 146": "NH1" <-> "NH2" Residue "K ARG 155": "NH1" <-> "NH2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 173": "NH1" <-> "NH2" Residue "K ARG 223": "NH1" <-> "NH2" Residue "K ARG 224": "NH1" <-> "NH2" Residue "K ARG 233": "NH1" <-> "NH2" Residue "K PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "K TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 285": "NH1" <-> "NH2" Residue "K ARG 297": "NH1" <-> "NH2" Residue "K ARG 366": "NH1" <-> "NH2" Residue "K ARG 413": "NH1" <-> "NH2" Residue "K ARG 418": "NH1" <-> "NH2" Residue "K ARG 420": "NH1" <-> "NH2" Residue "K ARG 505": "NH1" <-> "NH2" Residue "K ARG 533": "NH1" <-> "NH2" Residue "K ARG 534": "NH1" <-> "NH2" Residue "K ARG 536": "NH1" <-> "NH2" Residue "K ARG 576": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "L ARG 87": "NH1" <-> "NH2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L ARG 117": "NH1" <-> "NH2" Residue "L ARG 146": "NH1" <-> "NH2" Residue "L ARG 155": "NH1" <-> "NH2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 173": "NH1" <-> "NH2" Residue "L ARG 223": "NH1" <-> "NH2" Residue "L ARG 224": "NH1" <-> "NH2" Residue "L ARG 233": "NH1" <-> "NH2" Residue "L PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 259": "NH1" <-> "NH2" Residue "L ARG 270": "NH1" <-> "NH2" Residue "L TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 285": "NH1" <-> "NH2" Residue "L ARG 297": "NH1" <-> "NH2" Residue "L ARG 366": "NH1" <-> "NH2" Residue "L ARG 413": "NH1" <-> "NH2" Residue "L ARG 418": "NH1" <-> "NH2" Residue "L ARG 420": "NH1" <-> "NH2" Residue "L ARG 505": "NH1" <-> "NH2" Residue "L ARG 533": "NH1" <-> "NH2" Residue "L ARG 534": "NH1" <-> "NH2" Residue "L ARG 536": "NH1" <-> "NH2" Residue "L ARG 576": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M ARG 160": "NH1" <-> "NH2" Residue "N ARG 5": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "N ARG 160": "NH1" <-> "NH2" Residue "O ARG 5": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 160": "NH1" <-> "NH2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 160": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 22": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 114": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ARG 22": "NH1" <-> "NH2" Residue "S ARG 114": "NH1" <-> "NH2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "T ARG 114": "NH1" <-> "NH2" Residue "T ARG 160": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ARG 114": "NH1" <-> "NH2" Residue "U ARG 160": "NH1" <-> "NH2" Residue "V ARG 5": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ARG 114": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "W ARG 5": "NH1" <-> "NH2" Residue "W ARG 22": "NH1" <-> "NH2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "W ARG 160": "NH1" <-> "NH2" Residue "X ARG 5": "NH1" <-> "NH2" Residue "X ARG 22": "NH1" <-> "NH2" Residue "X ARG 114": "NH1" <-> "NH2" Residue "X ARG 160": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 68076 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "B" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "C" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "D" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "E" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "F" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "G" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "H" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "I" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "J" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "K" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "L" Number of atoms: 4274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4274 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain breaks: 3 Chain: "M" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "N" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "O" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "P" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "Q" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "R" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "S" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "U" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "V" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "W" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "X" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1399 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Time building chain proxies: 27.99, per 1000 atoms: 0.41 Number of scatterers: 68076 At special positions: 0 Unit cell: (189.431, 189.431, 234.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 12996 8.00 N 12048 7.00 C 42720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.13 Conformation dependent library (CDL) restraints added in 7.5 seconds 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 84 sheets defined 37.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 53 " --> pdb=" O GLN A 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.611A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.574A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 364' Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 422' Processing helix chain 'A' and resid 424 through 433 removed outlier: 3.874A pdb=" N TYR A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL A 441 " --> pdb=" O PRO A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 481' Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 500 " --> pdb=" O GLN A 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.883A pdb=" N ALA A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS B 50 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 53 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 78 removed outlier: 3.609A pdb=" N GLY B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.527A pdb=" N SER B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.643A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 301 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.574A pdb=" N ALA B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 364' Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 422' Processing helix chain 'B' and resid 424 through 433 removed outlier: 3.872A pdb=" N TYR B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 430 " --> pdb=" O PRO B 426 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.551A pdb=" N VAL B 441 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.630A pdb=" N ASP B 480 " --> pdb=" O GLU B 476 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 476 through 481' Processing helix chain 'B' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU B 495 " --> pdb=" O ASN B 491 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.884A pdb=" N ALA B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 570 through 580 removed outlier: 3.942A pdb=" N GLN B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.801A pdb=" N PHE C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 removed outlier: 3.611A pdb=" N GLY C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 305 removed outlier: 3.617A pdb=" N ASN C 295 " --> pdb=" O GLN C 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.749A pdb=" N SER C 331 " --> pdb=" O ARG C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.786A pdb=" N PHE C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 364' Processing helix chain 'C' and resid 403 through 417 removed outlier: 3.671A pdb=" N TYR C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 422' Processing helix chain 'C' and resid 424 through 433 removed outlier: 3.874A pdb=" N TYR C 428 " --> pdb=" O LYS C 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG C 430 " --> pdb=" O PRO C 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL C 441 " --> pdb=" O PRO C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP C 480 " --> pdb=" O GLU C 476 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 481' Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.513A pdb=" N GLU C 495 " --> pdb=" O ASN C 491 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 500 " --> pdb=" O GLN C 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 506 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.884A pdb=" N ALA C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS C 532 " --> pdb=" O LYS C 528 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 535 " --> pdb=" O ALA C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 561 through 565 Processing helix chain 'C' and resid 570 through 580 removed outlier: 3.942A pdb=" N GLN C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 78 removed outlier: 3.610A pdb=" N GLY D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.591A pdb=" N GLY D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER D 331 " --> pdb=" O ARG D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA D 355 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 356 " --> pdb=" O GLY D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 364' Processing helix chain 'D' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR D 412 " --> pdb=" O GLU D 408 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D 414 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.920A pdb=" N GLN D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 422' Processing helix chain 'D' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR D 428 " --> pdb=" O LYS D 424 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG D 430 " --> pdb=" O PRO D 426 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL D 441 " --> pdb=" O PRO D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP D 480 " --> pdb=" O GLU D 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 476 through 481' Processing helix chain 'D' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU D 495 " --> pdb=" O ASN D 491 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D 499 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 500 " --> pdb=" O GLN D 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU D 503 " --> pdb=" O GLN D 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU D 506 " --> pdb=" O GLU D 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.883A pdb=" N ALA D 531 " --> pdb=" O THR D 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS D 532 " --> pdb=" O LYS D 528 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 561 through 565 Processing helix chain 'D' and resid 570 through 580 removed outlier: 3.942A pdb=" N GLN D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 53 " --> pdb=" O GLN E 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 removed outlier: 3.610A pdb=" N GLY E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 Processing helix chain 'E' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER E 109 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.642A pdb=" N