Starting phenix.real_space_refine
on Thu Mar 14 21:04:52 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/03_2024/6wx6_21951.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/03_2024/6wx6_21951.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/03_2024/6wx6_21951.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/03_2024/6wx6_21951.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/03_2024/6wx6_21951.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/03_2024/6wx6_21951.pdb"
  }
  resolution = 2.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.431
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      8      9.91       5
     S     120      5.16       5
     C   21000      2.51       5
     N    5808      2.21       5
     O    8732      1.98       5
     H   32664      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ASP   15": "OD1" <-> "OD2"
    Residue "A GLU   17": "OE1" <-> "OE2"
    Residue "A PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP   42": "OD1" <-> "OD2"
    Residue "A ASP   45": "OD1" <-> "OD2"
    Residue "A PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   60": "OE1" <-> "OE2"
    Residue "A TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   67": "OE1" <-> "OE2"
    Residue "A ASP   84": "OD1" <-> "OD2"
    Residue "A GLU   90": "OE1" <-> "OE2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  139": "OD1" <-> "OD2"
    Residue "A GLU  141": "OE1" <-> "OE2"
    Residue "A GLU  167": "OE1" <-> "OE2"
    Residue "A TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  171": "OE1" <-> "OE2"
    Residue "B ASP   15": "OD1" <-> "OD2"
    Residue "B GLU   17": "OE1" <-> "OE2"
    Residue "B PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP   42": "OD1" <-> "OD2"
    Residue "B ASP   45": "OD1" <-> "OD2"
    Residue "B PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU   60": "OE1" <-> "OE2"
    Residue "B TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU   67": "OE1" <-> "OE2"
    Residue "B ASP   84": "OD1" <-> "OD2"
    Residue "B GLU   90": "OE1" <-> "OE2"
    Residue "B ASP  116": "OD1" <-> "OD2"
    Residue "B PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B ASP  139": "OD1" <-> "OD2"
    Residue "B GLU  141": "OE1" <-> "OE2"
    Residue "B GLU  167": "OE1" <-> "OE2"
    Residue "B TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B GLU  171": "OE1" <-> "OE2"
    Residue "C ASP   15": "OD1" <-> "OD2"
    Residue "C GLU   17": "OE1" <-> "OE2"
    Residue "C PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ASP   42": "OD1" <-> "OD2"
    Residue "C ASP   45": "OD1" <-> "OD2"
    Residue "C PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU   60": "OE1" <-> "OE2"
    Residue "C TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU   67": "OE1" <-> "OE2"
    Residue "C ASP   84": "OD1" <-> "OD2"
    Residue "C GLU   90": "OE1" <-> "OE2"
    Residue "C ASP  116": "OD1" <-> "OD2"
    Residue "C PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C ASP  139": "OD1" <-> "OD2"
    Residue "C GLU  141": "OE1" <-> "OE2"
    Residue "C GLU  167": "OE1" <-> "OE2"
    Residue "C TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C GLU  171": "OE1" <-> "OE2"
    Residue "D ASP   15": "OD1" <-> "OD2"
    Residue "D GLU   17": "OE1" <-> "OE2"
    Residue "D PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP   42": "OD1" <-> "OD2"
    Residue "D ASP   45": "OD1" <-> "OD2"
    Residue "D PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU   60": "OE1" <-> "OE2"
    Residue "D TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU   67": "OE1" <-> "OE2"
    Residue "D ASP   84": "OD1" <-> "OD2"
    Residue "D GLU   90": "OE1" <-> "OE2"
    Residue "D ASP  116": "OD1" <-> "OD2"
    Residue "D PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D ASP  139": "OD1" <-> "OD2"
    Residue "D GLU  141": "OE1" <-> "OE2"
    Residue "D GLU  167": "OE1" <-> "OE2"
    Residue "D TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "D GLU  171": "OE1" <-> "OE2"
    Residue "E ASP   15": "OD1" <-> "OD2"
    Residue "E GLU   17": "OE1" <-> "OE2"
    Residue "E PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E ASP   42": "OD1" <-> "OD2"
    Residue "E ASP   45": "OD1" <-> "OD2"
    Residue "E PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU   60": "OE1" <-> "OE2"
    Residue "E TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU   67": "OE1" <-> "OE2"
    Residue "E ASP   84": "OD1" <-> "OD2"
    Residue "E GLU   90": "OE1" <-> "OE2"
    Residue "E ASP  116": "OD1" <-> "OD2"
    Residue "E PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E ASP  139": "OD1" <-> "OD2"
    Residue "E GLU  141": "OE1" <-> "OE2"
    Residue "E GLU  167": "OE1" <-> "OE2"
    Residue "E TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "E GLU  171": "OE1" <-> "OE2"
    Residue "F ASP   15": "OD1" <-> "OD2"
    Residue "F GLU   17": "OE1" <-> "OE2"
    Residue "F PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F ASP   42": "OD1" <-> "OD2"
    Residue "F ASP   45": "OD1" <-> "OD2"
    Residue "F PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F GLU   60": "OE1" <-> "OE2"
    Residue "F TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F GLU   67": "OE1" <-> "OE2"
    Residue "F ASP   84": "OD1" <-> "OD2"
    Residue "F GLU   90": "OE1" <-> "OE2"
    Residue "F ASP  116": "OD1" <-> "OD2"
    Residue "F PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F ASP  139": "OD1" <-> "OD2"
    Residue "F GLU  141": "OE1" <-> "OE2"
    Residue "F GLU  167": "OE1" <-> "OE2"
    Residue "F TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "F GLU  171": "OE1" <-> "OE2"
    Residue "G ASP   15": "OD1" <-> "OD2"
    Residue "G GLU   17": "OE1" <-> "OE2"
    Residue "G PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G ASP   42": "OD1" <-> "OD2"
    Residue "G ASP   45": "OD1" <-> "OD2"
    Residue "G PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU   60": "OE1" <-> "OE2"
    Residue "G TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU   67": "OE1" <-> "OE2"
    Residue "G ASP   84": "OD1" <-> "OD2"
    Residue "G GLU   90": "OE1" <-> "OE2"
    Residue "G ASP  116": "OD1" <-> "OD2"
    Residue "G PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G ASP  139": "OD1" <-> "OD2"
    Residue "G GLU  141": "OE1" <-> "OE2"
    Residue "G GLU  167": "OE1" <-> "OE2"
    Residue "G TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "G GLU  171": "OE1" <-> "OE2"
    Residue "H ASP   15": "OD1" <-> "OD2"
    Residue "H GLU   17": "OE1" <-> "OE2"
    Residue "H PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP   42": "OD1" <-> "OD2"
    Residue "H ASP   45": "OD1" <-> "OD2"
    Residue "H PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU   60": "OE1" <-> "OE2"
    Residue "H TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU   67": "OE1" <-> "OE2"
    Residue "H ASP   84": "OD1" <-> "OD2"
    Residue "H GLU   90": "OE1" <-> "OE2"
    Residue "H ASP  116": "OD1" <-> "OD2"
    Residue "H PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H ASP  139": "OD1" <-> "OD2"
    Residue "H GLU  141": "OE1" <-> "OE2"
    Residue "H GLU  167": "OE1" <-> "OE2"
    Residue "H TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "H GLU  171": "OE1" <-> "OE2"
    Residue "I ASP   15": "OD1" <-> "OD2"
    Residue "I GLU   17": "OE1" <-> "OE2"
    Residue "I PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I ASP   42": "OD1" <-> "OD2"
    Residue "I ASP   45": "OD1" <-> "OD2"
    Residue "I PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I GLU   60": "OE1" <-> "OE2"
    Residue "I TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I GLU   67": "OE1" <-> "OE2"
    Residue "I ASP   84": "OD1" <-> "OD2"
    Residue "I GLU   90": "OE1" <-> "OE2"
    Residue "I ASP  116": "OD1" <-> "OD2"
    Residue "I PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I ASP  139": "OD1" <-> "OD2"
    Residue "I GLU  141": "OE1" <-> "OE2"
    Residue "I GLU  167": "OE1" <-> "OE2"
    Residue "I TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "I GLU  171": "OE1" <-> "OE2"
    Residue "J ASP   15": "OD1" <-> "OD2"
    Residue "J GLU   17": "OE1" <-> "OE2"
    Residue "J PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J ASP   42": "OD1" <-> "OD2"
    Residue "J ASP   45": "OD1" <-> "OD2"
    Residue "J PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J GLU   60": "OE1" <-> "OE2"
    Residue "J TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J GLU   67": "OE1" <-> "OE2"
    Residue "J ASP   84": "OD1" <-> "OD2"
    Residue "J GLU   90": "OE1" <-> "OE2"
    Residue "J ASP  116": "OD1" <-> "OD2"
