{+ file: minimize_twin.inp +}
{+ directory: xtal_twin +}
{+ description: Crystallographic conjugate gradient minimization refinement
                for data with hemihedral twinning  +}
{+ authors: Axel T. Brunger, and Paul D. Adams +}
{+ copyright: Yale University +}

{+ reference: T.O. Yeates, Detecting and Overcoming Crystal Twinning,
              Methods in Enzymology 276, 344-358 (1997) +}
{+ reference: A.T. Brunger, The Free R Value: a Novel Statistical 
              Quantity for Assessing the Accuracy of Crystal Structures, 
              Nature 355, 472-474 (1992) +}

{- Guidelines for using this file:
   - all strings must be quoted by double-quotes
   - logical variables (true/false) are not quoted
   - do not remove any evaluate statements from the file 
   - the selections store1 through store8 are available for general use -}

{========================== IMPORTANT NOTE ===========================}

{* This input file requires that the test set has been generated with
   the CNS task file make_cv_twin.inp. This ensures that twin related
   reflections are part of the same set. *}

{- begin block parameter definition -} define(

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

{* coordinate file *}
{===>} coordinate_infile="porin.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="porin.mtf";

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

{* force field settings file *}
{===>} force_field_infile="";

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

{* space group *}
{* use International Table conventions with subscripts substituted
   by parenthesis *}
{===>} sg="R3";

{* unit cell parameters in Angstroms and degrees *}
{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
{===>} a=104.400;
{===>} b=104.400;
{===>} c=124.250;
{===>} alpha=90;
{===>} beta=90;
{===>} gamma=120;

{* 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="porin.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 *}
{* 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 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 *}
{+ 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 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=2.25;

{* 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="";

{============ initial 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;

{======================= twinning parameters =========================}

{* twinning operation *}
{===>} twin_oper="h,-h-k,-l";

{* twinning fraction *}
{===>} twin_frac=0.304;

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

{* select atoms to be included in refinement *}
{* this should include all conformations if multiple conformations are used *}
{===>} atom_select=(known and not hydrogen);

{* select fixed atoms *}
{* note: atoms at special positions are automatically fixed. So, 
   you don't have to explicitly fix them here. *}
{===>} atom_fixed=(none);

{* select atoms to be harmonically restrained during refinement *}
{===>} atom_harm=(none);

{* harmonic restraint constant - for harmonically restrained atoms *}
{===>} k_harmonic=10;

{* select atoms in alternate conformation 1 *}
{===>} conf_1=(none);

{* select atoms in alternate conformation 2 *}
{===>} conf_2=(none);

{* select atoms in alternate conformation 3 *}
{===>} conf_3=(none);

{* select atoms in alternate conformation 4 *}
{===>} conf_4=(none);

{* additional restraints file *}
{* eg. auxiliary/dna-rna_restraints.def *}
{===>} restraints_infile="";

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

{* number of minimization steps *}
{===>} minimize_nstep=200;

{* number of cycles *}
{===>} num_cycles=1;

{* refinement target *}
{+ list: twin_lsq: least squares residual for hemihedral twinning +}
{+ choice: "twin_lsq" +}
{===>} reftarget="twin_lsq";

{* Wa weight for X-ray term *}
{* this will be determined automatically if a negative value is given.
   Note: wa can be very different depending on the target - if it is not
         determined automatically make sure an appropriate value is used *}
{===>} wa=-1;

{* 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;

{* 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;

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

{* output coordinate file *}
{===>} coordinate_outfile="minimize_twin.pdb";

{===========================================================================}
{        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

   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

 set echo=off end
 if ( &twin_frac > 0.5 ) then
   display Error: twinning fraction must be less than or equal 0.5
   abort
 end if
 set echo=on end

 {- 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 )

   binresolution &low_res &high_res
   mapresolution &high_res

   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
                    ( $obs_low <= amplitude(remap[&STRIP%twin_oper]($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          

 {- MODIFIED 8/01/06 -}
 end
 

 show min ( b ) ( &atom_select )
 evaluate ($b_min=$result)
 @@CNS_XTALMODULE:fft_parameter_check ( 
                             d_min=&high_res; 
                             b_min=$b_min;
                             grid=auto;
                             fft_memory=&fft_memory;
                             fft_grid=$fft_grid;   
                             fft_b_add=$fft_b_add; 
                             fft_elim=$fft_elim; 
                                      )
                            
 xray
 {- END MODIFICATION -}

   tolerance=0.0 lookup=false

   if ( &wa >= 0 ) then
      wa=&wa
   end if

 end                  

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

 if ( &BLANK%restraints_infile = false ) then
     @&restraints_infile
 end if

 do (store9=0) (all)

 evaluate ($nalt=1)
 evaluate ($alt=1)
 evaluate ($done=false)
 while ( $done = false ) loop nalt
   if ( &exist_conf_$alt = true ) then
     show sum(1) ( &conf_$alt )
     if ( $result > 0 ) then
       evaluate ($nalt=$nalt+1)
     end if
   else
     evaluate ($done=true)
     evaluate ($nalt=$nalt-1)
   end if
   evaluate ($alt=$alt+1)
 end loop nalt