VAL E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 175 through 183 removed outlier: 3.591A pdb=" N GLY E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 358 removed outlier: 3.574A pdb=" N ALA E 355 " --> pdb=" O ASN E 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE E 363 " --> pdb=" O SER E 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 364 " --> pdb=" O ALA E 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 359 through 364' Processing helix chain 'E' and resid 403 through 417 removed outlier: 3.671A pdb=" N TYR E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN E 414 " --> pdb=" O ALA E 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 417 " --> pdb=" O ARG E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.920A pdb=" N GLN E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 417 through 422' Processing helix chain 'E' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR E 428 " --> pdb=" O LYS E 424 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG E 430 " --> pdb=" O PRO E 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 removed outlier: 3.549A pdb=" N VAL E 441 " --> pdb=" O PRO E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP E 480 " --> pdb=" O GLU E 476 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE E 481 " --> pdb=" O LEU E 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 476 through 481' Processing helix chain 'E' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU E 495 " --> pdb=" O ASN E 491 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN E 499 " --> pdb=" O GLU E 495 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 500 " --> pdb=" O GLN E 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU E 506 " --> pdb=" O GLU E 502 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 507 " --> pdb=" O LEU E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 526 through 535 removed outlier: 3.884A pdb=" N ALA E 531 " --> pdb=" O THR E 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU E 535 " --> pdb=" O ALA E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 547 Processing helix chain 'E' and resid 561 through 565 Processing helix chain 'E' and resid 570 through 580 removed outlier: 3.942A pdb=" N GLN E 578 " --> pdb=" O ALA E 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN E 579 " --> pdb=" O ALA E 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE F 32 " --> pdb=" O ARG F 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 53 " --> pdb=" O GLN F 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 78 removed outlier: 3.610A pdb=" N GLY F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 74 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 115 removed outlier: 3.653A pdb=" N GLU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.642A pdb=" N VAL F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 305 removed outlier: 3.617A pdb=" N ASN F 295 " --> pdb=" O GLN F 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU F 301 " --> pdb=" O ARG F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER F 331 " --> pdb=" O ARG F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 358 removed outlier: 3.574A pdb=" N ALA F 355 " --> pdb=" O ASN F 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE F 363 " --> pdb=" O SER F 359 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE F 364 " --> pdb=" O ALA F 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 359 through 364' Processing helix chain 'F' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE F 422 " --> pdb=" O ARG F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 417 through 422' Processing helix chain 'F' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR F 428 " --> pdb=" O LYS F 424 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG F 430 " --> pdb=" O PRO F 426 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL F 441 " --> pdb=" O PRO F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP F 480 " --> pdb=" O GLU F 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE F 481 " --> pdb=" O LEU F 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 476 through 481' Processing helix chain 'F' and resid 491 through 508 removed outlier: 3.513A pdb=" N GLU F 495 " --> pdb=" O ASN F 491 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 499 " --> pdb=" O GLU F 495 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 500 " --> pdb=" O GLN F 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU F 503 " --> pdb=" O GLN F 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F 506 " --> pdb=" O GLU F 502 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 535 removed outlier: 3.884A pdb=" N ALA F 531 " --> pdb=" O THR F 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS F 532 " --> pdb=" O LYS F 528 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 533 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 547 Processing helix chain 'F' and resid 561 through 565 Processing helix chain 'F' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN F 578 " --> pdb=" O ALA F 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 579 " --> pdb=" O ALA F 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 removed outlier: 3.525A pdb=" N LYS G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 53 " --> pdb=" O GLN G 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 removed outlier: 3.609A pdb=" N GLY G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU G 71 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 Processing helix chain 'G' and resid 104 through 109 removed outlier: 3.527A pdb=" N SER G 109 " --> pdb=" O VAL G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 Processing helix chain 'G' and resid 175 through 183 removed outlier: 3.591A pdb=" N GLY G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN G 295 " --> pdb=" O GLN G 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS G 296 " --> pdb=" O ASP G 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER G 331 " --> pdb=" O ARG G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA G 355 " --> pdb=" O ASN G 351 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU G 356 " --> pdb=" O GLY G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 364 removed outlier: 3.786A pdb=" N PHE G 363 " --> pdb=" O SER G 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 364 " --> pdb=" O ALA G 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 359 through 364' Processing helix chain 'G' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR G 412 " --> pdb=" O GLU G 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG G 413 " --> pdb=" O LEU G 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN G 414 " --> pdb=" O ALA G 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU G 417 " --> pdb=" O ARG G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN G 421 " --> pdb=" O LEU G 417 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE G 422 " --> pdb=" O ARG G 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 417 through 422' Processing helix chain 'G' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR G 428 " --> pdb=" O LYS G 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG G 430 " --> pdb=" O PRO G 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL G 431 " --> pdb=" O ASP G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL G 441 " --> pdb=" O PRO G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.630A pdb=" N ASP G 480 " --> pdb=" O GLU G 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE G 481 " --> pdb=" O LEU G 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 476 through 481' Processing helix chain 'G' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU G 495 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN G 499 " --> pdb=" O GLU G 495 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 500 " --> pdb=" O GLN G 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU G 503 " --> pdb=" O GLN G 499 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU G 506 " --> pdb=" O GLU G 502 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 535 removed outlier: 3.883A pdb=" N ALA G 531 " --> pdb=" O THR G 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 533 " --> pdb=" O LEU G 529 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU G 535 " --> pdb=" O ALA G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 547 Processing helix chain 'G' and resid 561 through 565 Processing helix chain 'G' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN G 578 " --> pdb=" O ALA G 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN G 579 " --> pdb=" O ALA G 575 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 18 through 23 Processing helix chain 'H' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS H 50 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA H 53 " --> pdb=" O GLN H 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 78 removed outlier: 3.609A pdb=" N GLY H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL H 74 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 102 Processing helix chain 'H' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER H 109 " --> pdb=" O VAL H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY H 179 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU H 181 " --> pdb=" O GLU H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN H 295 " --> pdb=" O GLN H 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS H 296 " --> pdb=" O ASP H 292 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU H 301 " --> pdb=" O ARG H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER H 331 " --> pdb=" O ARG H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA H 355 " --> pdb=" O ASN H 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU H 356 " --> pdb=" O GLY H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 364 removed outlier: 3.786A pdb=" N PHE H 363 " --> pdb=" O SER H 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE H 364 " --> pdb=" O ALA H 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 359 through 364' Processing helix chain 'H' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR H 412 " --> pdb=" O GLU H 408 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 414 " --> pdb=" O ALA H 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU H 417 " --> pdb=" O ARG H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 422 removed outlier: 3.920A pdb=" N GLN H 421 " --> pdb=" O LEU H 417 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE H 422 " --> pdb=" O ARG H 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 417 through 422' Processing helix chain 'H' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR H 428 " --> pdb=" O LYS H 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG H 430 " --> pdb=" O PRO H 