    Residue "J PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J ASP  139": "OD1" <-> "OD2"
    Residue "J GLU  141": "OE1" <-> "OE2"
    Residue "J GLU  167": "OE1" <-> "OE2"
    Residue "J TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "J GLU  171": "OE1" <-> "OE2"
    Residue "K ASP   15": "OD1" <-> "OD2"
    Residue "K GLU   17": "OE1" <-> "OE2"
    Residue "K PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "K ASP   42": "OD1" <-> "OD2"
    Residue "K ASP   45": "OD1" <-> "OD2"
    Residue "K PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "K GLU   60": "OE1" <-> "OE2"
    Residue "K TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "K GLU   67": "OE1" <-> "OE2"
    Residue "K ASP   84": "OD1" <-> "OD2"
    Residue "K GLU   90": "OE1" <-> "OE2"
    Residue "K ASP  116": "OD1" <-> "OD2"
    Residue "K PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "K PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "K ASP  139": "OD1" <-> "OD2"
    Residue "K GLU  141": "OE1" <-> "OE2"
    Residue "K GLU  167": "OE1" <-> "OE2"
    Residue "K TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "K GLU  171": "OE1" <-> "OE2"
    Residue "L ASP   15": "OD1" <-> "OD2"
    Residue "L GLU   17": "OE1" <-> "OE2"
    Residue "L PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L ASP   42": "OD1" <-> "OD2"
    Residue "L ASP   45": "OD1" <-> "OD2"
    Residue "L PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L GLU   60": "OE1" <-> "OE2"
    Residue "L TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L GLU   67": "OE1" <-> "OE2"
    Residue "L ASP   84": "OD1" <-> "OD2"
    Residue "L GLU   90": "OE1" <-> "OE2"
    Residue "L ASP  116": "OD1" <-> "OD2"
    Residue "L PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L ASP  139": "OD1" <-> "OD2"
    Residue "L GLU  141": "OE1" <-> "OE2"
    Residue "L GLU  167": "OE1" <-> "OE2"
    Residue "L TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "L GLU  171": "OE1" <-> "OE2"
    Residue "M ASP   15": "OD1" <-> "OD2"
    Residue "M GLU   17": "OE1" <-> "OE2"
    Residue "M PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "M ASP   42": "OD1" <-> "OD2"
    Residue "M ASP   45": "OD1" <-> "OD2"
    Residue "M PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "M GLU   60": "OE1" <-> "OE2"
    Residue "M TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "M GLU   67": "OE1" <-> "OE2"
    Residue "M ASP   84": "OD1" <-> "OD2"
    Residue "M GLU   90": "OE1" <-> "OE2"
    Residue "M ASP  116": "OD1" <-> "OD2"
    Residue "M PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "M PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "M ASP  139": "OD1" <-> "OD2"
    Residue "M GLU  141": "OE1" <-> "OE2"
    Residue "M GLU  167": "OE1" <-> "OE2"
    Residue "M TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "M GLU  171": "OE1" <-> "OE2"
    Residue "N ASP   15": "OD1" <-> "OD2"
    Residue "N GLU   17": "OE1" <-> "OE2"
    Residue "N PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N ASP   42": "OD1" <-> "OD2"
    Residue "N ASP   45": "OD1" <-> "OD2"
    Residue "N PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N GLU   60": "OE1" <-> "OE2"
    Residue "N TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N GLU   67": "OE1" <-> "OE2"
    Residue "N ASP   84": "OD1" <-> "OD2"
    Residue "N GLU   90": "OE1" <-> "OE2"
    Residue "N ASP  116": "OD1" <-> "OD2"
    Residue "N PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N ASP  139": "OD1" <-> "OD2"
    Residue "N GLU  141": "OE1" <-> "OE2"
    Residue "N GLU  167": "OE1" <-> "OE2"
    Residue "N TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "N GLU  171": "OE1" <-> "OE2"
    Residue "O ASP   15": "OD1" <-> "OD2"
    Residue "O GLU   17": "OE1" <-> "OE2"
    Residue "O PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O ASP   42": "OD1" <-> "OD2"
    Residue "O ASP   45": "OD1" <-> "OD2"
    Residue "O PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O GLU   60": "OE1" <-> "OE2"
    Residue "O TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O GLU   67": "OE1" <-> "OE2"
    Residue "O ASP   84": "OD1" <-> "OD2"
    Residue "O GLU   90": "OE1" <-> "OE2"
    Residue "O ASP  116": "OD1" <-> "OD2"
    Residue "O PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O ASP  139": "OD1" <-> "OD2"
    Residue "O GLU  141": "OE1" <-> "OE2"
    Residue "O GLU  167": "OE1" <-> "OE2"
    Residue "O TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "O GLU  171": "OE1" <-> "OE2"
    Residue "P ASP   15": "OD1" <-> "OD2"
    Residue "P GLU   17": "OE1" <-> "OE2"
    Residue "P PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P ASP   42": "OD1" <-> "OD2"
    Residue "P ASP   45": "OD1" <-> "OD2"
    Residue "P PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P GLU   60": "OE1" <-> "OE2"
    Residue "P TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P GLU   67": "OE1" <-> "OE2"
    Residue "P ASP   84": "OD1" <-> "OD2"
    Residue "P GLU   90": "OE1" <-> "OE2"
    Residue "P ASP  116": "OD1" <-> "OD2"
    Residue "P PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P ASP  139": "OD1" <-> "OD2"
    Residue "P GLU  141": "OE1" <-> "OE2"
    Residue "P GLU  167": "OE1" <-> "OE2"
    Residue "P TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "P GLU  171": "OE1" <-> "OE2"
    Residue "Q ASP   15": "OD1" <-> "OD2"
    Residue "Q GLU   17": "OE1" <-> "OE2"
    Residue "Q PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q ASP   42": "OD1" <-> "OD2"
    Residue "Q ASP   45": "OD1" <-> "OD2"
    Residue "Q PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q GLU   60": "OE1" <-> "OE2"
    Residue "Q TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q GLU   67": "OE1" <-> "OE2"
    Residue "Q ASP   84": "OD1" <-> "OD2"
    Residue "Q GLU   90": "OE1" <-> "OE2"
    Residue "Q ASP  116": "OD1" <-> "OD2"
    Residue "Q PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q ASP  139": "OD1" <-> "OD2"
    Residue "Q GLU  141": "OE1" <-> "OE2"
    Residue "Q GLU  167": "OE1" <-> "OE2"
    Residue "Q TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "Q GLU  171": "OE1" <-> "OE2"
    Residue "R ASP   15": "OD1" <-> "OD2"
    Residue "R GLU   17": "OE1" <-> "OE2"
    Residue "R PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "R ASP   42": "OD1" <-> "OD2"
    Residue "R ASP   45": "OD1" <-> "OD2"
    Residue "R PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "R GLU   60": "OE1" <-> "OE2"
    Residue "R TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "R GLU   67": "OE1" <-> "OE2"
    Residue "R ASP   84": "OD1" <-> "OD2"
    Residue "R GLU   90": "OE1" <-> "OE2"
    Residue "R ASP  116": "OD1" <-> "OD2"
    Residue "R PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "R PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "R ASP  139": "OD1" <-> "OD2"
    Residue "R GLU  141": "OE1" <-> "OE2"
    Residue "R GLU  167": "OE1" <-> "OE2"
    Residue "R TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "R GLU  171": "OE1" <-> "OE2"
    Residue "S ASP   15": "OD1" <-> "OD2"
    Residue "S GLU   17": "OE1" <-> "OE2"
    Residue "S PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S ASP   42": "OD1" <-> "OD2"
    Residue "S ASP   45": "OD1" <-> "OD2"
    Residue "S PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S GLU   60": "OE1" <-> "OE2"
    Residue "S TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S GLU   67": "OE1" <-> "OE2"
    Residue "S ASP   84": "OD1" <-> "OD2"
    Residue "S GLU   90": "OE1" <-> "OE2"
    Residue "S ASP  116": "OD1" <-> "OD2"
    Residue "S PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S ASP  139": "OD1" <-> "OD2"
    Residue "S GLU  141": "OE1" <-> "OE2"
    Residue "S GLU  167": "OE1" <-> "OE2"
    Residue "S TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "S GLU  171": "OE1" <-> "OE2"
    Residue "T ASP   15": "OD1" <-> "OD2"
    Residue "T GLU   17": "OE1" <-> "OE2"
    Residue "T PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "T ASP   42": "OD1" <-> "OD2"
    Residue "T ASP   45": "OD1" <-> "OD2"
    Residue "T PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "T GLU   60": "OE1" <-> "OE2"
    Residue "T TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "T GLU   67": "OE1" <-> "OE2"
    Residue "T ASP   84": "OD1" <-> "OD2"
    Residue "T GLU   90": "OE1" <-> "OE2"
    Residue "T ASP  116": "OD1" <-> "OD2"
    Residue "T PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "T PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "T ASP  139": "OD1" <-> "OD2"
    Residue "T GLU  141": "OE1" <-> "OE2"
    Residue "T GLU  167": "OE1" <-> "OE2"
    Residue "T TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "T GLU  171": "OE1" <-> "OE2"
