Starting phenix.real_space_refine
on Mon Dec 11 04:58:22 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/12_2023/6wx6_21951.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/12_2023/6wx6_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_21951/12_2023/6wx6_21951.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/12_2023/6wx6_21951.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/12_2023/6wx6_21951.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wx6_21951/12_2023/6wx6_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-1.21rc1-5172/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: 22.40, per 1000 atoms: 0.33
  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: 49.78
  Conformation dependent library (CDL) restraints added in 5.0 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: 3.11
  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: 23.33

  Time building geometry restraints manager: 52.19 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: 27748
       17.48 -    34.97: 1725
       34.97 -    52.45: 360
       52.45 -    69.93: 95
       69.93 -    87.41: 96
  Dihedral angle restraints: 30024
    sinusoidal: 15864
      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 30021 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:             1.960
  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:             1.070
  Extract box with map and model:          8.020
  Check model and map are aligned:         0.760
  Set scattering table:                    0.470
  Process input model:                     175.460
  Find NCS groups from input model:        2.910
  Set up NCS constraints:                  0.450
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.020
  Load rotamer database and sin/cos tables:11.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  202.970
-------------------------------------------------------------------------------
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  : 4.228 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 720
  average time/residue: 4.5016
  time to fit residues: 3643.0421
Evaluate side-chains
  532 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 532
  time to evaluate  : 4.268 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.3793
-------------------------------------------------------------------------------
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:    5.9990
   chunk 165 optimal weight:    6.9990
   chunk 319 optimal weight:    4.9990
   chunk 123 optimal weight:    5.9990
   chunk 194 optimal weight:    7.9990
   chunk 238 optimal weight:    7.9990
   chunk 370 optimal weight:    6.9990
   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
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: 0.8680
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  33864  Z= 0.245
  Angle     :  0.569   4.914  45552  Z= 0.318
  Chirality :  0.035   0.136   4872
  Planarity :  0.004   0.029   5976
  Dihedral  :  4.394  17.560   4536
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  4.14 %
    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 :  0.06 (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 E  41 
   TYR   0.026   0.003   TYR O  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
  607 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 559
  time to evaluate  : 4.292 
Fit side-chains
  outliers start: 48
  outliers final: 0
  residues processed: 583
  average time/residue: 3.9815
  time to fit residues: 2653.0302
Evaluate side-chains
  541 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 541
  time to evaluate  : 4.655 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2554
-------------------------------------------------------------------------------
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:    5.9990
   chunk 308 optimal weight:    5.9990
   chunk 252 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   chunk 371 optimal weight:    7.9990
   chunk 400 optimal weight:    6.9990
   chunk 330 optimal weight:    8.9990
   chunk 368 optimal weight:    9.9990
   chunk 126 optimal weight:    9.9990
   chunk 297 optimal weight:    0.6980
   overall best weight:    5.5388

-------------------------------------------------------------------------------
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
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: 48

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2358

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= 0.273
  Angle     :  0.580   5.442  45552  Z= 0.328
  Chirality :  0.036   0.143   4872
  Planarity :  0.005   0.036   5976
  Dihedral  :  4.431  17.807   4536
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  5.83 %
    Favored  : 93.07 %
  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:  4.46 (0.13), residues: 4080
  helix:  3.50 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.19 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.002   TRP O  93 
   HIS   0.004   0.002   HIS X 136 
   PHE   0.020   0.003   PHE R  41 
   TYR   0.025   0.002   TYR M  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
  586 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 548
  time to evaluate  : 4.281 
Fit side-chains
  outliers start: 38
  outliers final: 0
  residues processed: 548
  average time/residue: 3.9235
  time to fit residues: 2462.6717
Evaluate side-chains
  545 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 545
  time to evaluate  : 4.093 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.1671
-------------------------------------------------------------------------------
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:    3.9990
   chunk 41 optimal weight:    9.9990
   chunk 177 optimal weight:    6.9990
   chunk 249 optimal weight:    9.9990
   chunk 372 optimal weight:    7.9990
   chunk 394 optimal weight:    4.9990
   chunk 194 optimal weight:   10.0000
   chunk 353 optimal weight:    9.9990
   chunk 106 optimal weight:    8.9990
   overall best weight:    6.1990