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL H 441 " --> pdb=" O PRO H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 481 removed outlier: 3.630A pdb=" N ASP H 480 " --> pdb=" O GLU H 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE H 481 " --> pdb=" O LEU H 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 476 through 481' Processing helix chain 'H' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU H 495 " --> pdb=" O ASN H 491 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN H 499 " --> pdb=" O GLU H 495 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU H 500 " --> pdb=" O GLN H 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU H 503 " --> pdb=" O GLN H 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU H 506 " --> pdb=" O GLU H 502 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 535 removed outlier: 3.883A pdb=" N ALA H 531 " --> pdb=" O THR H 527 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS H 532 " --> pdb=" O LYS H 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 533 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU H 535 " --> pdb=" O ALA H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 542 through 547 Processing helix chain 'H' and resid 561 through 565 Processing helix chain 'H' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN H 578 " --> pdb=" O ALA H 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 579 " --> pdb=" O ALA H 575 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 18 Processing helix chain 'I' and resid 18 through 23 Processing helix chain 'I' and resid 27 through 36 removed outlier: 3.801A pdb=" N PHE I 32 " --> pdb=" O ARG I 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE I 33 " --> pdb=" O LYS I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 78 removed outlier: 3.609A pdb=" N GLY I 70 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU I 71 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY I 73 " --> pdb=" O ARG I 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 102 Processing helix chain 'I' and resid 104 through 109 removed outlier: 3.527A pdb=" N SER I 109 " --> pdb=" O VAL I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 115 removed outlier: 3.653A pdb=" N GLU I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 124 removed outlier: 3.642A pdb=" N VAL I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 Processing helix chain 'I' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN I 295 " --> pdb=" O GLN I 291 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 296 " --> pdb=" O ASP I 292 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG I 297 " --> pdb=" O ALA I 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU I 301 " --> pdb=" O ARG I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER I 331 " --> pdb=" O ARG I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 358 removed outlier: 3.574A pdb=" N ALA I 355 " --> pdb=" O ASN I 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU I 356 " --> pdb=" O GLY I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE I 363 " --> pdb=" O SER I 359 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I 364 " --> pdb=" O ALA I 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 359 through 364' Processing helix chain 'I' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR I 412 " --> pdb=" O GLU I 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG I 413 " --> pdb=" O LEU I 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN I 414 " --> pdb=" O ALA I 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU I 417 " --> pdb=" O ARG I 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN I 421 " --> pdb=" O LEU I 417 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE I 422 " --> pdb=" O ARG I 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 417 through 422' Processing helix chain 'I' and resid 424 through 433 removed outlier: 3.872A pdb=" N TYR I 428 " --> pdb=" O LYS I 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE I 429 " --> pdb=" O ALA I 425 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG I 430 " --> pdb=" O PRO I 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 437 through 441 removed outlier: 3.551A pdb=" N VAL I 441 " --> pdb=" O PRO I 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP I 480 " --> pdb=" O GLU I 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE I 481 " --> pdb=" O LEU I 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 476 through 481' Processing helix chain 'I' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU I 495 " --> pdb=" O ASN I 491 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN I 499 " --> pdb=" O GLU I 495 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU I 500 " --> pdb=" O GLN I 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU I 503 " --> pdb=" O GLN I 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU I 506 " --> pdb=" O GLU I 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR I 507 " --> pdb=" O LEU I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 535 removed outlier: 3.883A pdb=" N ALA I 531 " --> pdb=" O THR I 527 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS I 532 " --> pdb=" O LYS I 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG I 533 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU I 535 " --> pdb=" O ALA I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 547 Processing helix chain 'I' and resid 561 through 565 Processing helix chain 'I' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN I 578 " --> pdb=" O ALA I 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN I 579 " --> pdb=" O ALA I 575 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 27 through 36 removed outlier: 3.801A pdb=" N PHE J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS J 50 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA J 53 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 78 removed outlier: 3.610A pdb=" N GLY J 70 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU J 71 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 102 Processing helix chain 'J' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 115 removed outlier: 3.651A pdb=" N GLU J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 Processing helix chain 'J' and resid 175 through 183 removed outlier: 3.591A pdb=" N GLY J 179 " --> pdb=" O ALA J 175 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN J 295 " --> pdb=" O GLN J 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS J 296 " --> pdb=" O ASP J 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG J 297 " --> pdb=" O ALA J 293 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU J 301 " --> pdb=" O ARG J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER J 331 " --> pdb=" O ARG J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA J 355 " --> pdb=" O ASN J 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU J 356 " --> pdb=" O GLY J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 364 removed outlier: 3.786A pdb=" N PHE J 363 " --> pdb=" O SER J 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE J 364 " --> pdb=" O ALA J 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 359 through 364' Processing helix chain 'J' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR J 412 " --> pdb=" O GLU J 408 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG J 413 " --> pdb=" O LEU J 409 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN J 414 " --> pdb=" O ALA J 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU J 417 " --> pdb=" O ARG J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN J 421 " --> pdb=" O LEU J 417 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE J 422 " --> pdb=" O ARG J 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 417 through 422' Processing helix chain 'J' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR J 428 " --> pdb=" O LYS J 424 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE J 429 " --> pdb=" O ALA J 425 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG J 430 " --> pdb=" O PRO J 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL J 431 " --> pdb=" O ASP J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL J 441 " --> pdb=" O PRO J 438 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 481 removed outlier: 3.630A pdb=" N ASP J 480 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE J 481 " --> pdb=" O LEU J 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 476 through 481' Processing helix chain 'J' and resid 491 through 508 removed outlier: 3.513A pdb=" N GLU J 495 " --> pdb=" O ASN J 491 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN J 499 " --> pdb=" O GLU J 495 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU J 500 " --> pdb=" O GLN J 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU J 503 " --> pdb=" O GLN J 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU J 506 " --> pdb=" O GLU J 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR J 507 " --> pdb=" O LEU J 503 " (cutoff:3.500A) Processing helix chain 'J' and resid 526 through 535 removed outlier: 3.884A pdb=" N ALA J 531 " --> pdb=" O THR J 527 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS J 532 " --> pdb=" O LYS J 528 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 533 " --> pdb=" O LEU J 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU J 535 " --> pdb=" O ALA J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 542 through 547 Processing helix chain 'J' and resid 561 through 565 Processing helix chain 'J' and resid 570 through 580 removed outlier: 3.942A pdb=" N GLN J 578 " --> pdb=" O ALA J 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN J 579 " --> pdb=" O ALA J 575 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 18 Processing helix chain 'K' and resid 18 through 23 Processing helix chain 'K' and resid 27 through 36 removed outlier: 3.800A pdb=" N PHE K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K 54 " --> pdb=" O LYS K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 removed outlier: 3.610A pdb=" N GLY K 70 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 102 Processing helix chain 'K' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER K 109 " --> pdb=" O VAL K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY K 179 " --> pdb=" O ALA K 175 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU K 181 " --> pdb=" O GLU K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN K 295 " --> pdb=" O GLN K 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS K 296 " --> pdb=" O ASP K 292 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG K 297 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU K 301 " --> pdb=" O ARG K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER K 331 " --> pdb=" O