    Residue "U ASP   15": "OD1" <-> "OD2"
    Residue "U GLU   17": "OE1" <-> "OE2"
    Residue "U PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "U ASP   42": "OD1" <-> "OD2"
    Residue "U ASP   45": "OD1" <-> "OD2"
    Residue "U PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "U GLU   60": "OE1" <-> "OE2"
    Residue "U TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "U GLU   67": "OE1" <-> "OE2"
    Residue "U ASP   84": "OD1" <-> "OD2"
    Residue "U GLU   90": "OE1" <-> "OE2"
    Residue "U ASP  116": "OD1" <-> "OD2"
    Residue "U PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "U PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "U ASP  139": "OD1" <-> "OD2"
    Residue "U GLU  141": "OE1" <-> "OE2"
    Residue "U GLU  167": "OE1" <-> "OE2"
    Residue "U TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "U GLU  171": "OE1" <-> "OE2"
    Residue "V ASP   15": "OD1" <-> "OD2"
    Residue "V GLU   17": "OE1" <-> "OE2"
    Residue "V PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "V ASP   42": "OD1" <-> "OD2"
    Residue "V ASP   45": "OD1" <-> "OD2"
    Residue "V PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "V GLU   60": "OE1" <-> "OE2"
    Residue "V TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "V GLU   67": "OE1" <-> "OE2"
    Residue "V ASP   84": "OD1" <-> "OD2"
    Residue "V GLU   90": "OE1" <-> "OE2"
    Residue "V ASP  116": "OD1" <-> "OD2"
    Residue "V PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "V PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "V ASP  139": "OD1" <-> "OD2"
    Residue "V GLU  141": "OE1" <-> "OE2"
    Residue "V GLU  167": "OE1" <-> "OE2"
    Residue "V TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "V GLU  171": "OE1" <-> "OE2"
    Residue "W ASP   15": "OD1" <-> "OD2"
    Residue "W GLU   17": "OE1" <-> "OE2"
    Residue "W PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "W ASP   42": "OD1" <-> "OD2"
    Residue "W ASP   45": "OD1" <-> "OD2"
    Residue "W PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "W GLU   60": "OE1" <-> "OE2"
    Residue "W TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "W GLU   67": "OE1" <-> "OE2"
    Residue "W ASP   84": "OD1" <-> "OD2"
    Residue "W GLU   90": "OE1" <-> "OE2"
    Residue "W ASP  116": "OD1" <-> "OD2"
    Residue "W PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "W PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "W ASP  139": "OD1" <-> "OD2"
    Residue "W GLU  141": "OE1" <-> "OE2"
    Residue "W GLU  167": "OE1" <-> "OE2"
    Residue "W TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "W GLU  171": "OE1" <-> "OE2"
    Residue "X ASP   15": "OD1" <-> "OD2"
    Residue "X GLU   17": "OE1" <-> "OE2"
    Residue "X PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "X ASP   42": "OD1" <-> "OD2"
    Residue "X ASP   45": "OD1" <-> "OD2"
    Residue "X PHE   55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "X GLU   60": "OE1" <-> "OE2"
    Residue "X TYR   66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "X GLU   67": "OE1" <-> "OE2"
    Residue "X ASP   84": "OD1" <-> "OD2"
    Residue "X GLU   90": "OE1" <-> "OE2"
    Residue "X ASP  116": "OD1" <-> "OD2"
    Residue "X PHE  132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "X PHE  137": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "X ASP  139": "OD1" <-> "OD2"
    Residue "X GLU  141": "OE1" <-> "OE2"
    Residue "X GLU  167": "OE1" <-> "OE2"
    Residue "X TYR  168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "X GLU  171": "OE1" <-> "OE2"
  Time to flip residues: 0.11s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 68332
  Number of models: 1
  Model: ""
    Number of chains: 56
    Chain: "A"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "B"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "C"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "E"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "F"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "G"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "H"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "I"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "J"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "K"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "L"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "M"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "N"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "O"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "P"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "Q"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "R"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "S"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "T"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "U"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "V"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "W"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "X"
      Number of atoms: 2746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 2746
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "N"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "O"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "B"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 105
          Classifications: {'water': 105}
          Link IDs: {None: 104}
    Chain: "C"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 99
          Classifications: {'water': 99}
          Link IDs: {None: 98}
    Chain: "D"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 102
          Classifications: {'water': 102}
          Link IDs: {None: 101}
    Chain: "E"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 100
          Classifications: {'water': 100}
          Link IDs: {None: 99}
    Chain: "F"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "G"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 102
          Classifications: {'water': 102}
          Link IDs: {None: 101}
    Chain: "H"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "I"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 100
          Classifications: {'water': 100}
          Link IDs: {None: 99}
    Chain: "J"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 97
          Classifications: {'water': 97}
          Link IDs: {None: 96}
    Chain: "K"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 101
          Classifications: {'water': 101}
          Link IDs: {None: 100}
    Chain: "L"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 97
          Classifications: {'water': 97}
          Link IDs: {None: 96}
    Chain: "M"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 102
          Classifications: {'water': 102}
          Link IDs: {None: 101}
    Chain: "N"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 97
          Classifications: {'water': 97}
          Link IDs: {None: 96}
    Chain: "O"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "P"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 102
          Classifications: {'water': 102}
          Link IDs: {None: 101}
    Chain: "Q"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 97
          Classifications: {'water': 97}
          Link IDs: {None: 96}
    Chain: "R"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 99
          Classifications: {'water': 99}
          Link IDs: {None: 98}
    Chain: "S"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "T"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 101
          Classifications: {'water': 101}
          Link IDs: {None: 100}
    Chain: "U"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 103
          Classifications: {'water': 103}
          Link IDs: {None: 102}
    Chain: "V"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 99
          Classifications: {'water': 99}
          Link IDs: {None: 98}
    Chain: "W"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 100
          Classifications: {'water': 100}
          Link IDs: {None: 99}
    Chain: "X"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 102
          Classifications: {'water': 102}
          Link IDs: {None: 101}
  Time building chain proxies: 21.99, per 1000 atoms: 0.32
  Number of scatterers: 68332
  At special positions: 0
  Unit cell: (139.536, 139.536, 139.536, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      8     19.99
     S     120     16.00
     O    8732      8.00
     N    5808      7.00
     C   21000      6.00
     H   32664      1.00
    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: 46.27
  Conformation dependent library (CDL) restraints added in 4.8 seconds
  

