{+ file: gradient_map.inp +}
{+ directory: xtal_refine +}
{+ description: Make a gradient electron density map  +}
{+ authors: Axel T. Brunger and Paul D. Adams +}
{+ copyright: Yale University +}

{+ reference: R.J. Read, Improved Fourier coefficients for maps using 
              phases from partial structures with errors. Acta Cryst. 
              A42, 140-149 (1986) +}
{+ reference: G.J. Kleywegt and A.T. Brunger, Checking your imagination:
              Applications of the free R value, Structure 4,
              897-904 (1996) +}
{+ reference: A.T. Brunger, P.D. Adams and L.M. Rice, New applications
              of simulated annealing in X-ray crystallography and
              solution NMR, Structure 5, 325-336, (1997) +}

{- Guidelines for using this file:
   - all strings must be quoted by double-quotes
   - logical variables (true/false) must not be quoted
   - do not remove any evaluate statements from the file -}

{- begin block parameter definition -} define(

{============================ coordinates ============================}

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

{==================== molecular information ==========================}

{* topology files *}
{===>} topology_infile_1="CNS_TOPPAR:protein.top";
{===>} topology_infile_2="CNS_TOPPAR:dna-rna.top";
{===>} topology_infile_3="CNS_TOPPAR:water.top";
{===>} topology_infile_4="CNS_TOPPAR:ion.top";
{===>} topology_infile_5="CNS_TOPPAR:carbohydrate.top";
{===>} topology_infile_6="";
{===>} topology_infile_7="";
{===>} topology_infile_8="";

{* linkage files for linear, continuous polymers (protein, DNA, RNA) *}
{===>} link_infile_1="CNS_TOPPAR:protein.link";
{===>} link_infile_2="CNS_TOPPAR:dna-rna-pho.link";
{===>} link_infile_3="";

{* parameter files *}
{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";
{===>} parameter_infile_2="CNS_TOPPAR:dna-rna_rep.param";
{===>} parameter_infile_3="CNS_TOPPAR:water_rep.param";
{===>} parameter_infile_4="CNS_TOPPAR:ion.param";
{===>} parameter_infile_5="CNS_TOPPAR:carbohydrate.param";
{===>} parameter_infile_6="";
{===>} parameter_infile_7="";
{===>} parameter_infile_8="";

{* molecular topology file: optional (leave blank for auto generation) *}
{* 
   Auto generation of the molecular topology from the coordinates should only 
   be used if:
   (1) Each distinct protein, DNA, or RNA chain must have a separate segid 
       (or chainid if the chainid is non-blank). 
   (2) Each contiguous protein, RNA, or RNA chain must not be disrupted by 
       other types of residues or ligands.  Rather, these other residues 
       should be listed after protein, RNA/DNA chains. 
   (3) Disulphides are automatically detected based on distances between the sulfur atoms
      (must be less than 3 A apart).
   (4) Broken protein/RNA/DNA chains without terminii must be more than 2.5 A apart to be recognized as such.
   (5) N-linked glycan links are automatically recognized if the bonded atoms are less than 2.5 A apart.
   (6) Automatic generation cannot be used with alternate conformations. 
   For ligands, the user must make suitable topology and parameter files.
   For non-standard covalent linkages, the custom patch file should be used.
   Alternatively, the generate.inp or generate_easy.inp task files
   can be used to generated the mtf prior to running this task file.
    *}
{===>} structure_infile="amy.mtf";

{* for auto generation: extra linkages and modifications by custom patches *}
{===>} patch_infile="";

{====================== 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;

{* anomalous f' f'' library file *}
{* If a file is not specified, no anomalous contribution will be included *}
{+ choice: "CNS_XRAYLIB:anom_cu.lib" "CNS_XRAYLIB:anom_mo.lib" "" user_file +}
{===>} anom_library="";

{* 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="";
{===>} reflection_infile_4="";

{* 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 for calculation of cross-validated sigmaA values *}
{===>} 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 weighting scheme for observed
   amplitudes: optional *}
{* only used for the "residual" and "vector" targets - this will
   default to a constant value of 1 if array is not present *}
{===>} obs_w="";

