phenix.eff

refinement {
  crystal_symmetry {
    unit_cell = 34.297 45.552 99.035 90 90 90
    space_group = P 21 21 21
  }
  input {
    pdb {
      file_name = "reference_data/7LVC.pdb"
    }
    xray_data {
      file_name = "merge/dhfr_0.mtz"
      labels = F,SigF
      r_free_flags {
        generate = True
      }
    }
    monomers {
      file_name = "reference_data/CSD.cif"
      file_name = "reference_data/FOL.cif"
      file_name = "reference_data/NAP.cif"
    }
    symmetry_safety_check = error *warning
  }
  output {
    prefix = """phenix_refine/DHFR_Laue_refine"""
    serial = 1
    serial_format = "%d"
    write_def_file = False
  }
  electron_density_maps {
    map_coefficients {
      map_type = 2mFo-DFc
      mtz_label_amplitudes = 2FOFCWT
      mtz_label_phases = PH2FOFCWT
      fill_missing_f_obs = True
    }
    map_coefficients {
      map_type = 2mFo-DFc
      mtz_label_amplitudes = 2FOFCWT_no_fill
      mtz_label_phases = PH2FOFCWT_no_fill
    }
    map_coefficients {
      map_type = mFo-DFc
      mtz_label_amplitudes = FOFCWT
      mtz_label_phases = PHFOFCWT
    }
    map_coefficients {
      map_type = anomalous
      mtz_label_amplitudes = ANOM
      mtz_label_phases = PHANOM
    }
  }
  refine {
    strategy = individual_sites individual_sites_real_space *rigid_body \
               *individual_adp group_adp tls *occupancies group_anomalous
  }
  main {
    number_of_macro_cycles = 5
  }
}