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  7680

  Finding SS restraints...
    Secondary structure from input PDB file:
      144 helices and 0 sheets defined
      78.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 41
    Processing helix  chain 'A' and resid 48 through 76
    Processing helix  chain 'A' and resid 95 through 124
    Processing helix  chain 'A' and resid 126 through 137
    Processing helix  chain 'A' and resid 137 through 158
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'B' and resid 13 through 41
    Processing helix  chain 'B' and resid 48 through 76
    Processing helix  chain 'B' and resid 95 through 124
    Processing helix  chain 'B' and resid 126 through 137
    Processing helix  chain 'B' and resid 137 through 158
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'C' and resid 13 through 41
    Processing helix  chain 'C' and resid 48 through 76
    Processing helix  chain 'C' and resid 95 through 124
    Processing helix  chain 'C' and resid 126 through 137
    Processing helix  chain 'C' and resid 137 through 158
    Processing helix  chain 'C' and resid 162 through 174
    Processing helix  chain 'D' and resid 13 through 41
    Processing helix  chain 'D' and resid 48 through 76
    Processing helix  chain 'D' and resid 95 through 124
    Processing helix  chain 'D' and resid 126 through 137
    Processing helix  chain 'D' and resid 137 through 158
    Processing helix  chain 'D' and resid 162 through 174
    Processing helix  chain 'E' and resid 13 through 41
    Processing helix  chain 'E' and resid 48 through 76
    Processing helix  chain 'E' and resid 95 through 124
    Processing helix  chain 'E' and resid 126 through 137
    Processing helix  chain 'E' and resid 137 through 158
    Processing helix  chain 'E' and resid 162 through 174
    Processing helix  chain 'F' and resid 13 through 41
    Processing helix  chain 'F' and resid 48 through 76
    Processing helix  chain 'F' and resid 95 through 124
    Processing helix  chain 'F' and resid 126 through 137
    Processing helix  chain 'F' and resid 137 through 158
    Processing helix  chain 'F' and resid 162 through 174
    Processing helix  chain 'G' and resid 13 through 41
    Processing helix  chain 'G' and resid 48 through 76
    Processing helix  chain 'G' and resid 95 through 124
    Processing helix  chain 'G' and resid 126 through 137
    Processing helix  chain 'G' and resid 137 through 158
    Processing helix  chain 'G' and resid 162 through 174
    Processing helix  chain 'H' and resid 13 through 41
    Processing helix  chain 'H' and resid 48 through 76
    Processing helix  chain 'H' and resid 95 through 124
    Processing helix  chain 'H' and resid 126 through 137
    Processing helix  chain 'H' and resid 137 through 158
    Processing helix  chain 'H' and resid 162 through 174
    Processing helix  chain 'I' and resid 13 through 41
    Processing helix  chain 'I' and resid 48 through 76
    Processing helix  chain 'I' and resid 95 through 124
    Processing helix  chain 'I' and resid 126 through 137
    Processing helix  chain 'I' and resid 137 through 158
    Processing helix  chain 'I' and resid 162 through 174
    Processing helix  chain 'J' and resid 13 through 41
    Processing helix  chain 'J' and resid 48 through 76
    Processing helix  chain 'J' and resid 95 through 124
    Processing helix  chain 'J' and resid 126 through 137
    Processing helix  chain 'J' and resid 137 through 158
    Processing helix  chain 'J' and resid 162 through 174
    Processing helix  chain 'K' and resid 13 through 41
    Processing helix  chain 'K' and resid 48 through 76
    Processing helix  chain 'K' and resid 95 through 124
    Processing helix  chain 'K' and resid 126 through 137
    Processing helix  chain 'K' and resid 137 through 158
    Processing helix  chain 'K' and resid 162 through 174
    Processing helix  chain 'L' and resid 13 through 41
    Processing helix  chain 'L' and resid 48 through 76
    Processing helix  chain 'L' and resid 95 through 124
    Processing helix  chain 'L' and resid 126 through 137
    Processing helix  chain 'L' and resid 137 through 158
    Processing helix  chain 'L' and resid 162 through 174
    Processing helix  chain 'M' and resid 13 through 41
    Processing helix  chain 'M' and resid 48 through 76
    Processing helix  chain 'M' and resid 95 through 124
    Processing helix  chain 'M' and resid 126 through 137
    Processing helix  chain 'M' and resid 137 through 158
    Processing helix  chain 'M' and resid 162 through 174
    Processing helix  chain 'N' and resid 13 through 41
    Processing helix  chain 'N' and resid 48 through 76
    Processing helix  chain 'N' and resid 95 through 124
    Processing helix  chain 'N' and resid 126 through 137
    Processing helix  chain 'N' and resid 137 through 158
    Processing helix  chain 'N' and resid 162 through 174
    Processing helix  chain 'O' and resid 13 through 41
    Processing helix  chain 'O' and resid 48 through 76
    Processing helix  chain 'O' and resid 95 through 124
    Processing helix  chain 'O' and resid 126 through 137
    Processing helix  chain 'O' and resid 137 through 158
    Processing helix  chain 'O' and resid 162 through 174
    Processing helix  chain 'P' and resid 13 through 41
    Processing helix  chain 'P' and resid 48 through 76
    Processing helix  chain 'P' and resid 95 through 124
    Processing helix  chain 'P' and resid 126 through 137
    Processing helix  chain 'P' and resid 137 through 158
    Processing helix  chain 'P' and resid 162 through 174
    Processing helix  chain 'Q' and resid 13 through 41
    Processing helix  chain 'Q' and resid 48 through 76
    Processing helix  chain 'Q' and resid 95 through 124
    Processing helix  chain 'Q' and resid 126 through 137
    Processing helix  chain 'Q' and resid 137 through 158
    Processing helix  chain 'Q' and resid 162 through 174
    Processing helix  chain 'R' and resid 13 through 41
    Processing helix  chain 'R' and resid 48 through 76
    Processing helix  chain 'R' and resid 95 through 124
    Processing helix  chain 'R' and resid 126 through 137
    Processing helix  chain 'R' and resid 137 through 158
    Processing helix  chain 'R' and resid 162 through 174
    Processing helix  chain 'S' and resid 13 through 41
    Processing helix  chain 'S' and resid 48 through 76
    Processing helix  chain 'S' and resid 95 through 124
    Processing helix  chain 'S' and resid 126 through 137
    Processing helix  chain 'S' and resid 137 through 158
    Processing helix  chain 'S' and resid 162 through 174
    Processing helix  chain 'T' and resid 13 through 41
    Processing helix  chain 'T' and resid 48 through 76
    Processing helix  chain 'T' and resid 95 through 124
    Processing helix  chain 'T' and resid 126 through 137
    Processing helix  chain 'T' and resid 137 through 158
    Processing helix  chain 'T' and resid 162 through 174
    Processing helix  chain 'U' and resid 13 through 41
    Processing helix  chain 'U' and resid 48 through 76
    Processing helix  chain 'U' and resid 95 through 124
    Processing helix  chain 'U' and resid 126 through 137
    Processing helix  chain 'U' and resid 137 through 158
    Processing helix  chain 'U' and resid 162 through 174
    Processing helix  chain 'V' and resid 13 through 41
    Processing helix  chain 'V' and resid 48 through 76
    Processing helix  chain 'V' and resid 95 through 124
    Processing helix  chain 'V' and resid 126 through 137
    Processing helix  chain 'V' and resid 137 through 158
    Processing helix  chain 'V' and resid 162 through 174
    Processing helix  chain 'W' and resid 13 through 41
    Processing helix  chain 'W' and resid 48 through 76
    Processing helix  chain 'W' and resid 95 through 124
    Processing helix  chain 'W' and resid 126 through 137
    Processing helix  chain 'W' and resid 137 through 158
    Processing helix  chain 'W' and resid 162 through 174
    Processing helix  chain 'X' and resid 13 through 41
    Processing helix  chain 'X' and resid 48 through 76
    Processing helix  chain 'X' and resid 95 through 124
    Processing helix  chain 'X' and resid 126 through 137
    Processing helix  chain 'X' and resid 137 through 158
    Processing helix  chain 'X' and resid 162 through 174