{* 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 and phase combined or observed maps *}
{+ table: rows=1 "HL coefficients" cols=4 "A" "B" "C" "D" +}
{===>} obs_pa="";
{===>} obs_pb="";
{===>} obs_pc="";
{===>} obs_pd="";

{* complex reciprocal space array containing experimental phases: optional *}
{* required for the "mixed" and "vector" targets *}
{===>} obs_phase="";

{* reciprocal space array containing experimental figures of merit: optional *}
{* required for the "mixed" target *}
{===>} obs_fom="";

{* resolution limits for data included in map calculation *}
{* all data available should be included in the map calculation *}
{+ table: rows=1 "resolution" cols=2 "lowest" "highest" +}
{===>} low_res=500.0;
{===>} high_res=2.0;

{* apply rejection criteria to amplitudes or intensities *}
{+ choice: "amplitude" "intensity" +}
{===>} obs_type="amplitude";

{* Observed data cutoff criteria: applied to amplitudes or intensities *}
{* reflections with magnitude(Obs)/sigma < cutoff are rejected. *}
{===>} sigma_cut=0.0;

{* rms outlier cutoff: applied to amplitudes or intensities *}
{* reflections with magnitude(Obs) > cutoff*rms(Obs) will be rejected *}
{===>} obs_rms=10000;

{=================== non-crystallographic symmetry ===================}

{* NCS-restraints/constraints file *}
{* see auxiliary/ncs.def *}
{===>} ncs_infile="";

{============ overall B-factor and bulk solvent corrections ==========}

{* overall B-factor correction *}
{+ choice: "no" "isotropic" "anisotropic" +}
{===>} bscale="anisotropic";

{* bulk solvent correction *}
{* a mask is required around the molecule(s). The region
   outside this mask is the solvent region *}
{+ choice: true false +}
{===>} bulk_sol=true;

{* bulk solvent mask file *}
{* mask will be read from O type mask file if a name is given
   otherwise calculated from coordinates of selected atoms *}
{===>} bulk_mask_infile="";

{* automatic bulk solvent parameter optimization for e-density level sol_k (e/A^3) and B-factor sol_b (A^2) *}
{+ choice: true false +}
{===>} sol_auto=true;

{* fixed solvent parameters (used if the automatic option is turned off) *}
{+ table: rows=1 "bulk solvent" cols=2 "e-density level sol_k (e/A^3)" "B-factor sol_b (A^2) " +}
{===>} sol_k=0.3;
{===>} sol_b=50.0;

{* optional file with a listing of the results of the automatic bulk solvent optimization *}
{===>} sol_output="";

{* solvent mask parameters *}
{+ table: rows=1 "bulk solvent" cols=2 "probe radius (A) (usually set to 1)" "shrink radius (A) (usually set to 1)" +}
{===>} sol_rad=1.0;
{===>} sol_shrink=1.0;

{========================== atom selection ===========================}

{* select atoms to be included in map calculation *}
{===>} atom_select=(known and not hydrogen);

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

{* 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";

{* number of bins for refinement target *}
{* this will be determined automatically if a negative value is given
   otherwise the specified number of bins will be used *}
{===>} target_bins=-1;

{* use model amplitudes for unmeasured data *}
{* this will not be applied to gradient or difference maps *}
{+ choice: true false +}
{===>} fill_in=false;

{* scale map by dividing by the rms sigma of the map *}
{* otherwise map will be on an absolute fobs scale *}
{+ choice: true false +}
{===>} map_scale=true;

{* map format *}
{+ choice: "cns" "ezd" +}
{===>} map_format="cns";

{* b-factor sharpening (A^2), for example, -100 *}
{===>} bsharp=0;

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

{* memory allocation for FFT calculation *}
{* this will be determined automatically if a negative value is given
   otherwise the specified number of words will be allocated *}
{===>} fft_memory=-1;

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

{* select atoms around which map will be written *}
{* change if different to atoms selected for map calculation *}
{===>} atom_map=(known and not hydrogen);