ARG K 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA K 355 " --> pdb=" O ASN K 351 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU K 356 " --> pdb=" O GLY K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 364 removed outlier: 3.788A pdb=" N PHE K 363 " --> pdb=" O SER K 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE K 364 " --> pdb=" O ALA K 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 359 through 364' Processing helix chain 'K' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG K 413 " --> pdb=" O LEU K 409 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU K 417 " --> pdb=" O ARG K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 422 removed outlier: 3.920A pdb=" N GLN K 421 " --> pdb=" O LEU K 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE K 422 " --> pdb=" O ARG K 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 417 through 422' Processing helix chain 'K' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR K 428 " --> pdb=" O LYS K 424 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE K 429 " --> pdb=" O ALA K 425 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG K 430 " --> pdb=" O PRO K 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL K 431 " --> pdb=" O ASP K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 437 through 441 removed outlier: 3.549A pdb=" N VAL K 441 " --> pdb=" O PRO K 438 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 481 removed outlier: 3.630A pdb=" N ASP K 480 " --> pdb=" O GLU K 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE K 481 " --> pdb=" O LEU K 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 476 through 481' Processing helix chain 'K' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU K 495 " --> pdb=" O ASN K 491 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN K 499 " --> pdb=" O GLU K 495 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU K 500 " --> pdb=" O GLN K 496 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU K 503 " --> pdb=" O GLN K 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU K 506 " --> pdb=" O GLU K 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR K 507 " --> pdb=" O LEU K 503 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 535 removed outlier: 3.884A pdb=" N ALA K 531 " --> pdb=" O THR K 527 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS K 532 " --> pdb=" O LYS K 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG K 533 " --> pdb=" O LEU K 529 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU K 535 " --> pdb=" O ALA K 531 " (cutoff:3.500A) Processing helix chain 'K' and resid 542 through 547 Processing helix chain 'K' and resid 561 through 565 Processing helix chain 'K' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN K 578 " --> pdb=" O ALA K 574 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN K 579 " --> pdb=" O ALA K 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 18 Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 27 through 36 removed outlier: 3.801A pdb=" N PHE L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 33 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 54 removed outlier: 3.524A pdb=" N LYS L 50 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA L 53 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG L 54 " --> pdb=" O LYS L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 78 removed outlier: 3.610A pdb=" N GLY L 70 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 102 Processing helix chain 'L' and resid 104 through 109 removed outlier: 3.526A pdb=" N SER L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 115 removed outlier: 3.652A pdb=" N GLU L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 124 removed outlier: 3.641A pdb=" N VAL L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 175 through 183 removed outlier: 3.590A pdb=" N GLY L 179 " --> pdb=" O ALA L 175 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 305 removed outlier: 3.618A pdb=" N ASN L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS L 296 " --> pdb=" O ASP L 292 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG L 297 " --> pdb=" O ALA L 293 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU L 301 " --> pdb=" O ARG L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER L 331 " --> pdb=" O ARG L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 358 removed outlier: 3.575A pdb=" N ALA L 355 " --> pdb=" O ASN L 351 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU L 356 " --> pdb=" O GLY L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 364 removed outlier: 3.787A pdb=" N PHE L 363 " --> pdb=" O SER L 359 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE L 364 " --> pdb=" O ALA L 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 359 through 364' Processing helix chain 'L' and resid 403 through 417 removed outlier: 3.672A pdb=" N TYR L 412 " --> pdb=" O GLU L 408 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN L 414 " --> pdb=" O ALA L 410 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU L 417 " --> pdb=" O ARG L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 422 removed outlier: 3.921A pdb=" N GLN L 421 " --> pdb=" O LEU L 417 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE L 422 " --> pdb=" O ARG L 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 417 through 422' Processing helix chain 'L' and resid 424 through 433 removed outlier: 3.873A pdb=" N TYR L 428 " --> pdb=" O LYS L 424 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE L 429 " --> pdb=" O ALA L 425 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG L 430 " --> pdb=" O PRO L 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL L 431 " --> pdb=" O ASP L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 441 removed outlier: 3.550A pdb=" N VAL L 441 " --> pdb=" O PRO L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 481 removed outlier: 3.631A pdb=" N ASP L 480 " --> pdb=" O GLU L 476 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE L 481 " --> pdb=" O LEU L 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 476 through 481' Processing helix chain 'L' and resid 491 through 508 removed outlier: 3.514A pdb=" N GLU L 495 " --> pdb=" O ASN L 491 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN L 499 " --> pdb=" O GLU L 495 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 500 " --> pdb=" O GLN L 496 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU L 503 " --> pdb=" O GLN L 499 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU L 506 " --> pdb=" O GLU L 502 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR L 507 " --> pdb=" O LEU L 503 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 535 removed outlier: 3.883A pdb=" N ALA L 531 " --> pdb=" O THR L 527 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS L 532 " --> pdb=" O LYS L 528 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG L 533 " --> pdb=" O LEU L 529 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU L 535 " --> pdb=" O ALA L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 542 through 547 Processing helix chain 'L' and resid 561 through 565 Processing helix chain 'L' and resid 570 through 580 removed outlier: 3.941A pdb=" N GLN L 578 " --> pdb=" O ALA L 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN L 579 " --> pdb=" O ALA L 575 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE M 7 " --> pdb=" O THR M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR M 34 " --> pdb=" O ASP M 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE M 44 " --> pdb=" O TYR M 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA M 45 " --> pdb=" O ASP M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU M 144 " --> pdb=" O LEU M 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA M 146 " --> pdb=" O ALA M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA M 159 " --> pdb=" O PRO M 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG M 160 " --> pdb=" O ARG M 156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE M 168 " --> pdb=" O PHE M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.906A pdb=" N ILE N 7 " --> pdb=" O THR N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR N 34 " --> pdb=" O ASP N 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL N 35 " --> pdb=" O ALA N 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE N 44 " --> pdb=" O TYR N 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA N 45 " --> pdb=" O ASP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU N 144 " --> pdb=" O LEU N 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA N 146 " --> pdb=" O ALA N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA N 159 " --> pdb=" O PRO N 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG N 160 " --> pdb=" O ARG N 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY N 161 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY N 166 " --> pdb=" O PHE N 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE N 168 " --> pdb=" O PHE N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE O 7 " --> pdb=" O THR O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 45 removed outlier: 3.581A pdb=" N ALA O 31 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR O 34 " --> pdb=" O ASP O 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE O 44 " --> pdb=" O TYR O 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA O 45 " --> pdb=" O ASP O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 146 removed outlier: 4.618A pdb=" N GLU O 144 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 146 " --> pdb=" O ALA O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA O 159 " --> pdb=" O PRO O 155 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG O 160 " --> pdb=" O ARG O 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY O 161 " --> pdb=" O THR O 157 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY O 166 " --> pdb=" O PHE O 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE O 168 " --> pdb=" O PHE O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE P 7 " --> pdb=" O THR P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR P 34 " --> pdb=" O ASP P 30 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL P 35 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE P 44 " --> pdb=" O TYR P 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA P 45 " --> pdb=" O ASP P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU P 144 " --> pdb=" O LEU P 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA P 146 " --> pdb=" O ALA P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA P 159 " --> pdb=" O PRO P 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG P 160 " --> pdb=" O ARG P 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY P 161 " --> pdb=" O THR