Params.eff

From CCP4 wiki
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
 }
}