{* cushion (in Angstroms) around selected atoms in "molecule" mode *}
{===>} map_cushion=3.0;

{* 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 file will be in: <output_root>.map
         positive peaks in: <output_root>_positive.peaks
         negative peaks in: <output_root>_negative.peaks
         Fourier coefficients will be in: <output_root>.hkl +}
{===>} output_root="gradient_map";

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

{* do peak picking on map *}
{* optional - use water_pick.inp to pick waters *} 
{+ choice: true false +}
{===>} peak_search=true;

{* number of peaks to pick from map *}
{===>} peak_num=30;

{* write a reflection file with the Fourier coefficients of the map *}
{+ list: arrays written:
         map_coeff: Fourier map coefficients - map=ft(map_coeff) +}
{+ choice: true false +}
{===>} write_coeff=true;

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

 ) {- end block parameter definition -}

 checkversion 1.3

 evaluate ($log_level=quiet)

 if ( $log_level = verbose ) then
   set message=normal echo=on end
 else
   set message=off echo=off end
 end if

 if ( &BLANK%structure_infile = true ) then
 
    {- read topology files -}
    topology
     evaluate ($counter=1)
     evaluate ($done=false)
     while ( $done = false ) loop read
      if ( &exist_topology_infile_$counter = true ) then
         if ( &BLANK%topology_infile_$counter = false ) then
            @@&topology_infile_$counter
         end if
      else
        evaluate ($done=true)
      end if
      evaluate ($counter=$counter+1)
     end loop read
    end
    
    @CNS_XTALMODULE:mtfautogenerate (
                                  coordinate_infile=&coordinate_infile;
                                  convert=true;
                                  separate=true;
                                  atom_delete=(not known);
                                  hydrogen_flag=true;
                                  break_cutoff=2.5;
                                  disulphide_dist=3.0;
                                  carbo_dist=2.5;
                                  patch_infile=&patch_infile;
                                  O5_becomes="O";
                                 )

 else

   structure @&structure_infile end
   coordinates @&coordinate_infile

 end if

 {- read parameter files -}
 parameter
  evaluate ($counter=1)
  evaluate ($done=false)
  while ( $done = false ) loop read
   if ( &exist_parameter_infile_$counter = true ) then
      if ( &BLANK%parameter_infile_$counter = false ) then
         @@&parameter_infile_$counter
      end if
   else
     evaluate ($done=true)
   end if
   evaluate ($counter=$counter+1)
  end loop read
 end

 set message=normal echo=on end

 xray

   @CNS_XTALLIB:spacegroup.lib (sg=&sg;sgparam=$sgparam;)

   a=&a b=&b c=&c  alpha=&alpha beta=&beta gamma=&gamma
  
   @CNS_XRAYLIB:scatter.lib

   binresolution &low_res &high_res
   mapresolution &high_res

   generate &low_res &high_res

   evaluate ($counter=1)
   evaluate ($done=false)
   while ( $done = false ) loop read
    if ( &exist_reflection_infile_$counter = true ) then
      if ( &BLANK%reflection_infile_$counter = false ) then
       reflection
         @@&reflection_infile_$counter
       end
      end if
   else
     evaluate ($done=true)
   end if
   evaluate ($counter=$counter+1)
  end loop read

 end

 if ( &BLANK%anom_library = false ) then
   @@&anom_library
 else
   set echo=off end
   xray anomalous=? end
   if ( $result = true ) then
     display Warning: no anomalous library has been specified
     display          no anomalous contribution will used in refinement
   end if
   set echo=on end
 end if

