Starting phenix.real_space_refine (version: dev)
on Sun Feb 26 22:51:01 2023 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/02_2023/7eep_31079.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/02_2023/7eep_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_31079/02_2023/7eep_31079.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/02_2023/7eep_31079.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/02_2023/7eep_31079.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eep_31079/02_2023/7eep_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
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-4877/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: 27.79, 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: 19.15
  Conformation dependent library (CDL) restraints added in 7.3 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: 2.76
  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: 21.82

  Time building geometry restraints manager: 21.24 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:             1.280
  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:             0.050
  Extract box with map and model:          10.510
  Check model and map are aligned:         0.760
  Process input model:                     125.720
  Find NCS groups from input model:        3.490
  Set up NCS constraints:                  0.500
  Set refine NCS operators:                0.000
  Set scattering table:                    0.460
  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:2.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  144.950
-------------------------------------------------------------------------------
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  : 6.093 
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: 0.7074
  time to fit residues: 2559.2346
Evaluate side-chains
  1446 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 1414
  time to evaluate  : 6.115 
Switching outliers to nearest non-outliers
  outliers start: 32
  outliers final: 0
  residues processed: 32
  average time/residue: 0.4986
  time to fit residues: 39.3443
-------------------------------------------------------------------------------
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  : 6.311 
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
  outliers start: 223
  outliers final: 96
  residues processed: 1742
  average time/residue: 0.6726
  time to fit residues: 1957.9584
Evaluate side-chains
  1441 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 96
    poor density    : 1345
  time to evaluate  : 6.062 
Switching outliers to nearest non-outliers
  outliers start: 96
  outliers final: 0
  residues processed: 96
  average time/residue: 0.4799
  time to fit residues: 97.3351
-------------------------------------------------------------------------------
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:    6.9990
   chunk 519 optimal weight:    9.9990
   chunk 210 optimal weight:    3.9990
   chunk 764 optimal weight:    4.9990
   chunk 825 optimal weight:    1.9990
   chunk 680 optimal weight:   10.0000
   chunk 757 optimal weight:    0.0370
   chunk 260 optimal weight:   10.0000
   chunk 613 optimal weight:    0.1980
   overall best weight:    2.2464

-------------------------------------------------------------------------------
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 414 GLN
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 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 414 GLN
L 542 GLN
M  64 GLN
** Q  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 0.8371
moved from start:          0.2754

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= 0.210
  Angle     :  0.648  13.670  93864  Z= 0.320
  Chirality :  0.043   0.210   9948
  Planarity :  0.005   0.048  12564
  Dihedral  :  5.327  21.299   9456
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer Outliers :  2.36 %
  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: -4.64 (0.07), residues: 8412
  helix: -3.40 (0.07), residues: 3288
  sheet: -0.61 (0.26), residues: 384
  loop : -3.15 (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
  1606 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 166
    poor density    : 1440
  time to evaluate  : 6.022 
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: 166
  outliers final: 75
  residues processed: 1571
  average time/residue: 0.6441
  time to fit residues: 1724.5943
Evaluate side-chains
  1414 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 75
    poor density    : 1339
  time to evaluate  : 6.061 
Switching outliers to nearest non-outliers
  outliers start: 75
  outliers final: 0
  residues processed: 75
  average time/residue: 0.4843
  time to fit residues: 78.1992
-------------------------------------------------------------------------------
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:    0.9990
   chunk 574 optimal weight:    0.9990
   chunk 396 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 364 optimal weight:   10.0000
   chunk 513 optimal weight:    8.9990
   chunk 766 optimal weight:    8.9990
   chunk 811 optimal weight:    4.9990
   chunk 400 optimal weight:   10.0000
   chunk 726 optimal weight:    7.9990
   chunk 218 optimal weight:    6.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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**
C 306 ASN
C 320 ASN
** C 414 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**
F 320 ASN
G 320 ASN
** G 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**
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 306 ASN
** L 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  13 GLN
** S 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 124 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.048  69432  Z= 0.334
  Angle     :  0.700  11.859  93864  Z= 0.351
  Chirality :  0.046   0.234   9948
  Planarity :  0.005   0.051  12564
  Dihedral  :  5.512  22.116   9456
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer Outliers :  4.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.38 (0.08), residues: 8412
  helix: -3.05 (0.08), residues: 3240
  sheet: -1.25 (0.22), residues: 528
  loop : -3.08 (0.07), residues: 4644