    2664 hydrogen bonds defined for protein.
    7992 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: 22.79

  Time building geometry restraints manager: 48.39 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.77 -     0.98: 32608
        0.98 -     1.19: 32
        1.19 -     1.39: 14222
        1.39 -     1.60: 19450
        1.60 -     1.80: 216
  Bond restraints: 66528
  Sorted by residual:
  bond pdb=" CB  SER F   5 "
       pdb=" HB2 SER F   5 "
    ideal  model  delta    sigma   weight residual
    0.970  1.036 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" OG  SER F   5 "
       pdb=" HG  SER F   5 "
    ideal  model  delta    sigma   weight residual
    0.840  0.774  0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" CB  SER B   5 "
       pdb=" HB2 SER B   5 "
    ideal  model  delta    sigma   weight residual
    0.970  1.035 -0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" OG  SER B   5 "
       pdb=" HG  SER B   5 "
    ideal  model  delta    sigma   weight residual
    0.840  0.775  0.065 2.00e-02 2.50e+03 1.04e+01
  bond pdb=" CB  SER F   5 "
       pdb=" HB3 SER F   5 "
    ideal  model  delta    sigma   weight residual
    0.970  1.022 -0.052 2.00e-02 2.50e+03 6.64e+00
  ... (remaining 66523 not shown)

  Histogram of bond angle deviations from ideal:
       79.52 -    90.43: 4
       90.43 -   101.33: 99
      101.33 -   112.23: 75143
      112.23 -   123.13: 38473
      123.13 -   134.03: 6257
  Bond angle restraints: 119976
  Sorted by residual:
  angle pdb=" OG  SER B   5 "
        pdb=" CB  SER B   5 "
        pdb=" HB3 SER B   5 "
      ideal   model   delta    sigma   weight residual
     109.00   79.52   29.48 3.00e+00 1.11e-01 9.65e+01
  angle pdb=" OG  SER F   5 "
        pdb=" CB  SER F   5 "
        pdb=" HB3 SER F   5 "
      ideal   model   delta    sigma   weight residual
     109.00   79.62   29.38 3.00e+00 1.11e-01 9.59e+01
  angle pdb=" HB2 SER F   5 "
        pdb=" CB  SER F   5 "
        pdb=" HB3 SER F   5 "
      ideal   model   delta    sigma   weight residual
     110.00   89.28   20.72 3.00e+00 1.11e-01 4.77e+01
  angle pdb=" HB2 SER B   5 "
        pdb=" CB  SER B   5 "
        pdb=" HB3 SER B   5 "
      ideal   model   delta    sigma   weight residual
     110.00   89.30   20.70 3.00e+00 1.11e-01 4.76e+01
  angle pdb=" OG  SER B   5 "
        pdb=" CB  SER B   5 "
        pdb=" HB2 SER B   5 "
      ideal   model   delta    sigma   weight residual
     109.00  126.01  -17.01 3.00e+00 1.11e-01 3.22e+01
  ... (remaining 119971 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 28180
       17.48 -    34.97: 1773
       34.97 -    52.45: 672
       52.45 -    69.93: 263
       69.93 -    87.41: 96
  Dihedral angle restraints: 30984
    sinusoidal: 16824
      harmonic: 14160
  Sorted by residual:
  dihedral pdb=" CA  VAL J  46 "
           pdb=" C   VAL J  46 "
           pdb=" N   ALA J  47 "
           pdb=" CA  ALA J  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.85   16.15     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  VAL Q  46 "
           pdb=" C   VAL Q  46 "
           pdb=" N   ALA Q  47 "
           pdb=" CA  ALA Q  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.87   16.13     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  VAL U  46 "
           pdb=" C   VAL U  46 "
           pdb=" N   ALA U  47 "
           pdb=" CA  ALA U  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.87   16.13     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 30981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 2974
       0.028 -    0.057: 1221
       0.057 -    0.085: 509
       0.085 -    0.114: 98
       0.114 -    0.142: 70
  Chirality restraints: 4872
  Sorted by residual:
  chirality pdb=" CA  PRO O 127 "
            pdb=" N   PRO O 127 "
            pdb=" C   PRO O 127 "
            pdb=" CB  PRO O 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CA  PRO E 127 "
            pdb=" N   PRO E 127 "
            pdb=" C   PRO E 127 "
            pdb=" CB  PRO E 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  PRO X 127 "
            pdb=" N   PRO X 127 "
            pdb=" C   PRO X 127 "
            pdb=" CB  PRO X 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 5.02e-01
  ... (remaining 4869 not shown)