P 157 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY P 166 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE P 168 " --> pdb=" O PHE P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE Q 7 " --> pdb=" O THR Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA Q 31 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU Q 33 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR Q 34 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL Q 35 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE Q 44 " --> pdb=" O TYR Q 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Q 45 " --> pdb=" O ASP Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 146 removed outlier: 4.618A pdb=" N GLU Q 144 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA Q 146 " --> pdb=" O ALA Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA Q 159 " --> pdb=" O PRO Q 155 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG Q 160 " --> pdb=" O ARG Q 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY Q 161 " --> pdb=" O THR Q 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY Q 166 " --> pdb=" O PHE Q 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE Q 168 " --> pdb=" O PHE Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE R 7 " --> pdb=" O THR R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE R 44 " --> pdb=" O TYR R 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA R 45 " --> pdb=" O ASP R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 146 removed outlier: 4.618A pdb=" N GLU R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA R 146 " --> pdb=" O ALA R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA R 159 " --> pdb=" O PRO R 155 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG R 160 " --> pdb=" O ARG R 156 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY R 161 " --> pdb=" O THR R 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE R 168 " --> pdb=" O PHE R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 15 removed outlier: 3.906A pdb=" N ILE S 7 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 45 removed outlier: 3.581A pdb=" N ALA S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU S 33 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR S 34 " --> pdb=" O ASP S 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL S 35 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE S 44 " --> pdb=" O TYR S 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA S 45 " --> pdb=" O ASP S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU S 144 " --> pdb=" O LEU S 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA S 146 " --> pdb=" O ALA S 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA S 159 " --> pdb=" O PRO S 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG S 160 " --> pdb=" O ARG S 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY S 161 " --> pdb=" O THR S 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY S 166 " --> pdb=" O PHE S 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE S 168 " --> pdb=" O PHE S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 15 removed outlier: 3.906A pdb=" N ILE T 7 " --> pdb=" O THR T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 45 removed outlier: 3.581A pdb=" N ALA T 31 " --> pdb=" O LYS T 27 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR T 34 " --> pdb=" O ASP T 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL T 35 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE T 44 " --> pdb=" O TYR T 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA T 45 " --> pdb=" O ASP T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU T 144 " --> pdb=" O LEU T 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA T 146 " --> pdb=" O ALA T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 154 through 168 removed outlier: 3.684A pdb=" N ALA T 159 " --> pdb=" O PRO T 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG T 160 " --> pdb=" O ARG T 156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY T 161 " --> pdb=" O THR T 157 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY T 166 " --> pdb=" O PHE T 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE T 168 " --> pdb=" O PHE T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 15 removed outlier: 3.906A pdb=" N ILE U 7 " --> pdb=" O THR U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA U 31 " --> pdb=" O LYS U 27 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR U 34 " --> pdb=" O ASP U 30 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE U 44 " --> pdb=" O TYR U 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU U 144 " --> pdb=" O LEU U 140 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA U 146 " --> pdb=" O ALA U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA U 159 " --> pdb=" O PRO U 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG U 160 " --> pdb=" O ARG U 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY U 161 " --> pdb=" O THR U 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY U 166 " --> pdb=" O PHE U 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE U 168 " --> pdb=" O PHE U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE V 7 " --> pdb=" O THR V 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA V 31 " --> pdb=" O LYS V 27 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU V 33 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR V 34 " --> pdb=" O ASP V 30 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL V 35 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE V 44 " --> pdb=" O TYR V 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA V 45 " --> pdb=" O ASP V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU V 144 " --> pdb=" O LEU V 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA V 146 " --> pdb=" O ALA V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA V 159 " --> pdb=" O PRO V 155 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG V 160 " --> pdb=" O ARG V 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY V 161 " --> pdb=" O THR V 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY V 166 " --> pdb=" O PHE V 162 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE V 168 " --> pdb=" O PHE V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 15 removed outlier: 3.907A pdb=" N ILE W 7 " --> pdb=" O THR W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA W 31 " --> pdb=" O LYS W 27 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU W 33 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR W 34 " --> pdb=" O ASP W 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE W 44 " --> pdb=" O TYR W 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA W 45 " --> pdb=" O ASP W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 146 removed outlier: 4.619A pdb=" N GLU W 144 " --> pdb=" O LEU W 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA W 146 " --> pdb=" O ALA W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA W 159 " --> pdb=" O PRO W 155 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG W 160 " --> pdb=" O ARG W 156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY W 161 " --> pdb=" O THR W 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY W 166 " --> pdb=" O PHE W 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE W 168 " --> pdb=" O PHE W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 15 removed outlier: 3.906A pdb=" N ILE X 7 " --> pdb=" O THR X 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 27 through 45 removed outlier: 3.580A pdb=" N ALA X 31 " --> pdb=" O LYS X 27 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU X 33 " --> pdb=" O ALA X 29 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR X 34 " --> pdb=" O ASP X 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL X 35 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE X 44 " --> pdb=" O TYR X 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA X 45 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 146 removed outlier: 4.620A pdb=" N GLU X 144 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 168 removed outlier: 3.685A pdb=" N ALA X 159 " --> pdb=" O PRO X 155 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG X 160 " --> pdb=" O ARG X 156 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY X 161 " --> pdb=" O THR X 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY X 166 " --> pdb=" O PHE X 162 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE X 168 " --> pdb=" O PHE X 164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.599A pdb=" N ASP A 81 " --> pdb=" O VAL L 486 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL L 486 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 144 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 removed outlier: 3.759A pdb=" N PHE A 151 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 167 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.636A pdb=" N GLN A 309 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 337 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 312 " --> pdb=" O ILE L 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 337 removed outlier: 7.574A pdb=" N ILE A 337 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 309 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 486 removed outlier: 3.551A pdb=" N VAL A 486 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 81 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 140 through 144 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE B 151 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 167 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 250 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'B' and resid 336 through 337 removed outlier: 7.576A pdb=" N ILE B 337 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 309 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 483 through 486 removed outlier: 3.558A pdb=" N VAL B 486 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 81 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 140 through 144 Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 152 removed outlier: 3.759A pdb=" N PHE C 151 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 167 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 337 removed outlier: 7.558A pdb=" N ILE C 337 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D 309 " --> pdb=" O ALA D 344 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 483 through 486 removed outlier: 3.554A pdb=" N VAL C 486 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP D 81 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 140 through 144 Processing sheet with id=AC1, first strand: chain 'D' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE D 151 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 