*********************** 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
  1669 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 304
    poor density    : 1365
  time to evaluate  : 6.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 304
  outliers final: 179
  residues processed: 1565
  average time/residue: 0.6578
  time to fit residues: 1750.7790
Evaluate side-chains
  1425 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 179
    poor density    : 1246
  time to evaluate  : 6.602 
Switching outliers to nearest non-outliers
  outliers start: 179
  outliers final: 0
  residues processed: 179
  average time/residue: 0.5091
  time to fit residues: 182.3605
-------------------------------------------------------------------------------
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:   10.0000
   chunk 460 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 604 optimal weight:    5.9990
   chunk 335 optimal weight:    8.9990
   chunk 692 optimal weight:    0.0670
   chunk 561 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 414 optimal weight:   20.0000
   chunk 728 optimal weight:    7.9990
   chunk 204 optimal weight:    1.9990
   overall best weight:    4.0126

-------------------------------------------------------------------------------
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**
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 370 ASN
F 542 GLN
** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 542 GLN
** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 542 GLN
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T 124 ASN
V  66 ASN
W  64 GLN
X 124 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.047  69432  Z= 0.318
  Angle     :  0.691  12.669  93864  Z= 0.344
  Chirality :  0.046   0.161   9948
  Planarity :  0.005   0.051  12564
  Dihedral  :  5.408  21.667   9456
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer Outliers :  2.42 %
  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: -4.25 (0.08), residues: 8412
  helix: -2.83 (0.08), residues: 3168
  sheet: -1.48 (0.19), residues: 648
  loop : -3.11 (0.07), residues: 4596

*********************** 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
  1521 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 170
    poor density    : 1351
  time to evaluate  : 6.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 170
  outliers final: 96
  residues processed: 1477
  average time/residue: 0.6442
  time to fit residues: 1624.6603
Evaluate side-chains
  1369 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 96
    poor density    : 1273
  time to evaluate  : 6.025 
Switching outliers to nearest non-outliers
  outliers start: 96
  outliers final: 0
  residues processed: 96
  average time/residue: 0.5024
  time to fit residues: 99.9294
-------------------------------------------------------------------------------
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:    9.9990
   chunk 731 optimal weight:    9.9990
   chunk 160 optimal weight:    0.8980
   chunk 476 optimal weight:    0.9980
   chunk 200 optimal weight:   10.0000
   chunk 812 optimal weight:    6.9990
   chunk 674 optimal weight:    4.9990
   chunk 376 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 268 optimal weight:   10.0000
   chunk 426 optimal weight:    3.9990
   overall best weight:    3.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 ASN
** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 121 ASN
C 542 GLN
D 121 ASN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 121 ASN
** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 121 ASN
F 542 GLN
G 121 ASN
G 402 ASN
** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 121 ASN
** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 121 ASN
I 542 GLN
J 121 ASN
** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 121 ASN
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 542 GLN
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
X 124 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3387

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= 0.275
  Angle     :  0.668  12.993  93864  Z= 0.332
  Chirality :  0.045   0.161   9948
  Planarity :  0.005   0.050  12564
  Dihedral  :  5.270  21.340   9456
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer Outliers :  2.82 %
  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: -4.08 (0.08), residues: 8412
  helix: -2.72 (0.08), residues: 3240
  sheet: -1.15 (0.19), residues: 624
  loop : -3.00 (0.08), residues: 4548