  Planarity restraints: 9984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  66 "    0.015 2.00e-02 2.50e+03   9.09e-03 2.48e+00
        pdb=" CG  TYR F  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  66 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  66 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  66 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  66 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR F  66 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR F  66 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR F  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 TYR F  66 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR F  66 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR I  66 "    0.015 2.00e-02 2.50e+03   9.08e-03 2.48e+00
        pdb=" CG  TYR I  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR I  66 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR I  66 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR I  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR I  66 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR I  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR I  66 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 TYR I  66 "    0.002 2.00e-02 2.50e+03
        pdb=" HD2 TYR I  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 TYR I  66 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR I  66 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR V  66 "    0.015 2.00e-02 2.50e+03   9.08e-03 2.47e+00
        pdb=" CG  TYR V  66 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR V  66 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR V  66 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR V  66 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR V  66 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR V  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR V  66 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD1 TYR V  66 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR V  66 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 TYR V  66 "    0.003 2.00e-02 2.50e+03
        pdb=" HE2 TYR V  66 "    0.001 2.00e-02 2.50e+03
  ... (remaining 9981 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.28: 9681
        2.28 -     2.86: 155771
        2.86 -     3.44: 200894
        3.44 -     4.02: 281067
        4.02 -     4.60: 411336
  Nonbonded interactions: 1058749
  Sorted by model distance:
  nonbonded pdb=" HE  ARG J  68 "
            pdb=" O   HOH J 203 "
     model   vdw
     1.694 1.850
  nonbonded pdb=" HH  TYR D 168 "
            pdb=" OG1 THR T 174 "
     model   vdw
     1.732 1.850
  nonbonded pdb=" HH  TYR F 168 "
            pdb=" OG1 THR N 174 "
     model   vdw
     1.736 1.850
  nonbonded pdb=" OG1 THR H 174 "
            pdb=" HH  TYR P 168 "
     model   vdw
     1.739 1.850
  nonbonded pdb=" HH  TYR K 168 "
            pdb=" OG1 THR U 174 "
     model   vdw
     1.740 1.850
  ... (remaining 1058744 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' and resid 5 through 176)
  selection = (chain 'B' and resid 5 through 176)
  selection = (chain 'C' and resid 5 through 176)
  selection = (chain 'D' and resid 5 through 176)
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = (chain 'M' and resid 5 through 176)
  selection = (chain 'N' and resid 5 through 176)
  selection = (chain 'O' and resid 5 through 176)
  selection = (chain 'P' and resid 5 through 176)
  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
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  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:             1.290
  Extract box with map and model:          8.210
  Check model and map are aligned:         0.730
  Set scattering table:                    0.490
  Process input model:                     167.890
  Find NCS groups from input model:        2.750
  Set up NCS constraints:                  0.400
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  192.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
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      :  0.006   0.044  33864  Z= 0.404
  Angle     :  0.690   6.123  45552  Z= 0.363
  Chirality :  0.038   0.142   4872
  Planarity :  0.003   0.025   5976
  Dihedral  : 14.942  87.413  12768
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.12), residues: 4080
  helix:  1.54 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop : -0.95 (0.18), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP J  93 
 HIS   0.003   0.001   HIS O 118 
 PHE   0.013   0.003   PHE L  41 
 TYR   0.024   0.002   TYR F  66 
 ARG   0.004   0.001   ARG L  43 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  720 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 720
  time to evaluate  : 4.214 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 720
  average time/residue: 4.4504
  time to fit residues: 3597.9222
Evaluate side-chains
  532 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 532
  time to evaluate  : 4.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 344 optimal weight:    6.9990
   chunk 309 optimal weight:    3.9990
   chunk 171 optimal weight:    3.9990
   chunk 105 optimal weight:    4.9990
   chunk 208 optimal weight:    4.9990
   chunk 165 optimal weight:    6.9990
   chunk 319 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 194 optimal weight:    5.9990
   chunk 238 optimal weight:    7.9990
   chunk 370 optimal weight:    6.9990
   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  29 GLN
A  75 GLN
B  29 GLN
B  75 GLN
B  83 GLN
C  25 ASN
C  29 GLN
C  75 GLN
C  83 GLN
D  25 ASN
D  29 GLN
D  75 GLN
D  83 GLN
E  25 ASN
E  29 GLN
E  75 GLN
E  83 GLN
F  25 ASN
F  29 GLN
F  75 GLN
G  25 ASN
G  29 GLN
G  75 GLN
G  83 GLN
H  25 ASN
H  29 GLN
H  75 GLN
H  83 GLN
I  25 ASN
I  29 GLN
I  75 GLN
I  83 GLN
J  25 ASN
J  29 GLN
J  75 GLN
J  83 GLN
K  25 ASN
K  29 GLN
K  75 GLN
K  83 GLN
L  25 ASN
L  29 GLN
L  75 GLN
L  83 GLN
M  25 ASN
M  29 GLN
M  75 GLN
M  83 GLN
N  25 ASN
N  29 GLN
N  75 GLN
N  83 GLN
O  25 ASN
O  29 GLN
O  75 GLN
O  83 GLN
P  25 ASN
P  29 GLN
P  75 GLN
Q  25 ASN
Q  29 GLN
Q  75 GLN
Q  83 GLN
R  25 ASN
R  29 GLN
R  75 GLN
R  83 GLN
S  25 ASN
S  29 GLN
S  75 GLN
S  83 GLN
T  25 ASN
T  29 GLN
T  75 GLN
T  83 GLN
U  25 ASN
U  29 GLN
U  75 GLN
U  83 GLN
V  25 ASN
V  29 GLN
V  75 GLN
V  83 GLN
W  25 ASN
W  29 GLN
W  75 GLN
W  83 GLN
X  25 ASN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 91

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  33864  Z= 0.239
  Angle     :  0.562   4.898  45552  Z= 0.314
  Chirality :  0.035   0.135   4872
  Planarity :  0.004   0.028   5976
  Dihedral  :  4.364  17.399   4536
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 1.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  4.17 %
    Favored  : 94.48 %
  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:  4.21 (0.13), residues: 4080
  helix:  3.34 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.04 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP L  93 
 HIS   0.004   0.001   HIS W 151 
 PHE   0.020   0.003   PHE J  41 
 TYR   0.026   0.003   TYR U  66 
 ARG   0.003   0.001   ARG N  76 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  604 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 557
  time to evaluate  : 4.144 
Fit side-chains
  outliers start: 47
  outliers final: 0
  residues processed: 580
  average time/residue: 3.9181
  time to fit residues: 2591.8760
Evaluate side-chains
  533 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 533
  time to evaluate  : 4.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 205 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 308 optimal weight:    5.9990
   chunk 252 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 371 optimal weight:    5.9990
   chunk 400 optimal weight:    6.9990
   chunk 330 optimal weight:   10.0000
   chunk 368 optimal weight:   10.0000
   chunk 126 optimal weight:   10.0000
   chunk 297 optimal weight:    2.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
A  29 GLN
A  75 GLN
B  25 ASN
B  29 GLN
B  75 GLN
C  29 GLN
C  75 GLN
D  29 GLN
D  75 GLN
E  29 GLN
E  75 GLN
F  29 GLN
F  75 GLN
G  29 GLN
G  75 GLN
H  29 GLN
H  75 GLN
I  29 GLN
I  75 GLN
J  29 GLN
J  75 GLN
K  29 GLN
K  75 GLN
L  29 GLN
L  75 GLN
M  29 GLN
M  75 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  75 GLN
P  29 GLN
P  75 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
R  75 GLN
S  29 GLN
S  75 GLN
T  29 GLN
U  29 GLN
U  75 GLN
V  29 GLN
V  75 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN