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

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

Total number of N/Q/H flips: 31

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  33864  Z= 0.290
  Angle     :  0.579   5.394  45552  Z= 0.330
  Chirality :  0.037   0.148   4872
  Planarity :  0.005   0.038   5976
  Dihedral  :  4.481  18.298   4536
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  4.94 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.39 (0.13), residues: 4080
  helix:  3.47 (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 V  93 
   HIS   0.004   0.002   HIS Q 136 
   PHE   0.020   0.004   PHE B  41 
   TYR   0.022   0.003   TYR F  66 
   ARG   0.005   0.001   ARG H  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: 28
    poor density    : 533
  time to evaluate  : 4.316 
Fit side-chains
  outliers start: 28
  outliers final: 0
  residues processed: 533
  average time/residue: 4.0078
  time to fit residues: 2435.1134
Evaluate side-chains
  528 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 528
  time to evaluate  : 4.253 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2695
-------------------------------------------------------------------------------
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:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 201 optimal weight:    6.9990
   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  83 GLN
B  29 GLN
C  29 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 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
P  29 GLN
Q  29 GLN
R  29 GLN
S  29 GLN
T  29 GLN
U  29 GLN
V  29 GLN
W  29 GLN
X  29 GLN
X  75 GLN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2456

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= 0.238
  Angle     :  0.540   5.437  45552  Z= 0.307
  Chirality :  0.035   0.141   4872
  Planarity :  0.004   0.033   5976
  Dihedral  :  4.388  17.397   4536
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.03 %
    Favored  : 94.28 %
  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:  4.63 (0.13), residues: 4080
  helix:  3.61 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.29 (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 C 128 
   PHE   0.018   0.003   PHE D  41 
   TYR   0.022   0.002   TYR J  66 
   ARG   0.003   0.001   ARG D  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
  570 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 546
  time to evaluate  : 4.819 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 546
  average time/residue: 3.9098
  time to fit residues: 2447.2890
Evaluate side-chains
  544 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 544
  time to evaluate  : 4.179 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2218
-------------------------------------------------------------------------------
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:    3.9990
   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:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  83 GLN
B  29 GLN
C  29 GLN
D  29 GLN
D  75 GLN
E  29 GLN
F  29 GLN
G  29 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
N  29 GLN
O  29 GLN
P  29 GLN
Q  29 GLN
R  29 GLN
S  29 GLN
T  29 GLN
U  29 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: 31

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  33864  Z= 0.285
  Angle     :  0.577   5.450  45552  Z= 0.329
  Chirality :  0.036   0.147   4872
  Planarity :  0.005   0.037   5976
  Dihedral  :  4.482  18.154   4536
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.06 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.39 (0.13), residues: 4080
  helix:  3.46 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.16 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.002   TRP G  93 
   HIS   0.004   0.002   HIS J 128 
   PHE   0.020   0.004   PHE J  41 
   TYR   0.022   0.002   TYR T  66 
   ARG   0.005   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
  563 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 539
  time to evaluate  : 4.383 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 539
  average time/residue: 3.8914
  time to fit residues: 2400.0175
Evaluate side-chains
  539 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 539
  time to evaluate  : 4.148 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2250
-------------------------------------------------------------------------------
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:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 224 optimal weight:    7.9990
   chunk 288 optimal weight:    5.9990
   chunk 223 optimal weight:    3.9990
   chunk 332 optimal weight:    3.9990
   chunk 220 optimal weight:    4.9990
   chunk 393 optimal weight:    5.9990
   chunk 246 optimal weight:    2.9990
   chunk 239 optimal weight:    9.9990
   chunk 181 optimal weight:    6.9990
   overall best weight:    4.3990

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

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

Total number of N/Q/H flips: 29

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  33864  Z= 0.223
  Angle     :  0.528   5.449  45552  Z= 0.301
  Chirality :  0.035   0.139   4872
  Planarity :  0.004   0.032   5976
  Dihedral  :  4.376  17.289   4536
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.06 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.66 (0.13), residues: 4080
  helix:  3.63 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.31 (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 A  66 
   ARG   0.003   0.000   ARG V  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
  570 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 546
  time to evaluate  : 4.262 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 546
  average time/residue: 3.9236
  time to fit residues: 2454.5346
Evaluate side-chains
  533 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 533
  time to evaluate  : 4.156 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2008
-------------------------------------------------------------------------------
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:    8.9990
   chunk 118 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 250 optimal weight:    8.9990
   chunk 267 optimal weight:    9.9990
   chunk 194 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 309 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 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
M  29 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  83 GLN
P  29 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
S  29 GLN
T  29 GLN
T  75 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: 40

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.2499

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= 0.262
  Angle     :  0.558   5.444  45552  Z= 0.318
  Chirality :  0.036   0.144   4872
  Planarity :  0.005   0.035   5976
  Dihedral  :  4.426  17.814   4536
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 2.73
  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:  4.54 (0.13), residues: 4080
  helix:  3.56 (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 R 128 
   PHE   0.020   0.003   PHE R  41 
   TYR   0.021   0.002   TYR A  66 
   ARG   0.004   0.001   ARG E  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  : 4.426 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 537
  average time/residue: 3.8778
  time to fit residues: 2384.8844
Evaluate side-chains
  537 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 537
  time to evaluate  : 4.141 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2861
-------------------------------------------------------------------------------
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:    4.9990
   chunk 159 optimal weight:    5.9990
   chunk 287 optimal weight:    7.9990
   chunk 112 optimal weight:    9.9990
   chunk 331 optimal weight:    6.9990
   chunk 346 optimal weight:    7.9990
   chunk 365 optimal weight:    0.8980
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  29 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
F  75 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  75 GLN
M  29 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  83 GLN
P  29 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
R  29 GLN
R  75 GLN
S  29 GLN
T  29 GLN
T  75 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: 43