*********************** 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
  1513 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 198
    poor density    : 1315
  time to evaluate  : 7.284 
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: 198
  outliers final: 130
  residues processed: 1434
  average time/residue: 0.6524
  time to fit residues: 1601.9926
Evaluate side-chains
  1408 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 130
    poor density    : 1278
  time to evaluate  : 6.042 
Switching outliers to nearest non-outliers
  outliers start: 130
  outliers final: 0
  residues processed: 130
  average time/residue: 0.5119
  time to fit residues: 133.4069
-------------------------------------------------------------------------------
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:    0.7980
   chunk 91 optimal weight:    0.0470
   chunk 463 optimal weight:    0.0570
   chunk 593 optimal weight:    8.9990
   chunk 459 optimal weight:    6.9990
   chunk 684 optimal weight:    7.9990
   chunk 453 optimal weight:    0.1980
   chunk 809 optimal weight:    6.9990
   chunk 506 optimal weight:   10.0000
   chunk 493 optimal weight:    0.9980
   chunk 373 optimal weight:    4.9990
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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**
** B 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 402 ASN
C 542 GLN
** 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**
I 542 GLN
** 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
M 108 HIS
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  80 GLN
S 108 HIS
W  13 GLN
X 124 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033  69432  Z= 0.140
  Angle     :  0.588  10.850  93864  Z= 0.292
  Chirality :  0.042   0.163   9948
  Planarity :  0.004   0.049  12564
  Dihedral  :  4.637  19.143   9456
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer Outliers :  0.74 %
  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: -3.71 (0.08), residues: 8412
  helix: -2.41 (0.08), residues: 3420
  sheet: -0.77 (0.19), residues: 624
  loop : -2.80 (0.08), residues: 4368

*********************** 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
  1515 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 1463
  time to evaluate  : 6.075 
Fit side-chains
   revert: symmetry clash
  outliers start: 52
  outliers final: 17
  residues processed: 1494
  average time/residue: 0.6688
  time to fit residues: 1698.1882
Evaluate side-chains
  1367 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 1350
  time to evaluate  : 6.043 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.5539
  time to fit residues: 25.5218
-------------------------------------------------------------------------------
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:    8.9990
   chunk 323 optimal weight:    7.9990
   chunk 483 optimal weight:    2.9990
   chunk 243 optimal weight:    8.9990
   chunk 159 optimal weight:   10.0000
   chunk 156 optimal weight:   10.0000
   chunk 514 optimal weight:    9.9990
   chunk 551 optimal weight:    4.9990
   chunk 400 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 636 optimal weight:    3.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
A 402 ASN
** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 567 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**
C 137 ASN
D 137 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 137 ASN
** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 137 ASN
** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 137 ASN
** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 137 ASN
J 402 ASN
** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 137 ASN
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O  13 GLN
P  13 GLN
P 124 ASN
** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  13 GLN
T 124 ASN
U 124 ASN
W  13 GLN
X  13 GLN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.057  69432  Z= 0.360
  Angle     :  0.710  14.305  93864  Z= 0.353
  Chirality :  0.048   0.168   9948
  Planarity :  0.005   0.055  12564
  Dihedral  :  5.165  21.210   9456
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer Outliers :  2.05 %
  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: -3.84 (0.08), residues: 8412
  helix: -2.43 (0.08), residues: 3372
  sheet: -0.98 (0.19), residues: 624
  loop : -2.93 (0.08), residues: 4416

*********************** 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
  1445 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 144
    poor density    : 1301
  time to evaluate  : 6.187 
Fit side-chains
  outliers start: 144
  outliers final: 84
  residues processed: 1371
  average time/residue: 0.6633
  time to fit residues: 1553.8235
Evaluate side-chains
  1349 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 1265
  time to evaluate  : 6.040 
Switching outliers to nearest non-outliers
  outliers start: 84
  outliers final: 0
  residues processed: 84
  average time/residue: 0.5241
  time to fit residues: 91.0049
-------------------------------------------------------------------------------
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:    6.9990
   chunk 775 optimal weight:    0.1980
   chunk 707 optimal weight:    5.9990
   chunk 754 optimal weight:    5.9990
   chunk 454 optimal weight:    7.9990
   chunk 328 optimal weight:    6.9990
   chunk 592 optimal weight:    2.9990
   chunk 231 optimal weight:    0.6980
   chunk 681 optimal weight:    2.9990
   chunk 713 optimal weight:   10.0000
   chunk 751 optimal weight:    6.9990
   overall best weight:    2.5786