Total number of N/Q/H flips: 49

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  33864  Z= 0.283
  Angle     :  0.591   5.445  45552  Z= 0.334
  Chirality :  0.036   0.145   4872
  Planarity :  0.005   0.037   5976
  Dihedral  :  4.457  17.976   4536
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  5.75 %
    Favored  : 92.84 %
  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:  4.41 (0.13), residues: 4080
  helix:  3.46 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.18 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP V  93 
 HIS   0.004   0.002   HIS Q 136 
 PHE   0.020   0.003   PHE D  41 
 TYR   0.025   0.003   TYR S  66 
 ARG   0.004   0.001   ARG G  56 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  581 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 532
  time to evaluate  : 4.313 
Fit side-chains
  outliers start: 49
  outliers final: 0
  residues processed: 533
  average time/residue: 3.9455
  time to fit residues: 2394.6495
Evaluate side-chains
  534 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 534
  time to evaluate  : 4.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 366 optimal weight:    6.9990
   chunk 279 optimal weight:   10.0000
   chunk 192 optimal weight:    6.9990
   chunk 41 optimal weight:    9.9990
   chunk 177 optimal weight:   10.0000
   chunk 249 optimal weight:   10.0000
   chunk 372 optimal weight:    7.9990
   chunk 394 optimal weight:    3.9990
   chunk 194 optimal weight:    9.9990
   chunk 353 optimal weight:   10.0000
   chunk 106 optimal weight:    8.9990
   overall best weight:    6.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
B  29 GLN
C  29 GLN
C  75 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 GLN
G  75 GLN
H  29 GLN
I  29 GLN
J  29 GLN
K  29 GLN
K  75 GLN
L  29 GLN
M  29 GLN
N  29 GLN
O  29 GLN
O  75 GLN
P  29 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
S  29 GLN
T  29 GLN
U  29 GLN
U  75 GLN
V  29 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN

Total number of N/Q/H flips: 35

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029  33864  Z= 0.322
  Angle     :  0.606   5.415  45552  Z= 0.344
  Chirality :  0.038   0.151   4872
  Planarity :  0.005   0.041   5976
  Dihedral  :  4.547  18.551   4536
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  5.23 %
    Favored  : 93.82 %
  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:  4.23 (0.13), residues: 4080
  helix:  3.36 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.04 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP G  93 
 HIS   0.005   0.002   HIS X 136 
 PHE   0.021   0.004   PHE R  41 
 TYR   0.022   0.003   TYR O  66 
 ARG   0.006   0.001   ARG G  56 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 528
  time to evaluate  : 4.244 
Fit side-chains
  outliers start: 33
  outliers final: 0
  residues processed: 528
  average time/residue: 4.0766
  time to fit residues: 2467.7903
Evaluate side-chains
  525 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 525
  time to evaluate  : 4.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 328 optimal weight:    4.9990
   chunk 223 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 293 optimal weight:    1.9990
   chunk 162 optimal weight:    6.9990
   chunk 336 optimal weight:    8.9990
   chunk 272 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 201 optimal weight:    7.9990
   chunk 353 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
C  29 GLN
C  75 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 GLN
G  75 GLN
H  29 GLN
I  29 GLN
J  29 GLN
K  29 GLN
K  75 GLN
L  29 GLN
M  29 GLN
N  29 GLN
O  29 GLN
O  75 GLN
P  29 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
S  29 GLN
T  29 GLN
U  29 GLN
V  29 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN

Total number of N/Q/H flips: 34

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  33864  Z= 0.236
  Angle     :  0.540   5.468  45552  Z= 0.307
  Chirality :  0.035   0.143   4872
  Planarity :  0.004   0.032   5976
  Dihedral  :  4.394  17.376   4536
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.52 %
    Favored  : 93.79 %
  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:  4.60 (0.13), residues: 4080
  helix:  3.59 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.28 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP G  93 
 HIS   0.004   0.002   HIS S 128 
 PHE   0.018   0.003   PHE L  41 
 TYR   0.023   0.002   TYR U  66 
 ARG   0.004   0.001   ARG V  56 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  569 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 545
  time to evaluate  : 4.200 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 545
  average time/residue: 3.8757
  time to fit residues: 2411.7385
Evaluate side-chains
  539 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 539
  time to evaluate  : 4.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 132 optimal weight:    7.9990
   chunk 355 optimal weight:    9.9990
   chunk 77 optimal weight:    6.9990
   chunk 231 optimal weight:   10.0000
   chunk 97 optimal weight:    7.9990
   chunk 394 optimal weight:    5.9990
   chunk 327 optimal weight:    8.9990
   chunk 182 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 207 optimal weight:    5.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
C  29 GLN
C  75 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 GLN
G  75 GLN
H  29 GLN
H  83 GLN
I  29 GLN
J  29 GLN
K  29 GLN
K  75 GLN
L  29 GLN
M  29 GLN
M  75 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  75 GLN
O  83 GLN
P  29 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
S  29 GLN
S  83 GLN
T  29 GLN
U  29 GLN
U  75 GLN
U  83 GLN
V  29 GLN
V  75 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 43

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  33864  Z= 0.308
  Angle     :  0.596   5.484  45552  Z= 0.339
  Chirality :  0.037   0.151   4872
  Planarity :  0.005   0.039   5976
  Dihedral  :  4.520  18.401   4536
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.46 %
    Favored  : 93.85 %
  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:  4.31 (0.13), residues: 4080
  helix:  3.40 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.15 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP G  93 
 HIS   0.005   0.002   HIS R 128 
 PHE   0.021   0.004   PHE N  41 
 TYR   0.021   0.002   TYR J  66 
 ARG   0.006   0.001   ARG E  56 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  556 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 532
  time to evaluate  : 4.225 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 532
  average time/residue: 3.8417
  time to fit residues: 2336.6828
Evaluate side-chains
  526 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 526
  time to evaluate  : 4.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 380 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 224 optimal weight:    6.9990
   chunk 288 optimal weight:    6.9990
   chunk 223 optimal weight:    5.9990
   chunk 332 optimal weight:    2.9990
   chunk 220 optimal weight:    6.9990
   chunk 393 optimal weight:    6.9990
   chunk 246 optimal weight:    4.9990
   chunk 239 optimal weight:    9.9990
   chunk 181 optimal weight:    6.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
C  29 GLN
C  75 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 GLN
G  75 GLN
H  29 GLN
H  83 GLN
I  29 GLN
I  75 GLN
J  29 GLN
K  29 GLN
K  75 GLN
L  29 GLN
M  29 GLN
M  75 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  75 GLN
O  83 GLN
P  29 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
S  29 GLN
S  83 GLN
T  29 GLN
U  29 GLN
U  75 GLN
U  83 GLN
V  29 GLN
V  75 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 44

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  33864  Z= 0.266
  Angle     :  0.560   5.495  45552  Z= 0.319
  Chirality :  0.036   0.147   4872
  Planarity :  0.005   0.037   5976
  Dihedral  :  4.463  17.973   4536
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.55 %
    Favored  : 93.76 %
  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:  4.43 (0.13), residues: 4080
  helix:  3.48 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.22 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP E  93 
 HIS   0.004   0.002   HIS P 136 
 PHE   0.019   0.003   PHE H  41 
 TYR   0.022   0.002   TYR F  66 
 ARG   0.005   0.001   ARG J  56 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  558 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 534
  time to evaluate  : 4.349 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 534
  average time/residue: 3.8326
  time to fit residues: 2341.8068
Evaluate side-chains
  529 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 529
  time to evaluate  : 4.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 243 optimal weight:    4.9990
   chunk 157 optimal weight:    8.9990
   chunk 234 optimal weight:    7.9990
   chunk 118 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 250 optimal weight:    8.9990
   chunk 267 optimal weight:    8.9990
   chunk 194 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 309 optimal weight:    5.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
C  29 GLN
C  75 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 GLN
G  75 GLN
G  83 GLN
H  29 GLN
H  83 GLN
I  29 GLN
J  29 GLN
K  29 GLN
K  75 GLN
L  29 GLN
L  83 GLN
M  29 GLN
M  75 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  75 GLN
O  83 GLN
P  29 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
S  29 GLN
S  83 GLN
T  29 GLN
T  83 GLN
U  29 GLN
U  83 GLN
V  29 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 44