 {- copy define parameters of optional arrays into symbols so 
    we can redefine them -}
    
 evaluate ($obs_i=&obs_i)
 evaluate ($obs_sigi=&obs_sigi)
 evaluate ($obs_w=&obs_w)
 xray
   @@CNS_XTALMODULE:checkrefinput (
                                  reftarget=&reftarget;
                                  obs_f=&obs_f;
                                  obs_sigf=&obs_sigf;
                                  test_set=&test_set;
                                  obs_pa=&obs_pa;
                                  obs_pb=&obs_pb;
                                  obs_pc=&obs_pc;
                                  obs_pd=&obs_pd;
                                  obs_phase=&obs_phase;
                                  obs_fom=&obs_fom;
                                  obs_w=$obs_w;
                                  obs_i=$obs_i;
                                  obs_sigi=$obs_sigi;
                                  )

   query name=fcalc domain=reciprocal end
   if ( $object_exist = false ) then
      declare name=fcalc domain=reciprocal type=complex end
   end if
   declare name=fbulk domain=reciprocal type=complex end
   do (fbulk=0) ( all )

   query name=&STRIP%obs_f domain=reciprocal end
   declare name=fobs_orig domain=reciprocal type=$object_type end
   declare name=sigma_orig domain=reciprocal type=real end

   do (fobs_orig=&STRIP%obs_f) (all)
   do (sigma_orig=&STRIP%obs_sigf) (all)

   if ( &BLANK%obs_i = false ) then
     query name=&STRIP%obs_i domain=reciprocal end
     declare name=iobs_orig domain=reciprocal type=$object_type end
     declare name=sigi_orig domain=reciprocal type=real end
     do (iobs_orig=&STRIP%obs_i) (all)
     do (sigi_orig=&STRIP%obs_sigi) (all)
   end if

   if ( &obs_type = "intensity" ) then
     if ( &BLANK%obs_i = true ) then
       display  Error: observed intensity array is undefined
       display         aborting script
       abort
     end if
     evaluate ($reject_obs=&obs_i)
     evaluate ($reject_sig=&obs_sigi)
   else
     evaluate ($reject_obs=&obs_f)
     evaluate ($reject_sig=&obs_sigf)
   end if

   declare name=ref_active domain=reciprocal type=integer end
   declare name=tst_active domain=reciprocal type=integer end

   do (ref_active=0) ( all )
   do (ref_active=1) ( ( $STRIP%reject_sig # 0 ) and
                      ( &low_res >= d >= &high_res ) )

   statistics overall
     completeness
     selection=( ref_active=1 )
   end
   evaluate ($total_compl=$expression1)

   show sum(1) ( ref_active=1 )
   evaluate ($total_read=$select)
   evaluate ($total_theor=int(1./$total_compl * $total_read))

   show rms (amplitude($STRIP%reject_obs)) ( ref_active=1 )
   evaluate ($obs_high=$result*&obs_rms)
   show min (amplitude($STRIP%reject_obs)) ( ref_active=1 )
   evaluate ($obs_low=$result)

   do (ref_active=0) ( all )
   do (ref_active=1)
                  ( ( amplitude($STRIP%reject_obs) > &sigma_cut*$STRIP%reject_sig ) and
                    ( $STRIP%reject_sig # 0 ) and
                    ( $obs_low <= amplitude($STRIP%reject_obs) <= $obs_high ) and
                    ( &low_res >= d >= &high_res ) )

   do (tst_active=0) (all)
   if ( &BLANK%test_set = false ) then
     do (tst_active=1) (ref_active=1 and &STRIP%test_set=&test_flag)
   end if

   show sum(1) ( ref_active=1 and tst_active=0 )
   evaluate ($total_work=$select)
   show sum(1) ( ref_active=1 and tst_active=1 )
   evaluate ($total_test=$select)
   evaluate ($total_used=$total_work+$total_test)

   evaluate ($unobserved=$total_theor-$total_read)
   evaluate ($rejected=$total_read-$total_used)
   evaluate ($per_unobs=100*($unobserved/$total_theor))
   evaluate ($per_reject=100*($rejected/$total_theor))
   evaluate ($per_used=100*($total_used/$total_theor))
   evaluate ($per_work=100*($total_work/$total_theor))
   evaluate ($per_test=100*($total_test/$total_theor))

   associate fcalc ( &atom_select )

   tselection=( ref_active=1 )

   cvselection=( tst_active=1 )

