View source for Params.eff

 verbose = False
 dry_run = False
 show_script = False
 show_defaults = False
 test_mode = False
 phaser {
  mode = ANO EP_AUTO EP_SAD *MR_AUTO MR_BRF MR_BTF MR_FRF MR_FTF MR_LLG \
         MR_PAK MR_RNP NMA
  sad_mode = *SAD MR_SAD
  hklin = None
  labin = None
  crystal {
    xtal_id = None
    pdb_file = None
    ha_file = None
    dataset {
      wave_id = None
      hklin = None
      labin = None
      wavelength = None
      energy = None
    }
  }
  crystal_symmetry {
    unit_cell = None
    space_group = None
  }
  composition {
    solvent = None
    chain {
      chain_type = *protein na
      sequence_file = None
      sequence = None
      nres = None
      mw = None
      num = 1
    }
    atom {
      element = None
      num = None
    }
  }
  ensemble {
    model_id = None
    coordinates {
      pdb = None
      rmsd = None
      identity = None
    }
    map_hklin = None
    map_labels = None
    map_extent = None
    map_rms = 1.0
    map_centre = None
    map_protein_mw = 0
    map_nucleic_mw = 0
    fractional_comp = none
  }
  search {
    ensembles = None
    copies = 1
  }
  solution = None
  output_dir = None
  keywords {
    general {
      root = "PHASER"
      title = "[no title set]"
      verbose = None
      debug = None
      mute = None
      xyzout = None
      hklout = None
      jobs = 2
    }
    atoms {
      change_scatterer = False
      change_scatterer_type = "Se"
      change_bfac_wilson = False
    }
    bfactor {
      wilson_restraint = True
      wilson_sigma = 5
      sphericity_restraint = True
      sphericity_sigma = 5
      refine_restraint = True
      refine_sigma = 10
    }
    bins {
      minimum = 6
      maximum = 50
      width = 500
      cubic = 0,1,0
    }
    boxscale = 4.0
    clmn {
      sphere = 0
      lmin = 4
      lmax = 100
    }
    cluster_pdb {
      id = None
      file_name = None
    }
    eigen {
      read = None
      write = True
    }
    ffts {
      minimum = 20
      maximum = 80
    }
    hand = off on *both
    integration {
      fixed = False
      step = None
    }
    llgcompletion {
      complete = True
      scatterer = None
      clash = 0
      sigma = 6
      ncycle = 50
      maps = False
    }
    macano {
      protocol = *default off custom
      macrocycle {
        ref_anis = None
        ref_bins = None
        ref_solk = None
        ref_solb = None
        ncycle = None
        minimiser = *BFGS NEWTON DESCENT
      }
    }
    macmr {
      protocol = *default off custom
      macrocycle {
        ref_rota = None
        ref_tran = None
        ref_bfac = None
        ref_vrms = None
        ncycle = None
        minimizer = *BFGS NEWTON DESCENT
      }
    }
    macsad {
      protocol = *default off custom
      macrocycle {
        ref_k = None
        ref_b = None
        ref_sigma = None
        ref_xyz = None
        ref_occ = None
        ref_bfac = None
        ref_fdp = None
        ref_sa = None
        ref_sb = None
        ref_sp = None
        ref_sd = None
        ncycle = None
        minimizer = *bfgs newton descent
      }
    }
    nmamethod {
      oscillators = *rtb ca all
      rtb_maxblocks = 125
      rtb_nresidues = 0
      radius = 5
      force = 1
    }
    nmapdb {
      mode = None
      combination = None
      perturb = *rms dq
      rms {
        step = None
        stretch = None
        clash = None
        maxrms = None
        direction = *forward backward tofro
      }
      dq = None
    }
    normalization {
      bins = None
      aniso = None
      solk = None
      solb = None
    }
    outlier {
      reject = True
      probability = 1e-06
    }
    pack {
      select = *percent best allow all
      cutoff = 5
      quick = True
      distance = 3.0
    }
    partial {
      pdb = None
      hklin = None
      variance = rms *id
      deviation = None
    }
    peaks_rotation {
      select = *percent sigma number all
      cutoff = 75
      cluster = True
    }
    peaks_translation {
      select = *percent sigma number all
      cutoff = 75
      cluster = True
    }
    permutations = False
    ptgroup {
      coverage = 0.90
      identity = 0.95
      rmsd = 1.00
      tolerance_angular = 0.035
      tolerance_spatial = 0.5
    }
    purge {
      enable = True
      percent = 0.75
    }
    rescore_rotation = True
    rescore_translation = True
    resharpen_percent = 100
    resolution {
      high = None
      low = None
      auto {
        high = None
        low = None
      }
    }
    rotate {
      volume = *full around
      euler = None
      range = None
    }
    sampling_rotation = None
    sampling_translation = None
    scattering {
      scatterer {
        type = None
        fp = None
        fdp = None
        fixfdp = *EDGE ON OFF
      }
      restraint = True
      sigma = 0.2
    }
    search_order_auto = True
    search_method = *full fast
    sgalternative {
      select = all *hand list none
      test = None
      sort = True
    }
    solparameters {
      fsol = 0.95
      bsol = 300
    }
    solution_origin_ensemble = None
    sort = None
    target_frf = *lerf1 lerf2 crowther
    target_ftf = *letf1 letf2 correlation
    topfiles = 1
    translate {
      volume = *full line region around
      fractional = None
      start = None
      end = None
      range = None
    }
    zscore_solved = 8
  }
 }