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  33864  Z= 0.252
  Angle     :  0.552   5.478  45552  Z= 0.314
  Chirality :  0.036   0.144   4872
  Planarity :  0.005   0.035   5976
  Dihedral  :  4.441  17.750   4536
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.60 %
    Favored  : 93.71 %
  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:  4.48 (0.13), residues: 4080
  helix:  3.51 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.25 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP E  93 
 HIS   0.004   0.002   HIS J 128 
 PHE   0.019   0.003   PHE L  41 
 TYR   0.022   0.002   TYR I  66 
 ARG   0.004   0.001   ARG J  56 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 537
  time to evaluate  : 4.309 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 537
  average time/residue: 3.9424
  time to fit residues: 2437.3039
Evaluate side-chains
  526 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 526
  time to evaluate  : 4.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 357 optimal weight:    8.9990
   chunk 376 optimal weight:    5.9990
   chunk 343 optimal weight:    6.9990
   chunk 366 optimal weight:    2.9990
   chunk 220 optimal weight:    6.9990
   chunk 159 optimal weight:    9.9990
   chunk 287 optimal weight:    7.9990
   chunk 112 optimal weight:    9.9990
   chunk 331 optimal weight:    3.9990
   chunk 346 optimal weight:    7.9990
   chunk 365 optimal weight:    0.9980
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
B  83 GLN
C  29 GLN
C  75 GLN
C  83 GLN
D  29 GLN
D  75 GLN
E  29 GLN
E  75 GLN
E  83 GLN
F  29 GLN
G  29 GLN
G  75 GLN
G  83 GLN
H  29 GLN
H  83 GLN
I  29 GLN
I  83 GLN
J  29 GLN
K  29 GLN
K  75 GLN
L  29 GLN
L  83 GLN
M  29 GLN
M  75 GLN
M  83 GLN
N  29 GLN
N  75 GLN
N  83 GLN
O  29 GLN
O  75 GLN
O  83 GLN
P  29 GLN
P  75 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
Q  83 GLN
R  29 GLN
R  83 GLN
S  29 GLN
S  83 GLN
T  29 GLN
T  83 GLN
U  29 GLN
U  83 GLN
V  29 GLN
V  83 GLN
W  29 GLN
W  75 GLN
W  83 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 57

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  33864  Z= 0.217
  Angle     :  0.526   5.424  45552  Z= 0.299
  Chirality :  0.035   0.139   4872
  Planarity :  0.004   0.032   5976
  Dihedral  :  4.367  17.227   4536
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.60 %
    Favored  : 93.71 %
  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:  4.69 (0.13), residues: 4080
  helix:  3.65 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.34 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP E  93 
 HIS   0.003   0.001   HIS Q 128 
 PHE   0.017   0.003   PHE B  41 
 TYR   0.022   0.002   TYR C  66 
 ARG   0.003   0.000   ARG J  56 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  563 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 539
  time to evaluate  : 4.265 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 539
  average time/residue: 3.7992
  time to fit residues: 2341.4786
Evaluate side-chains
  534 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 534
  time to evaluate  : 4.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 240 optimal weight:    6.9990
   chunk 387 optimal weight:   10.0000
   chunk 236 optimal weight:    8.9990
   chunk 183 optimal weight:    7.9990
   chunk 269 optimal weight:    6.9990
   chunk 406 optimal weight:    7.9990
   chunk 374 optimal weight:    8.9990
   chunk 323 optimal weight:    8.9990
   chunk 33 optimal weight:    8.9990
   chunk 250 optimal weight:   10.0000
   chunk 198 optimal weight:    7.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
B  83 GLN
C  29 GLN
C  75 GLN
C  83 GLN
D  29 GLN
D  75 GLN
D  83 GLN
E  29 GLN
E  75 GLN
E  83 GLN
F  29 GLN
G  29 GLN
G  75 GLN
G  83 GLN
H  29 GLN
H  83 GLN
I  29 GLN
I  75 GLN
I  83 GLN
J  29 GLN
J  83 GLN
K  29 GLN
K  75 GLN
K  83 GLN
L  29 GLN
L  83 GLN
M  29 GLN
M  75 GLN
M  83 GLN
N  29 GLN
N  75 GLN
N  83 GLN
O  29 GLN
O  75 GLN
O  83 GLN
P  29 GLN
P  75 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
Q  83 GLN
R  29 GLN
R  83 GLN
S  29 GLN
S  83 GLN
T  29 GLN
T  75 GLN
T  83 GLN
U  29 GLN
U  75 GLN
U  83 GLN
V  29 GLN
V  75 GLN
V  83 GLN
W  29 GLN
W  75 GLN
W  83 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 64

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  33864  Z= 0.345
  Angle     :  0.618   5.530  45552  Z= 0.352
  Chirality :  0.038   0.153   4872
  Planarity :  0.005   0.041   5976
  Dihedral  :  4.554  18.681   4536
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.72 %
    Favored  : 93.59 %
  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:  4.20 (0.13), residues: 4080
  helix:  3.32 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.10 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP E  93 
 HIS   0.005   0.002   HIS J 128 
 PHE   0.021   0.004   PHE A  39 
 TYR   0.020   0.003   TYR U  66 
 ARG   0.006   0.001   ARG E  56 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8160 Ramachandran restraints generated.
    4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  558 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 534
  time to evaluate  : 4.274 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 534
  average time/residue: 3.8490
  time to fit residues: 2347.8672
Evaluate side-chains
  531 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 531
  time to evaluate  : 4.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 408
   random chunks:
   chunk 257 optimal weight:    5.9990
   chunk 344 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 298 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 324 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 332 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  75 GLN
A  83 GLN
B  29 GLN
B  83 GLN
C  29 GLN
C  75 GLN
C  83 GLN
D  29 GLN
D  75 GLN
D  83 GLN
E  29 GLN
E  83 GLN
F  29 GLN
G  29 GLN
G  75 GLN
G  83 GLN
H  29 GLN
H  83 GLN
I  29 GLN
I  83 GLN
J  29 GLN
J  83 GLN
K  29 GLN
K  75 GLN
K  83 GLN
L  29 GLN
L  83 GLN
M  29 GLN
M  83 GLN
N  29 GLN
N  83 GLN
O  29 GLN
O  75 GLN
O  83 GLN
P  29 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
Q  83 GLN
R  29 GLN
R  83 GLN
S  29 GLN
S  83 GLN
T  29 GLN
T  83 GLN
U  29 GLN
U  83 GLN
V  29 GLN
V  75 GLN
V  83 GLN
W  29 GLN
W  75 GLN
W  83 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 57

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.114205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.104461 restraints weight = 81241.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 0.74
r_work: 0.2976 rms_B_bonded: 0.92 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 1.62 restraints_weight: 0.2500
r_work: 0.2620 rms_B_bonded: 4.24 restraints_weight: 0.1250
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  33864  Z= 0.197
  Angle     :  0.512   5.356  45552  Z= 0.291
  Chirality :  0.034   0.135   4872
  Planarity :  0.004   0.027   5976
  Dihedral  :  4.297  16.728   4536
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.72 %
    Favored  : 93.59 %
  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:  4.80 (0.13), residues: 4080
  helix:  3.73 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.33 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  93 
 HIS   0.003   0.001   HIS J 128 
 PHE   0.017   0.003   PHE M  41 
 TYR   0.024   0.002   TYR R  66 
 ARG   0.002   0.000   ARG E  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 32057.86 seconds
wall clock time: 550 minutes 24.00 seconds (33024.00 seconds total)