167 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 250 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 173 through 174 Processing sheet with id=AC3, first strand: chain 'D' and resid 336 through 337 removed outlier: 7.572A pdb=" N ILE D 337 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN E 309 " --> pdb=" O ALA E 344 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 483 through 486 removed outlier: 3.558A pdb=" N VAL D 486 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP E 81 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 140 through 144 Processing sheet with id=AC6, first strand: chain 'E' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE E 151 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 167 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU E 250 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AC8, first strand: chain 'E' and resid 336 through 337 removed outlier: 7.575A pdb=" N ILE E 337 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN F 309 " --> pdb=" O ALA F 344 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 483 through 486 removed outlier: 3.549A pdb=" N VAL E 486 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP F 81 " --> pdb=" O VAL E 486 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 140 through 144 Processing sheet with id=AD2, first strand: chain 'F' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE F 151 " --> pdb=" O GLY F 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 167 " --> pdb=" O TYR F 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 250 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 173 through 174 Processing sheet with id=AD4, first strand: chain 'F' and resid 336 through 337 removed outlier: 7.577A pdb=" N ILE F 337 " --> pdb=" O ALA G 312 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN G 309 " --> pdb=" O ALA G 344 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 483 through 486 removed outlier: 3.550A pdb=" N VAL F 486 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP G 81 " --> pdb=" O VAL F 486 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 140 through 144 Processing sheet with id=AD7, first strand: chain 'G' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE G 151 " --> pdb=" O GLY G 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS G 167 " --> pdb=" O TYR G 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU G 250 " --> pdb=" O LEU G 242 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 173 through 174 Processing sheet with id=AD9, first strand: chain 'G' and resid 336 through 337 removed outlier: 7.569A pdb=" N ILE G 337 " --> pdb=" O ALA H 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN H 309 " --> pdb=" O ALA H 344 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 483 through 486 removed outlier: 3.559A pdb=" N VAL G 486 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP H 81 " --> pdb=" O VAL G 486 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 140 through 144 Processing sheet with id=AE3, first strand: chain 'H' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE H 151 " --> pdb=" O GLY H 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS H 167 " --> pdb=" O TYR H 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU H 250 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 173 through 174 Processing sheet with id=AE5, first strand: chain 'H' and resid 336 through 337 removed outlier: 7.561A pdb=" N ILE H 337 " --> pdb=" O ALA I 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN I 309 " --> pdb=" O ALA I 344 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 483 through 486 removed outlier: 3.559A pdb=" N VAL H 486 " --> pdb=" O ASP I 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP I 81 " --> pdb=" O VAL H 486 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 140 through 144 Processing sheet with id=AE8, first strand: chain 'I' and resid 151 through 152 removed outlier: 3.759A pdb=" N PHE I 151 " --> pdb=" O GLY I 168 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS I 167 " --> pdb=" O TYR I 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 173 through 174 Processing sheet with id=AF1, first strand: chain 'I' and resid 336 through 337 removed outlier: 7.577A pdb=" N ILE I 337 " --> pdb=" O ALA J 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN J 309 " --> pdb=" O ALA J 344 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 483 through 486 removed outlier: 3.553A pdb=" N VAL I 486 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP J 81 " --> pdb=" O VAL I 486 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 140 through 144 Processing sheet with id=AF4, first strand: chain 'J' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE J 151 " --> pdb=" O GLY J 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 167 " --> pdb=" O TYR J 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU J 250 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 173 through 174 Processing sheet with id=AF6, first strand: chain 'J' and resid 336 through 337 removed outlier: 7.562A pdb=" N ILE J 337 " --> pdb=" O ALA K 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN K 309 " --> pdb=" O ALA K 344 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 483 through 486 removed outlier: 3.561A pdb=" N VAL J 486 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP K 81 " --> pdb=" O VAL J 486 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 140 through 144 Processing sheet with id=AF9, first strand: chain 'K' and resid 151 through 152 removed outlier: 3.758A pdb=" N PHE K 151 " --> pdb=" O GLY K 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS K 167 " --> pdb=" O TYR K 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU K 250 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 173 through 174 Processing sheet with id=AG2, first strand: chain 'K' and resid 336 through 337 removed outlier: 7.567A pdb=" N ILE K 337 " --> pdb=" O ALA L 312 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN L 309 " --> pdb=" O ALA L 344 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 483 through 486 removed outlier: 3.559A pdb=" N VAL K 486 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP L 81 " --> pdb=" O VAL K 486 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 140 through 144 Processing sheet with id=AG5, first strand: chain 'L' and resid 151 through 152 removed outlier: 3.759A pdb=" N PHE L 151 " --> pdb=" O GLY L 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS L 167 " --> pdb=" O TYR L 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU L 250 " --> pdb=" O LEU L 242 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 173 through 174 Processing sheet with id=AG7, first strand: chain 'M' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR M 53 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU M 67 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 98 " --> pdb=" O GLU M 67 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 82 through 83 Processing sheet with id=AG9, first strand: chain 'N' and resid 53 through 55 removed outlier: 6.212A pdb=" N THR N 53 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU N 67 " --> pdb=" O ALA N 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE N 98 " --> pdb=" O GLU N 67 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 82 through 83 Processing sheet with id=AH2, first strand: chain 'O' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU O 67 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE O 98 " --> pdb=" O GLU O 67 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 82 through 83 Processing sheet with id=AH4, first strand: chain 'P' and resid 53 through 55 removed outlier: 6.210A pdb=" N THR P 53 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU P 67 " --> pdb=" O ALA P 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE P 98 " --> pdb=" O GLU P 67 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 82 through 83 Processing sheet with id=AH6, first strand: chain 'Q' and resid 53 through 55 removed outlier: 6.212A pdb=" N THR Q 53 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU Q 67 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE Q 98 " --> pdb=" O GLU Q 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 82 through 83 Processing sheet with id=AH8, first strand: chain 'R' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR R 53 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU R 67 " --> pdb=" O ALA R 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE R 98 " --> pdb=" O GLU R 67 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 82 through 83 Processing sheet with id=AI1, first strand: chain 'S' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR S 53 " --> pdb=" O ARG S 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU S 67 " --> pdb=" O ALA S 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE S 98 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 82 through 83 Processing sheet with id=AI3, first strand: chain 'T' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR T 53 " --> pdb=" O ARG T 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU T 67 " --> pdb=" O ALA T 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE T 98 " --> pdb=" O GLU T 67 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 82 through 83 Processing sheet with id=AI5, first strand: chain 'U' and resid 53 through 55 removed outlier: 6.212A pdb=" N THR U 53 " --> pdb=" O ARG U 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU U 67 " --> pdb=" O ALA U 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE U 98 " --> pdb=" O GLU U 67 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 82 through 83 Processing sheet with id=AI7, first strand: chain 'V' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR V 53 " --> pdb=" O ARG V 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU V 67 " --> pdb=" O ALA V 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE V 98 " --> pdb=" O GLU V 67 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'V' and resid 82 through 83 Processing sheet with id=AI9, first strand: chain 'W' and resid 53 through 55 removed outlier: 6.212A pdb=" N THR W 53 " --> pdb=" O ARG W 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU W 67 " --> pdb=" O ALA W 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE W 98 " --> pdb=" O GLU W 67 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 82 through 83 Processing sheet with id=AJ2, first strand: chain 'X' and resid 53 through 55 removed outlier: 6.211A pdb=" N THR X 53 " --> pdb=" O ARG X 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU X 67 " --> pdb=" O ALA X 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE X 98 " --> pdb=" O GLU X 67 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'X' and resid 82 through 83 1512 hydrogen bonds defined for protein. 