   method=FFT          
   
 end
 

 show min ( b ) ( &atom_select )
 evaluate ($b_min=$result)
 @@CNS_XTALMODULE:fft_parameter_check ( 
                             d_min=&high_res; 
                             b_min=$b_min;
                             grid=&grid;
                             fft_memory=&fft_memory;
                             fft_grid=$fft_grid;   
                             fft_b_add=$fft_b_add; 
                             fft_elim=$fft_elim; 
                                      )
                            
 xray
 
   tolerance=0.0 lookup=false
   
 end                  

 if ( &reftarget = "mlhl" ) then
   evalaute ($test_hl=true)
 elseif ( &reftarget = "vector" ) then
   evalaute ($test_hl=true)
 elseif ( &reftarget = "combined" ) then
   evalaute ($test_hl=true)
 else
   evalaute ($test_hl=false)
 end if

 if ( $test_hl = true ) then
   xray
     @@CNS_XTALMODULE:check_abcd (pa=&obs_pa;
                                 pb=&obs_pb;
                                 pc=&obs_pc;
                                 pd=&obs_pd;)
   end
 end if

 if ( &BLANK%ncs_infile = false ) then
    inline @&ncs_infile
 end if

 xray
   declare name=dtarg domain=reciprocal type=complex end
   declare name=total domain=reciprocal type=complex end
   declare name=fmap domain=reciprocal type=complex end
 end

 xray
   do (&STRIP%obs_f=fobs_orig) (all)
   do (&STRIP%obs_sigf=sigma_orig) (all)
   if ( &BLANK%obs_i = false ) then
     do (&STRIP%obs_i=iobs_orig) (all)
     do (&STRIP%obs_sigi=sigi_orig) (all)
   end if
 end

 xray
    predict
      mode=reciprocal
      to=fcalc
      selection=(&low_res >= d >= &high_res)
      atomselection=( &atom_select ) 
    end
 end

  @CNS_XTALMODULE:scale_and_solvent_grid_search (
                             bscale=&bscale;
                             sel=( ref_active=1 );
                             sel_test=( tst_active=1 );
                             atom_select=( &atom_select );
                             bulk_sol=&bulk_sol;
                             bulk_mask=&bulk_mask_infile;
                             bulk_atoms=( &atom_select );
                             
                             sol_auto=&sol_auto;
                             sol_k=&sol_k;
                             sol_b=&sol_b;
                             sol_rad=&sol_rad;
                             sol_shrink=&sol_shrink;
  
                             fcalc=fcalc;
                             obs_f=&STRIP%obs_f;
                             obs_sigf=&STRIP%obs_sigf;
                             obs_i=$STRIP%obs_i;
                             obs_sigi=$STRIP%obs_sigi;                             
                             fpart=fbulk;
                             
                             Baniso_11=$Baniso_11;
                             Baniso_22=$Baniso_22;
                             Baniso_33=$Baniso_33;
                             Baniso_12=$Baniso_12;
                             Baniso_13=$Baniso_13;
                             Baniso_23=$Baniso_23;
                             Biso=$Biso_model;
                             
                             sol_k_best=$sol_k_ref;
                             sol_b_best=$sol_b_ref;
			     solrad_best=$solrad_best;
			     shrink_best=$shrink_best;
                             
                             b=b;

                             low_b_flag=$low_b_flag;
                            
                             sol_output=&sol_output;
                             
                             )
 xray
   @@CNS_XTALMODULE:calculate_r (
                                 fobs=&STRIP%obs_f;
                                 fcalc=fcalc;
                                 fpart=fbulk;
                                 sel=( ref_active=1 );
                                 sel_test=( tst_active=1 );
                                 print=true;
                                 output=OUTPUT;
                                 r=$map_r;
                                 test_r=$map_free_r;)
 end

