refinement.refine.strategy=individual_sites+individual_adp+occupancies
refinement.main.number_of_macro_cycles=7
refinement.main.nqh_flips=True
refinement.target_weights.optimize_xyz_weight=True
refinement.target_weights.optimize_adp_weight=True
#refinement.main.nproc=4
refinement.hydrogens.refine=riding
refinement.input.xray_data.labels="IMEAN,SIGIMEAN"
# NRQ
# chain E
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain E and resname PHE and resid 65 and name C
    atom_selection_2 = chain E and resname NRQ and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain E and resname PHE and resid 65 and name O
    atom_selection_2 = chain E and resname PHE and resid 65 and name C
    atom_selection_3 = chain E and resname NRQ and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain E and resname PHE and resid 65 and name CA
    atom_selection_2 = chain E and resname PHE and resid 65 and name C
    atom_selection_3 = chain E and resname NRQ and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain E and resname NRQ and resid 66 and name C3
    atom_selection_2 = chain E and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain E and resname NRQ and resid 66 and name O3
    atom_selection_2 = chain E and resname NRQ and resid 66 and name C3
    atom_selection_3 = chain E and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain E and resname NRQ and resid 66 and name CA3
    atom_selection_2 = chain E and resname NRQ and resid 66 and name C3
    atom_selection_3 = chain E and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain E and resname NRQ and resid 66 and name O3 
    atom_selection_2 = chain E and resname NRQ and resid 66 and name C3 
    atom_selection_3 = chain E and resname SER and resid 69 and name N 
    atom_selection_4 = chain E and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# chain H
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain H and resname PHE and resid 65 and name C
    atom_selection_2 = chain H and resname NRQ and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain H and resname PHE and resid 65 and name O
    atom_selection_2 = chain H and resname PHE and resid 65 and name C
    atom_selection_3 = chain H and resname NRQ and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain H and resname PHE and resid 65 and name CA
    atom_selection_2 = chain H and resname PHE and resid 65 and name C
    atom_selection_3 = chain H and resname NRQ and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain H and resname NRQ and resid 66 and name C3
    atom_selection_2 = chain H and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain H and resname NRQ and resid 66 and name O3
    atom_selection_2 = chain H and resname NRQ and resid 66 and name C3
    atom_selection_3 = chain H and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain H and resname NRQ and resid 66 and name CA3
    atom_selection_2 = chain H and resname NRQ and resid 66 and name C3
    atom_selection_3 = chain H and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain H and resname NRQ and resid 66 and name O3 
    atom_selection_2 = chain H and resname NRQ and resid 66 and name C3 
    atom_selection_3 = chain H and resname SER and resid 69 and name N 
    atom_selection_4 = chain H and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# CH6
# chain A
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain A and resname PHE and resid 65 and name C
    atom_selection_2 = chain A and resname CH6 and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain A and resname PHE and resid 65 and name O
    atom_selection_2 = chain A and resname PHE and resid 65 and name C
    atom_selection_3 = chain A and resname CH6 and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain A and resname PHE and resid 65 and name CA
    atom_selection_2 = chain A and resname PHE and resid 65 and name C
    atom_selection_3 = chain A and resname CH6 and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  angle {
    action = *add
    atom_selection_1 = chain A and resname PHE and resid 65 and name C
    atom_selection_2 = chain A and resname CH6 and resid 66 and name N1
    atom_selection_3 = chain A and resname CH6 and resid 66 and name HN11
    angle_ideal = 120.0
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain A and resname CH6 and resid 66 and name C3
    atom_selection_2 = chain A and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain A and resname CH6 and resid 66 and name O3
    atom_selection_2 = chain A and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain A and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain A and resname CH6 and resid 66 and name CA3
    atom_selection_2 = chain A and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain A and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain A and resname CH6 and resid 66 and name O3 
    atom_selection_2 = chain A and resname CH6 and resid 66 and name C3 
    atom_selection_3 = chain A and resname SER and resid 69 and name N 
    atom_selection_4 = chain A and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# chain B
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain B and resname PHE and resid 65 and name C
    atom_selection_2 = chain B and resname CH6 and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain B and resname PHE and resid 65 and name O
    atom_selection_2 = chain B and resname PHE and resid 65 and name C
    atom_selection_3 = chain B and resname CH6 and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain B and resname PHE and resid 65 and name CA
    atom_selection_2 = chain B and resname PHE and resid 65 and name C
    atom_selection_3 = chain B and resname CH6 and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  angle {
    action = *add
    atom_selection_1 = chain B and resname PHE and resid 65 and name C
    atom_selection_2 = chain B and resname CH6 and resid 66 and name N1
    atom_selection_3 = chain B and resname CH6 and resid 66 and name HN11
    angle_ideal = 120.0
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain B and resname CH6 and resid 66 and name C3
    atom_selection_2 = chain B and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain B and resname CH6 and resid 66 and name O3
    atom_selection_2 = chain B and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain B and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain B and resname CH6 and resid 66 and name CA3
    atom_selection_2 = chain B and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain B and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain B and resname CH6 and resid 66 and name O3 
    atom_selection_2 = chain B and resname CH6 and resid 66 and name C3 
    atom_selection_3 = chain B and resname SER and resid 69 and name N 
    atom_selection_4 = chain B and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# chain C
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain C and resname PHE and resid 65 and name C
    atom_selection_2 = chain C and resname CH6 and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain C and resname PHE and resid 65 and name O
    atom_selection_2 = chain C and resname PHE and resid 65 and name C