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8679
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  33864  Z= 0.214
  Angle     :  0.521   5.420  45552  Z= 0.297
  Chirality :  0.034   0.138   4872
  Planarity :  0.004   0.032   5976
  Dihedral  :  4.351  17.187   4536
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  5.49 %
    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:  4.73 (0.13), residues: 4080
  helix:  3.68 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.36 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.002   TRP C  93 
   HIS   0.003   0.001   HIS X 128 
   PHE   0.016   0.003   PHE R  41 
   TYR   0.022   0.002   TYR H  66 
   ARG   0.003   0.000   ARG N  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
  567 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 543
  time to evaluate  : 4.365 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 543
  average time/residue: 3.8972
  time to fit residues: 2424.9622
Evaluate side-chains
  533 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 533
  time to evaluate  : 4.262 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.2453
-------------------------------------------------------------------------------
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:    0.9990
   chunk 236 optimal weight:    7.9990
   chunk 183 optimal weight:    7.9990
   chunk 269 optimal weight:    8.9990
   chunk 406 optimal weight:    7.9990
   chunk 374 optimal weight:    8.9990
   chunk 323 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 250 optimal weight:    1.9990
   chunk 198 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  83 GLN
B  29 GLN
B  75 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
F  29 GLN
G  29 GLN
G  75 GLN
G  83 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
L  83 GLN
M  29 GLN
M  75 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  83 GLN
P  29 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
Q  83 GLN
R  29 GLN
R  75 GLN
S  29 GLN
S  75 GLN
S  83 GLN
T  29 GLN
T  75 GLN
T  83 GLN
U  29 GLN
U  83 GLN
V  29 GLN
V  83 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 54

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021  33864  Z= 0.234
  Angle     :  0.536   5.446  45552  Z= 0.305
  Chirality :  0.035   0.140   4872
  Planarity :  0.004   0.032   5976
  Dihedral  :  4.365  17.412   4536
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.87
  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:  4.68 (0.13), residues: 4080
  helix:  3.65 (0.08), residues: 3312
  sheet:  None (None), residues: 0
  loop :  0.32 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.002   TRP C  93 
   HIS   0.004   0.001   HIS S 128 
   PHE   0.018   0.003   PHE P  41 
   TYR   0.022   0.002   TYR T  66 
   ARG   0.003   0.001   ARG R  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
  566 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 542
  time to evaluate  : 4.276 
Fit side-chains
  outliers start: 24
  outliers final: 0
  residues processed: 542
  average time/residue: 3.9240
  time to fit residues: 2438.3985
Evaluate side-chains
  534 residues out of total 3480 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 534
  time to evaluate  : 4.286 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 5.3308
-------------------------------------------------------------------------------
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:    6.9990
   chunk 344 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 298 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 89 optimal weight:    7.9990
   chunk 324 optimal weight:   10.0000
   chunk 135 optimal weight:    5.9990
   chunk 332 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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  75 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
F  29 GLN
G  29 GLN
G  75 GLN
G  83 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
L  83 GLN
M  29 GLN
M  75 GLN
N  29 GLN
N  75 GLN
O  29 GLN
O  83 GLN
P  29 GLN
P  83 GLN
Q  29 GLN
Q  75 GLN
Q  83 GLN
R  29 GLN
R  75 GLN
S  29 GLN
S  75 GLN
S  83 GLN
T  29 GLN
T  75 GLN
T  83 GLN
U  29 GLN
U  83 GLN
V  29 GLN
V  83 GLN
W  29 GLN
W  75 GLN
X  29 GLN
X  75 GLN
X  83 GLN

Total number of N/Q/H flips: 55

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.111863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.101985 restraints weight = 80926.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 0.74
r_work: 0.2966 rms_B_bonded: 0.90 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 1.60 restraints_weight: 0.2500
r_work: 0.2607 rms_B_bonded: 4.21 restraints_weight: 0.1250
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.2482

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= 0.225
  Angle     :  0.529   5.417  45552  Z= 0.302
  Chirality :  0.035   0.138   4872
  Planarity :  0.004   0.032   5976
  Dihedral  :  4.362  17.342   4536
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 2.94
  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:  4.69 (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 C  93 
   HIS   0.004   0.002   HIS S 128 
   PHE   0.018   0.003   PHE R  41 
   TYR   0.022   0.002   TYR V  66 
   ARG   0.003   0.000   ARG E  56 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 33008.93 seconds
wall clock time: 567 minutes 39.88 seconds (34059.88 seconds total)