 {- check the gridding again since the minimum B-factor may have changed -}
 show min ( b ) ( &atom_select )
 evaluate ($b_min=$result)
 @@CNS_XTALMODULE:fft_parameter_check ( 
                             d_min=&high_res; 
                             b_min=$b_min;
                             grid=&grid;
                             fft_memory=&fft_memory;
                             fft_grid=$fft_grid;   
                             fft_b_add=$fft_b_add; 
                             fft_elim=$fft_elim; 
                                      )  
 xray
     @@CNS_XTALMODULE:refinementtarget (target=&reftarget;
                                        sig_sigacv=0.07;
                                        mbins=&target_bins;
                                        fobs=&STRIP%obs_f;
                                        sigma=&STRIP%obs_sigf;
                                        weight=$STRIP%obs_w;
                                        iobs=$STRIP%obs_i;
                                        sigi=$STRIP%obs_sigi;
                                        test=tst_active;
                                        fcalc=fcalc;
                                        fpart=fbulk;
                                        pa=&STRIP%obs_pa;
                                        pb=&STRIP%obs_pb;
                                        pc=&STRIP%obs_pc;
                                        pd=&STRIP%obs_pd;
                                        phase=&STRIP%obs_phase;
                                        fom=&STRIP%obs_fom;
                                        sel=(ref_active=1);
                                        sel_test=(tst_active=1);
                                        statistics=true;)
      predict
         mode=dtarget(fcalc)
         to=dtarg
         selection=(ref_active=1)
         atomselection=( &atom_select ) 
      end
 
  end

 xray
  {- take the negative of the gradient so the map is the same sign
     as a standard difference map -}
  do (fmap=-dtarg) (ref_active=1)
 end

 if (&bsharp # 0) then 
   {- b-factor sharpening -} 
    evaluate ($bsharp= (-1) * &bsharp) 
    xray
      do (fmap=exp( $bsharp * s^2/4) * fmap) ( all )
    end
 end if
 
 xray
   declare name=map domain=real end
     do (map=ft(fmap)) (ref_active=1)
 end

 xray
   undeclare name=dtarg domain=reciprocal end
   undeclare name=total domain=reciprocal end
 end

 if (&map_scale=true) then    
   xray                                        
     show rms (real(map)) ( all )
     do (map=map/$result) ( all )
     evaluate ($map_scale=$result)
   end
 end if
 
 set remarks=reset end
 set remarks=accumulate end

 xray
   show sum (1) (tst_active=1)
   if ( $result > 0 ) then
     evaluate ($test_exist=true)
   else
     evaluate ($test_exist=false)
   end if
 end

 evaluate ($remark="( d(" + &reftarget + ")/dFc )")
 
 evaluate ($remark=$remark + " map")

 if ( $total_test > 0 ) then
   remark $remark  r= $map_r[f6.4] free_r= $map_free_r[f6.4]
 else
   remark $remark  r= $map_r[f6.4]
 end if

 remark resolution range of map: &low_res - &high_res
 
 if ( &obs_type = "intensity" ) then
   remark reflections with Iobs/sigma_I < &sigma_cut rejected
   remark reflections with Iobs > &obs_rms * rms(Iobs) rejected
 else
   remark reflections with |Fobs|/sigma_F < &sigma_cut rejected
   remark reflections with |Fobs| > &obs_rms * rms(Fobs) rejected
 end if
 xray anomalous=? end
 if ( $result = true ) then
   remark anomalous diffraction data was input
 end if
 
 remark fft gridding factor = $fft_grid, B factor offset = $fft_b_add A^2, Elimit = $fft_elim
 
 remark theoretical total number of refl. in resol. range:    $total_theor[I6] ( 100.0 % )
 remark number of unobserved reflections (no entry):          $unobserved[I6] ( $per_unobs[f5.1] % )
 remark number of reflections rejected:                       $rejected[I6] ( $per_reject[f5.1] % )
 remark total number of reflections used:                     $total_used[I6] ( $per_used[f5.1] % )
 remark number of reflections in working set:                 $total_work[I6] ( $per_work[f5.1] % )
 remark number of reflections in test set:                    $total_test[I6] ( $per_test[f5.1] % )