-------------------------------------------------------------------------------
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**
A 547 GLN
** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 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**
D 547 GLN
** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 402 ASN
** G 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 547 GLN
** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 402 ASN
** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 547 GLN
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 124 ASN
** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  13 GLN
R  80 GLN
T  13 GLN
U 124 ASN
** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
W  13 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.048  69432  Z= 0.232
  Angle     :  0.659  15.638  93864  Z= 0.327
  Chirality :  0.045   0.177   9948
  Planarity :  0.004   0.055  12564
  Dihedral  :  4.982  20.442   9456
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer Outliers :  0.64 %
  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: -3.64 (0.08), residues: 8412
  helix: -2.24 (0.08), residues: 3384
  sheet: -0.87 (0.19), residues: 624
  loop : -2.84 (0.08), residues: 4404

*********************** 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
  1395 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 1350
  time to evaluate  : 6.157 
Fit side-chains
  outliers start: 45
  outliers final: 25
  residues processed: 1370
  average time/residue: 0.6655
  time to fit residues: 1565.2623
Evaluate side-chains
  1328 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 1303
  time to evaluate  : 6.077 
Switching outliers to nearest non-outliers
  outliers start: 25
  outliers final: 0
  residues processed: 25
  average time/residue: 0.5060
  time to fit residues: 32.6839
-------------------------------------------------------------------------------
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:    3.9990
   chunk 797 optimal weight:    9.9990
   chunk 486 optimal weight:    9.9990
   chunk 378 optimal weight:    3.9990
   chunk 554 optimal weight:    0.0270
   chunk 836 optimal weight:    6.9990
   chunk 770 optimal weight:    7.9990
   chunk 666 optimal weight:    8.9990
   chunk 69 optimal weight:    8.9990
   chunk 514 optimal weight:    2.9990
   chunk 408 optimal weight:    6.9990
   overall best weight:    3.6046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 ASN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 547 GLN
** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 547 GLN
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 124 ASN
** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
U 124 ASN
** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.047  69432  Z= 0.292
  Angle     :  0.694  15.748  93864  Z= 0.345
  Chirality :  0.046   0.163   9948
  Planarity :  0.005   0.056  12564
  Dihedral  :  5.116  20.868   9456
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer Outliers :  0.68 %
  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: -3.68 (0.08), residues: 8412
  helix: -2.16 (0.08), residues: 3384
  sheet: -1.49 (0.17), residues: 732
  loop : -2.89 (0.08), residues: 4296

********************** 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
  1340 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 1292
  time to evaluate  : 6.139 
Fit side-chains
  outliers start: 48
  outliers final: 26
  residues processed: 1316
  average time/residue: 0.6623
  time to fit residues: 1486.4815
Evaluate side-chains
  1304 residues out of total 7032 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 1278
  time to evaluate  : 6.077 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 0
  residues processed: 26
  average time/residue: 0.4971
  time to fit residues: 33.0191
-------------------------------------------------------------------------------
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:    0.6980
   chunk 709 optimal weight:    2.9990
   chunk 204 optimal weight:    2.9990
   chunk 614 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 185 optimal weight:    0.7980
   chunk 667 optimal weight:   10.0000
   chunk 279 optimal weight:    2.9990
   chunk 685 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 122 optimal weight:   20.0000
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 137 ASN
** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**
G 547 GLN
** H 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 547 GLN
** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 119 HIS
N 124 ASN
** P 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  80 GLN
** V 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.139068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.112751 restraints weight = 91284.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.115198 restraints weight = 54852.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.116785 restraints weight = 38992.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040  69432  Z= 0.203
  Angle     :  0.648  15.305  93864  Z= 0.322
  Chirality :  0.044   0.155   9948
  Planarity :  0.004   0.054  12564
  Dihedral  :  4.878  20.148   9456
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer Outliers :  0.43 %
  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: -3.35 (0.08), residues: 8412
  helix: -1.92 (0.09), residues: 3384
  sheet: -0.77 (0.19), residues: 624
  loop : -2.75 (0.08), residues: 4404

===============================================================================
Job complete
usr+sys time: 22257.56 seconds
wall clock time: 385 minutes 57.89 seconds (23157.89 seconds total)