    atom_selection_3 = chain C and resname CH6 and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain C and resname PHE and resid 65 and name CA
    atom_selection_2 = chain C and resname PHE and resid 65 and name C
    atom_selection_3 = chain C and resname CH6 and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  angle {
    action = *add
    atom_selection_1 = chain C and resname PHE and resid 65 and name C
    atom_selection_2 = chain C and resname CH6 and resid 66 and name N1
    atom_selection_3 = chain C and resname CH6 and resid 66 and name HN11
    angle_ideal = 120.0
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain C and resname CH6 and resid 66 and name C3
    atom_selection_2 = chain C and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain C and resname CH6 and resid 66 and name O3
    atom_selection_2 = chain C and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain C and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain C and resname CH6 and resid 66 and name CA3
    atom_selection_2 = chain C and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain C and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain C and resname CH6 and resid 66 and name O3 
    atom_selection_2 = chain C and resname CH6 and resid 66 and name C3 
    atom_selection_3 = chain C and resname SER and resid 69 and name N 
    atom_selection_4 = chain C and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# chain D
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain D and resname PHE and resid 65 and name C
    atom_selection_2 = chain D and resname CH6 and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain D and resname PHE and resid 65 and name O
    atom_selection_2 = chain D and resname PHE and resid 65 and name C
    atom_selection_3 = chain D and resname CH6 and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain D and resname PHE and resid 65 and name CA
    atom_selection_2 = chain D and resname PHE and resid 65 and name C
    atom_selection_3 = chain D and resname CH6 and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  angle {
    action = *add
    atom_selection_1 = chain D and resname PHE and resid 65 and name C
    atom_selection_2 = chain D and resname CH6 and resid 66 and name N1
    atom_selection_3 = chain D and resname CH6 and resid 66 and name HN11
    angle_ideal = 120.0
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain D and resname CH6 and resid 66 and name C3
    atom_selection_2 = chain D and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain D and resname CH6 and resid 66 and name O3
    atom_selection_2 = chain D and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain D and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain D and resname CH6 and resid 66 and name CA3
    atom_selection_2 = chain D and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain D and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain D and resname CH6 and resid 66 and name O3 
    atom_selection_2 = chain D and resname CH6 and resid 66 and name C3 
    atom_selection_3 = chain D and resname SER and resid 69 and name N 
    atom_selection_4 = chain D and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# chain F
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain F and resname PHE and resid 65 and name C
    atom_selection_2 = chain F and resname CH6 and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain F and resname PHE and resid 65 and name O
    atom_selection_2 = chain F and resname PHE and resid 65 and name C
    atom_selection_3 = chain F and resname CH6 and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain F and resname PHE and resid 65 and name CA
    atom_selection_2 = chain F and resname PHE and resid 65 and name C
    atom_selection_3 = chain F and resname CH6 and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  angle {
    action = *add
    atom_selection_1 = chain F and resname PHE and resid 65 and name C
    atom_selection_2 = chain F and resname CH6 and resid 66 and name N1
    atom_selection_3 = chain F and resname CH6 and resid 66 and name HN11
    angle_ideal = 120.0
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain F and resname CH6 and resid 66 and name C3
    atom_selection_2 = chain F and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain F and resname CH6 and resid 66 and name O3
    atom_selection_2 = chain F and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain F and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain F and resname CH6 and resid 66 and name CA3
    atom_selection_2 = chain F and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain F and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain F and resname CH6 and resid 66 and name O3 
    atom_selection_2 = chain F and resname CH6 and resid 66 and name C3 
    atom_selection_3 = chain F and resname SER and resid 69 and name N 
    atom_selection_4 = chain F and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}
# chain G
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = chain G and resname PHE and resid 65 and name C
    atom_selection_2 = chain G and resname CH6 and resid 66 and name N1
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
  }
  angle {
    action = *add
    atom_selection_1 = chain G and resname PHE and resid 65 and name O
    atom_selection_2 = chain G and resname PHE and resid 65 and name C
    atom_selection_3 = chain G and resname CH6 and resid 66 and name N1
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain G and resname PHE and resid 65 and name CA
    atom_selection_2 = chain G and resname PHE and resid 65 and name C
    atom_selection_3 = chain G and resname CH6 and resid 66 and name N1
    angle_ideal = 117.2
    sigma = 2.0
  }
  angle {
    action = *add
    atom_selection_1 = chain G and resname PHE and resid 65 and name C
    atom_selection_2 = chain G and resname CH6 and resid 66 and name N1
    atom_selection_3 = chain G and resname CH6 and resid 66 and name HN11
    angle_ideal = 120.0
    sigma = 2.0
  }
  bond {
    action = *add
    atom_selection_1 = chain G and resname CH6 and resid 66 and name C3
    atom_selection_2 = chain G and resname SER and resid 69 and name N
    symmetry_operation = None
    distance_ideal = 1.33
    sigma = 0.02
    slack = None
    }
  angle {
    action = *add
    atom_selection_1 = chain G and resname CH6 and resid 66 and name O3
    atom_selection_2 = chain G and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain G and resname SER and resid 69 and name N
    angle_ideal = 122.7
    sigma = 1.6
  }
  angle {
    action = *add
    atom_selection_1 = chain G and resname CH6 and resid 66 and name CA3
    atom_selection_2 = chain G and resname CH6 and resid 66 and name C3
    atom_selection_3 = chain G and resname SER and resid 69 and name N
    angle_ideal = 117.2
    sigma = 2.0
  }
  dihedral {
    action = *add
    atom_selection_1 = chain G and resname CH6 and resid 66 and name O3 
    atom_selection_2 = chain G and resname CH6 and resid 66 and name C3 
    atom_selection_3 = chain G and resname SER and resid 69 and name N 
    atom_selection_4 = chain G and resname SER and resid 69 and name CA
    angle_ideal = 0.0
    sigma = 2.0
  }
}