 if ( &bscale = "anisotropic" ) then
   REMARK Anisotropic B-factor tensor Ucart of atomic model without isotropic component :
   REMARK   B11=$Baniso_11[f8.3] B22=$Baniso_22[f8.3] B33=$Baniso_33[f8.3]
   REMARK   B12=$Baniso_12[f8.3] B13=$Baniso_13[f8.3] B23=$Baniso_23[f8.3]
   REMARK Isotropic component added to coordinate array B: $Biso_model[f8.3]
 elseif ( &bscale = "isotropic" ) then
   REMARK B-factor applied to coordinate array B: $Biso_model[f8.3]
 else
   REMARK initial B-factor correction: none
 end if
 
 if ( &bulk_sol = true ) then
   remark bulk solvent: probe radius=$solrad_best, shrink value=$solrad_best
   remark bulk solvent: density level= $sol_k_ref e/A^3, B-factor= $sol_b_ref A^2
 else
   remark bulk solvent: false
 end if
  
 if (&bsharp # 0) then
   remark B-factor sharpening applied to map: exp( Bsharp * S^2/4 ) where Bsharp = &bsharp
 end if

 if (&map_scale=true) then
      remarks map has been scaled by 1/rms (rms= $map_scale[F11.5] )
 end if

 remark a= &a b= &b c= &c alpha= &alpha beta= &beta gamma= &gamma sg= &STRIP%sg

 if ( &write_coeff = true ) then
   evaluate ($coeff_out=&output_root + ".hkl")
   xray
     declare name=map_coeff domain=reciprocal type=complex end
     do (map_coeff=fmap) (all)

     set display=$coeff_out end
   end
   
   @CNS_XTALMODULE:write_hkl_header (sg=&STRIP%sg;
                                     sgparam=$sgparam;)

   xray

     write reflection
       output=$coeff_out
       sele=(ref_active=1)
       map_coeff
     end
     
     set display=OUTPUT end

     undeclare name=map_coeff domain=reciprocal end
   end
 end if
 
 xray
   undeclare name=fmap  domain=reciprocal end
 end

 if ( &write_map = true ) then

   evaluate ($filename=&output_root + ".map") 

   if ( &map_mode = "asymmetric" ) then
     evaluate ($map_mode_string=ASYM)
   elseif ( &map_mode = "unit" ) then
     evaluate ($map_mode_string=UNIT)
   elseif ( &map_mode = "box" ) then
     evaluate ($map_mode_string=BOX)
   elseif ( &map_mode = "fract" ) then
     evaluate ($map_mode_string=FRAC)
   else
     evaluate ($map_mode_string=MOLE)
   end if

   xray
     write map
       if ( &map_format = "ezd" ) then
         type=ezd
       else
         type=cns
       end if
       automatic=false
       from=map
       output=$filename
       cushion=&map_cushion
       selection=&atom_map
       extend=$map_mode_string
       if ( &map_mode = "box" ) then
         xmin=&xmin xmax=&xmax
         ymin=&ymin ymax=&ymax
         zmin=&zmin zmax=&zmax
       end if
       if ( &map_mode = "fract" ) then
         xmin=&xmin xmax=&xmax
         ymin=&ymin ymax=&ymax
         zmin=&zmin zmax=&zmax
       end if
     end
   end
 end if

 if ( &peak_search = true ) then

   show sum ( x ) ( segid PEAK) 
   if ($SELECT > 0) then
      display
      display  WARNING: there are atoms that have the reserved segid PEAK. 
      display           They will be deleted prior to the peak search.
      display
   end if
   delete sele=(segid=PEAK) end

   evaluate ($filename=&output_root + "_positive.peaks")
   xray
     peakpik
       from=map
       mpeak=&peak_num
       selection=( all )
       atom=true
       proximity=(&atom_map)
     end
   end

   write coor output=$filename selection=(segid=PEAK) end

   delete sele=(segid=PEAK) end

   evaluate ($filename=&output_root + "_negative.peaks")
   xray
     do (map=-map) ( all )
     peakpik
       from=map
       mpeak=&peak_num
       selection=( all )
       atom=true
       proximity=(&atom_map)
     end
   end

   write coor output=$filename selection=(segid=PEAK) end
 end if

 stop