4248 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: 23.12 Time building geometry restraints manager: 22.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22132 1.33 - 1.45: 10625 1.45 - 1.57: 36111 1.57 - 1.69: 0 1.69 - 1.81: 564 Bond restraints: 69432 Sorted by residual: bond pdb=" C LYS D 583 " pdb=" N PRO D 584 " ideal model delta sigma weight residual 1.334 1.387 -0.053 8.40e-03 1.42e+04 4.06e+01 bond pdb=" C LYS H 583 " pdb=" N PRO H 584 " ideal model delta sigma weight residual 1.334 1.387 -0.053 8.40e-03 1.42e+04 4.04e+01 bond pdb=" C LYS I 583 " pdb=" N PRO I 584 " ideal model delta sigma weight residual 1.334 1.387 -0.053 8.40e-03 1.42e+04 3.98e+01 bond pdb=" C LYS G 583 " pdb=" N PRO G 584 " ideal model delta sigma weight residual 1.334 1.386 -0.053 8.40e-03 1.42e+04 3.97e+01 bond pdb=" C LYS K 583 " pdb=" N PRO K 584 " ideal model delta sigma weight residual 1.334 1.386 -0.053 8.40e-03 1.42e+04 3.95e+01 ... (remaining 69427 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.36: 1632 105.36 - 113.00: 34178 113.00 - 120.65: 33505 120.65 - 128.29: 23997 128.29 - 135.94: 552 Bond angle restraints: 93864 Sorted by residual: angle pdb=" C ASP P 177 " pdb=" N ASP P 178 " pdb=" CA ASP P 178 " ideal model delta sigma weight residual 121.57 132.25 -10.68 1.62e+00 3.81e-01 4.34e+01 angle pdb=" C ASP X 177 " pdb=" N ASP X 178 " pdb=" CA ASP X 178 " ideal model delta sigma weight residual 121.57 132.23 -10.66 1.62e+00 3.81e-01 4.33e+01 angle pdb=" C ASP R 177 " pdb=" N ASP R 178 " pdb=" CA ASP R 178 " ideal model delta sigma weight residual 121.57 132.23 -10.66 1.62e+00 3.81e-01 4.33e+01 angle pdb=" C ASP N 177 " pdb=" N ASP N 178 " pdb=" CA ASP N 178 " ideal model delta sigma weight residual 121.57 132.22 -10.65 1.62e+00 3.81e-01 4.32e+01 angle pdb=" C ASP M 177 " pdb=" N ASP M 178 " pdb=" CA ASP M 178 " ideal model delta sigma weight residual 121.57 132.21 -10.64 1.62e+00 3.81e-01 4.31e+01 ... (remaining 93859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 38759 15.14 - 30.28: 2763 30.28 - 45.42: 754 45.42 - 60.56: 12 60.56 - 75.69: 96 Dihedral angle restraints: 42384 sinusoidal: 17532 harmonic: 24852 Sorted by residual: dihedral pdb=" CA VAL F 479 " pdb=" C VAL F 479 " pdb=" N ASP F 480 " pdb=" CA ASP F 480 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL H 479 " pdb=" C VAL H 479 " pdb=" N ASP H 480 " pdb=" CA ASP H 480 " ideal model delta harmonic sigma weight residual -180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA VAL A 479 " pdb=" C VAL A 479 " pdb=" N ASP A 480 " pdb=" CA ASP A 480 " ideal model delta harmonic sigma weight residual 180.00 -153.95 -26.05 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 42381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 8104 0.080 - 0.161: 1566 0.161 - 0.241: 194 0.241 - 0.321: 60 0.321 - 0.401: 24 Chirality restraints: 9948 Sorted by residual: chirality pdb=" CB ILE D 142 " pdb=" CA ILE D 142 " pdb=" CG1 ILE D 142 " pdb=" CG2 ILE D 142 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB ILE F 142 " pdb=" CA ILE F 142 " pdb=" CG1 ILE F 142 " pdb=" CG2 ILE F 142 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE A 142 " pdb=" CA ILE A 142 " pdb=" CG1 ILE A 142 " pdb=" CG2 ILE A 142 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 9945 not shown) Planarity restraints: 12564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 139 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO K 140 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO K 140 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO K 140 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 139 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO E 140 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 140 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 140 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 139 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO L 140 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 140 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 140 " 0.041 5.00e-02 4.00e+02 ... (remaining 12561 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 17890 2.79 - 3.32: 57574 3.32 - 3.85: 102508 3.85 - 4.37: 120775 4.37 - 4.90: 208181 Nonbonded interactions: 506928 Sorted by model distance: nonbonded pdb=" NH2 ARG A 297 " pdb=" O TYR R 182 " model vdw 2.267 2.520 nonbonded pdb=" NH1 ARG S 163 " pdb=" OG SER U 42 " model vdw 2.268 2.520 nonbonded pdb=" NH2 ARG C 297 " pdb=" O TYR U 182 " model vdw 2.281 2.520 nonbonded pdb=" NH2 ARG E 297 " pdb=" O TYR X 182 " model vdw 2.294 2.520 nonbonded pdb=" NH2 ARG K 297 " pdb=" O TYR P 182 " model vdw 2.296 2.520 ... (remaining 506923 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' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 42720 2.51 5 N 12048 2.21 5 O 12996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 10.770 Check model and map are aligned: 0.830 Convert atoms to be neutral: 0.450 Process input model: 130.340 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.009 0.082 69432 Z= 0.603 Angle : 1.199 16.758 93864 Z= 0.644 Chirality : 0.068 0.401 9948 Planarity : 0.008 0.074 12564 Dihedral : 11.993 75.694 26304 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.27 % Favored : 89.59 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.29 (0.06), residues: 8412 helix: -5.06 (0.03), residues: 3444 sheet: -2.37 (0.20), residues: 696 loop : -3.73 (0.06), residues: 4272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2197 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 2113 time to evaluate : 7.311 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 outliers start: 84 outliers final: 32 residues processed: 2173 average time/residue: 0.6489 time to fit residues: 2339.3839 Evaluate side-chains 1446 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1414 time to evaluate : 6.110 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4483 time to fit residues: 36.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 2.9990 chunk 636 optimal weight: 5.9990 chunk 353 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 429 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 658 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 400 optimal weight: 0.9980 chunk 490 optimal weight: 0.4980 chunk 762 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS A 306 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 HIS B 306 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 HIS ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN D 303 HIS D 306 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 HIS ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 GLN G 303 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 GLN H 303 HIS ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 303 HIS I 306 ASN ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 494 GLN J 303 HIS ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 414 GLN K 303 HIS ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 GLN L 303 HIS ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 494 GLN M 66 ASN O 13 GLN O 119 HIS P 119 HIS Q 66 ASN Q 119 HIS R 13 GLN R 119 HIS S 13 GLN ** S 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 119 HIS U 119 HIS V 13 GLN V 66 ASN V 119 HIS ** W 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 119 HIS X 13 GLN ** X 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 119 HIS X 124 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 69432 Z= 0.168 Angle : 0.644 13.500 93864 Z= 0.329 Chirality : 0.043 0.203 9948 Planarity : 0.005 0.052 12564 Dihedral : 5.767 21.803 9456 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.07), residues: 8412 helix: -4.07 (0.05), residues: 3324 sheet: -0.77 (0.27), residues: 384 loop : -3.32 (0.07), residues: 4704 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1793 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1570 time to evaluate : 7.826 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 outliers start: 223 outliers final: 96 residues processed: 1742 average time/residue: 0.6439 time to fit residues: 1874.9824 Evaluate side-chains 1441 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1345 time to evaluate : 6.239 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.4602 time to fit residues: 93.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 634 optimal weight: 7.9990 chunk 519 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 764 optimal weight: 4.9990 chunk 825 optimal weight: 0.9990 chunk 680 optimal weight: 0.5980 chunk 757 optimal weight: 0.0770 chunk 260 optimal weight: 10.0000 chunk 613 optimal weight: 2.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN F 306 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 542 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 542 GLN J 320 ASN ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 542 GLN M 64 GLN Q 13 GLN Q 64 GLN S 13 GLN ** S 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 119 HIS U 13 GLN X 13 GLN X 108 HIS X 124 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 69432 Z= 0.194 Angle : 0.641 13.495 93864 Z= 0.316 Chirality : 0.043 0.210 9948 Planarity : 0.005 0.047 12564 Dihedral : 5.243 21.163 9456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.07), residues: 8412 helix: -3.36 (0.07), residues: 3288 sheet: -0.54 (0.26), residues: 384 loop : -3.12 (0.07), residues: 4740 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1441 time to evaluate : 6.234 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 outliers start: 162 outliers final: 73 residues processed: 1568 average time/residue: 0.6166 time to fit residues: 1649.0026 Evaluate side-chains 1407 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1334 time to evaluate : 6.176 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4838 time to fit residues: 76.6833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 0.7980 chunk 574 optimal weight: 1.9990 chunk 396 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 364 optimal weight: 10.0000 chunk 513 optimal weight: 1.9990 chunk 766 optimal weight: 0.9980 chunk 811 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 726 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 64 GLN S 108 HIS W 13 GLN X 124 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 69432 Z= 0.162 Angle : 0.598 10.704 93864 Z= 0.296 Chirality : 0.042 0.225 9948 Planarity : 0.004 0.048 12564 Dihedral : 4.912 19.903 9456 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.08), residues: 8412 helix: -2.88 (0.08), residues: 3228 sheet: -0.41 (0.26), residues: 384 loop : -2.95 (0.07), residues: 4800 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1429 time to evaluate : 6.102 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 outliers start: 158 outliers final: 80 residues processed: 1510 average time/residue: 0.6273 time to fit residues: 1618.7410 Evaluate side-chains 1417 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1337 time to evaluate : 6.045 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.4882 time to fit residues: 82.