{+ file: refine.def +}
{+ directory: auxiliary +}
{+ description: Defaults file which can be used to override input parameters
                for xtal_refine/refine.inp +}
{+ authors: Axel T. Brunger, and Paul D. Adams +}
{+ copyright: Yale University +}

{- begin block parameter definition -} define(

{======================= molecular structure =========================}

{* coordinate file *}
{===>} coordinate_infile="amy.pdb";

{====================== crystallographic data ========================}

{* space group *}
{* use International Table conventions with subscripts substituted
   by parenthesis *}
{===>} sg="P2(1)2(1)2(1)";

{* unit cell parameters in Angstroms and degrees *}
{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
{===>} a=61.76;
{===>} b=40.73;
{===>} c=26.74;
{===>} alpha=90;
{===>} beta=90;
{===>} gamma=90;

{* reflection files *}
{* specify non-anomalous reflection files before anomalous reflection files. *}
{* files must contain unique array names otherwise errors will occur *}
{===>} reflection_infile_1="amy.cv";
{===>} reflection_infile_2="";
{===>} reflection_infile_3="";

{* reciprocal space array containing observed amplitudes: required *}
{===>} obs_f="fobs";

{* reciprocal space array containing sigma values for amplitudes: required *}
{===>} obs_sigf="sigma";

{* reciprocal space array containing test set for cross-validation: required *}
{* cross-validation should always be used, with the possible exception
   of a final round of refinement including all data *}
{* cross-validation is always required for the maximum likelihood targets *}
{===>} test_set="test";

{* number for selection of test reflections: required for cross-validation *}
{* ie. reflections with the test set array equal to this number will be
       used for cross-validation, all other reflections form the working set *}
{===>} test_flag=1;

{* reciprocal space array containing observed intensities: optional *}
{* required for the "mli" target *}
{===>} obs_i="";

{* reciprocal space array containing sigma values for intensities: optional *}
{* required for the "mli" target *}
{===>} obs_sigi="";

{* reciprocal space arrays with experimental phase probability
   distribution: optional *}
{* Hendrickson-Lattman coefficients A,B,C,D *}
{* required for the "mlhl" target *}
{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +}
{===>} obs_pa="pa";
{===>} obs_pb="pb";
{===>} obs_pc="pc";
{===>} obs_pd="pd";

{* resolution limits to be used in refinement *}
{* the full resolution range of observed data should be used in refinement.
   A bulk solvent correction should be applied to allow the use of low
   resolution terms. If no bulk solvent correction is applied, data must
   be truncated at a lower resolution limit of between 8 and 6 Angstrom. *}
{+ table: rows=1 "resolution" cols=2 "lowest" "highest" +}
{===>} low_res=500.0;
{===>} high_res=2.0;

{====================== annealing parameters =========================}

{* carry out simulated annealing *}
{+ choice: true false +}
{===>} anneal=true;

{===================== minimization parameters =======================}

{* number of coordinate minimization steps *}
{===>} minimize_nstep=10;

{* number of restrained individual B-factor minimization steps *}
{===>} bfactor_nstep=10;

{====================== refinement parameters ========================}

{* number of cycles of refinement *}
{===>} num_cycles=2;

{* refinement target *}
{+ list: mlf: maximum likelihood target using amplitudes
         mli: maximum likelihood target using intensities
        mlhl: maximum likelihood target using amplitudes
              and phase probability distribution
    residual: standard crystallographic residual
      vector: vector residual
       mixed: (1-fom)*residual + fom*vector
        e2e2: correlation coefficient using normalized E^2
        e1e1: correlation coefficient using normalized E
        f2f2: correlation coefficient using F^2
        f1f1: correlation coefficient using F +}
{+ choice: "mlf" "mli" "mlhl" "residual" "vector" "mixed"
           "e2e2" "e1e1" "f2f2" "f1f1" +}
{===>} reftarget="mlf";

{==================== map generation parameters ======================}

{* write map files *}
{+ choice: true false +}
{===>} write_map=true;

{* type of map *}
{+ list:   sigmaa: (u m|Fo| - v D|Fc|)^exp(i phi_calc)
                    m and D calculated from sigmaa
       unweighted: (u |Fo| - v k|Fc|)^exp(i phi_calc)
                    no figure-of-merit weighting
         combined: (u m|Fo|^exp(i phi_comb) - v D|Fc|^exp(i phi_calc))
                    model and experimental phases combined, m and D from sigmaa
         observed: (u m|Fo|^exp(i phi_obs) - v k m|Fc|^exp(i phi_calc))
                    observed phases and fom from phase probability distribution
       NB. experimental phases must be supplied as a phase
           probability distribution in the Hendrickson-Lattman arrays +}
{+ choice: "sigmaa" "unweighted" "combined" "observed" +}
{===>} map_type="sigmaa";

{* coefficients for first map *}
{+ choice: "gradient" "fofc" "2fofc" "3fo2fc" +}
{===>} map_coeff_1="fofc";

{* coefficients for second map *}
{+ choice: "gradient" "fofc" "2fofc" "3fo2fc" +}
{===>} map_coeff_2="2fofc";

{* map grid size: dmin*grid *}
{* use grid=0.25 for better map appearance *}
{===>} grid=0.33;

{* extent of map *}
{+ choice: "molecule" "asymmetric" "unit" "box" "fract" +}
{===>} map_mode="molecule";

{* limits in orthogonal angstroms for box mode or 
   fractional coordinates for fract mode *}
{+ table: rows=3 "x" "y" "z" cols=2 "minimum" "maximum" +}
{===>} xmin=0;
{===>} xmax=0;
{===>} ymin=0;
{===>} ymax=0;
{===>} zmin=0;
{===>} zmax=0;

{=========================== output files ============================}

{* root name for output files *}
{+ list:
         map files will be in: <output_root>_<map_coeff_1>.map
                               <output_root>_<map_coeff_2>.map
         refined coordinates will be in: <output_root>.pdb +}
{===>} output_root="refine";

{===========================================================================}
{        things below this line do not normally need to be changed          }
{===========================================================================}

 ) {- end block parameter definition -}