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 9.9990 chunk 460 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 604 optimal weight: 7.9990 chunk 335 optimal weight: 9.9990 chunk 692 optimal weight: 10.0000 chunk 561 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 728 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 306 ASN C 414 GLN D 137 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** E 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN G 137 ASN ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 ASN ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 414 GLN ** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN P 13 GLN R 13 GLN T 13 GLN U 124 ASN W 13 GLN W 64 GLN X 124 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 69432 Z= 0.469 Angle : 0.780 11.926 93864 Z= 0.391 Chirality : 0.050 0.250 9948 Planarity : 0.006 0.053 12564 Dihedral : 5.691 22.416 9456 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer Outliers : 4.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.08), residues: 8412 helix: -2.93 (0.08), residues: 3240 sheet: -1.48 (0.19), residues: 648 loop : -3.11 (0.07), residues: 4524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1703 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1379 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 324 outliers final: 182 residues processed: 1613 average time/residue: 0.6196 time to fit residues: 1703.5315 Evaluate side-chains 1442 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1260 time to evaluate : 6.143 Switching outliers to nearest non-outliers outliers start: 182 outliers final: 0 residues processed: 182 average time/residue: 0.4759 time to fit residues: 174.4220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 0.0980 chunk 731 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 476 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 812 optimal weight: 9.9990 chunk 674 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 426 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 137 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN D 137 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 370 ASN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN F 542 GLN G 137 ASN ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN H 370 ASN ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN I 542 GLN J 137 ASN ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 GLN K 137 ASN ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN L 306 ASN L 320 ASN L 542 GLN ** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 HIS O 13 GLN ** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN T 13 GLN T 124 ASN U 124 ASN V 66 ASN W 13 GLN X 124 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 69432 Z= 0.168 Angle : 0.615 10.493 93864 Z= 0.307 Chirality : 0.043 0.167 9948 Planarity : 0.004 0.052 12564 Dihedral : 5.004 20.480 9456 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.08), residues: 8412 helix: -2.61 (0.08), residues: 3324 sheet: -1.09 (0.21), residues: 528 loop : -2.92 (0.07), residues: 4560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1402 time to evaluate : 6.089 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 outliers start: 135 outliers final: 92 residues processed: 1486 average time/residue: 0.6275 time to fit residues: 1590.5180 Evaluate side-chains 1430 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1338 time to evaluate : 6.176 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 0.4903 time to fit residues: 94.9962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 463 optimal weight: 8.9990 chunk 593 optimal weight: 0.4980 chunk 459 optimal weight: 0.9990 chunk 684 optimal weight: 8.9990 chunk 453 optimal weight: 10.0000 chunk 809 optimal weight: 0.7980 chunk 506 optimal weight: 4.9990 chunk 493 optimal weight: 2.9990 chunk 373 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 370 ASN ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 HIS P 108 HIS ** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN S 80 GLN X 124 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 69432 Z= 0.143 Angle : 0.583 10.062 93864 Z= 0.290 Chirality : 0.042 0.183 9948 Planarity : 0.004 0.047 12564 Dihedral : 4.560 19.352 9456 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.08), residues: 8412 helix: -2.23 (0.08), residues: 3336 sheet: -0.75 (0.22), residues: 528 loop : -2.76 (0.08), residues: 4548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1426 time to evaluate : 6.260 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 outliers start: 56 outliers final: 29 residues processed: 1452 average time/residue: 0.6339 time to fit residues: 1569.6872 Evaluate side-chains 1385 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1356 time to evaluate : 6.134 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5007 time to fit residues: 35.7890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 6.9990 chunk 323 optimal weight: 1.9990 chunk 483 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 chunk 156 optimal weight: 10.0000 chunk 514 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 chunk 400 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 636 optimal weight: 7.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 ASN F 542 GLN ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN L 542 GLN ** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 124 ASN V 13 GLN ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 124 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 69432 Z= 0.235 Angle : 0.638 12.185 93864 Z= 0.318 Chirality : 0.045 0.160 9948 Planarity : 0.004 0.050 12564 Dihedral : 4.778 19.443 9456 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.08), residues: 8412 helix: -2.08 (0.09), residues: 3264 sheet: -0.85 (0.21), residues: 528 loop : -2.72 (0.08), residues: 4620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1349 time to evaluate : 6.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 59 residues processed: 1397 average time/residue: 0.6334 time to fit residues: 1508.6425 Evaluate side-chains 1398 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1339 time to evaluate : 6.174 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.5070 time to fit residues: 64.3337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 0.3980 chunk 775 optimal weight: 9.9990 chunk 707 optimal weight: 9.9990 chunk 754 optimal weight: 9.9990 chunk 454 optimal weight: 0.0370 chunk 328 optimal weight: 6.9990 chunk 592 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 681 optimal weight: 1.9990 chunk 713 optimal weight: 0.0050 chunk 751 optimal weight: 4.9990 overall best weight: 1.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 542 GLN ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 542 GLN N 124 ASN ** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 69432 Z= 0.161 Angle : 0.604 11.209 93864 Z= 0.299 Chirality : 0.043 0.159 9948 Planarity : 0.004 0.048 12564 Dihedral : 4.547 19.356 9456 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.08), residues: 8412 helix: -1.84 (0.09), residues: 3312 sheet: -0.70 (0.22), residues: 528 loop : -2.62 (0.08), residues: 4572 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1344 time to evaluate : 6.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 1360 average time/residue: 0.6403 time to fit residues: 1479.2155 Evaluate side-chains 1335 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1321 time to evaluate : 6.099 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5046 time to fit residues: 21.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 0.0370 chunk 797 optimal weight: 0.9990 chunk 486 optimal weight: 20.0000 chunk 378 optimal weight: 1.9990 chunk 554 optimal weight: 6.9990 chunk 836 optimal weight: 0.6980 chunk 770 optimal weight: 10.0000 chunk 666 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 514 optimal weight: 7.9990 chunk 408 optimal weight: 9.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 542 GLN ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 542 GLN N 124 ASN ** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 69432 Z= 0.148 Angle : 0.591 11.181 93864 Z= 0.292 Chirality : 0.042 0.152 9948 Planarity : 0.004 0.047 12564 Dihedral : 4.341 18.548 9456 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.08), residues: 8412 helix: -1.59 (0.09), residues: 3468 sheet: -0.52 (0.22), residues: 528 loop : -2.56 (0.08), residues: 4416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16824 Ramachandran restraints generated. 8412 Oldfield, 0 Emsley, 8412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1361 time to evaluate : 6.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 1370 average time/residue: 0.6335 time to fit residues: 1472.2730 Evaluate side-chains 1350 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1336 time to evaluate : 6.078 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4803 time to fit residues: 21.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 4.9990 chunk 709 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 614 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 667 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 685 optimal weight: 0.0030 chunk 84 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 ASN ** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 542 GLN G 402 ASN ** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 510 GLN ** I 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN L 260 ASN L 542 GLN N 124 ASN ** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 13 GLN ** X 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.112531 restraints weight = 91215.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.114983 restraints weight = 55433.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.116540 restraints weight = 39567.409| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 69432 Z= 0.255 Angle : 0.663 13.683 93864 Z= 0.328 Chirality : 0.046 0.221 9948 Planarity : 0.004 0.049 12564 Dihedral : 4.707 19.410 9456 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.08), residues: 8412 helix: -1.66 (0.09), residues: 3444 sheet: -1.07 (0.21), residues: 564 loop : -2.60 (0.08), residues: 4404 =============================================================================== Job complete usr+sys time: 21383.22 seconds wall clock time: 370 minutes 53.06 seconds (22253.06 seconds total)