 evaluate ($alt=1)
 while ( $alt <= $nalt ) loop alt
   do (store9=$alt) ( &conf_$alt )
   evaluate ($alt=$alt+1)
 end loop alt

 igroup
   interaction ( &atom_select and not(attr store9 > 0))
               ( &atom_select and not(attr store9 > 0))
   evaluate ($alt=1)
   while ( $alt <= $nalt ) loop alcs
     interaction ( &atom_select and ( attr store9 = $alt or attr store9 = 0 ))
                 ( &atom_select and ( attr store9 = $alt ))
     evaluate ($alt=$alt+1)
   end loop alcs
 end
 
 {- check isolated atoms and atoms at special positions and add to
    list of fixed atoms if needed - store9 will be used -}
 
 @CNS_XTALMODULE:setupfixed (
                           mode="minimization";
                           atom_select=&atom_select;
                           atom_fixed=&atom_fixed;
                           atom_total_fixed=store9;
                           atom_multiplicity=rmsd;
                           )
 
 fix selection=( store9 ) end

 fastnb grid end

 flags                                       
    include xref                   
   ?                                        
 end      
 if ( &BLANK%force_field_infile = true ) then
    flags                                       
       exclude elec pele include vdw pvdw                 
      ?                                        
    end      
 else
     @&force_field_infile
 end if                                   

 show sum(1) (&atom_harm)
 if ( $result > 0 ) then
   evaluate ($harmonic=true)
 else
   evaluate ($harmonic=false)
 end if

 xray
   predict
     mode=reciprocal
     to=fcalc
     selection=(ref_active=1)
     atomselection=( &atom_select ) 
   end
 end

 {- BEGIN MODIFICATION 8/01/06 -}
 @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;
                             
                             )
 
 {- 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=$b_min;
                             grid=auto;
                             fft_memory=&fft_memory;
                             fft_grid=$fft_grid;   
                             fft_b_add=$fft_b_add; 
                             fft_elim=$fft_elim; 
                                      )
{- END MODIFICATION -}


 if ( $harmonic = true ) then
   do (refx=x) (all)
   do (refy=y) (all)
   do (refz=z) (all)
   do (harm=0) (all)
   do (harm=&k_harmonic) (&atom_harm)
   flags include harm end
 end if

 xray
   @@CNS_XTALMODULE:calculate_r_twin (fobs=&STRIP%obs_f;
                                      fcalc=fcalc;
                                      fpart=fbulk;
                                      twin_oper=&STRIP%twin_oper;
                                      twin_frac=&twin_frac;
                                      sel=(ref_active=1);
                                      sel_test=(tst_active=1);
                                      print=true;
                                      output=OUTPUT;
                                      r=$start_r;
                                      test_r=$start_test_r;)
 end

 evaluate ($cycle=1)

 while ($cycle <= &num_cycles) loop main

   xray
     @@CNS_XTALMODULE:refinementtarget_twin (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;
                                             twin_oper=&STRIP%twin_oper;
                                             twin_frac=&twin_frac;
                                             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;)
   end

   if ( &wa < 0 ) then
     @@CNS_XTALMODULE:getweight (selected=&atom_select;
                                 fixed=(store9);)
   end if

   if ( &minimize_nstep > 0 ) then
     minimize lbfgs                             
       nstep=&minimize_nstep                                             
       nprint=5
       drop=10.0
     end                                            
   end if

   evaluate ($cycle=$cycle+1)

 end loop main

 xray
    predict
      mode=reciprocal
      to=fcalc
      selection=(ref_active=1)
      atomselection=( &atom_select ) 
    end
    @@CNS_XTALMODULE:calculate_r_twin (fobs=&STRIP%obs_f;
                                       fcalc=fcalc;
                                       fpart=fbulk;
                                       twin_oper=&STRIP%twin_oper;
                                       twin_frac=&twin_frac;
                                       sel=(ref_active=1);
                                       sel_test=(tst_active=1);
                                       print=true;
                                       output=OUTPUT;
                                       r=$full_r;
                                       test_r=$full_test_r;)
 end

 print threshold=20.0 bond 
 evaluate ($rmsd_bond=$result)

 print threshold=50.0 angle 
 evaluate ($rmsd_angle=$result)

 set display=&coordinate_outfile end

 display REMARK coordinates from twinned data minimization refinement
 display REMARK twinning operator= &STRIP%twin_oper  twinning fraction= &twin_frac
 display REMARK refinement resolution: &low_res - &high_res A
 if ( $total_test > 0 ) then
   display REMARK starting twinned r= $start_r[f6.4] twinned free_r= $start_test_r[f6.4]
   display REMARK final    twinned r= $full_r[f6.4] twinned free_r= $full_test_r[f6.4]
 else
   display REMARK starting twinned r= $start_r[f6.4]
   display REMARK final    twinned r= $full_r[f6.4]
 end if
 display REMARK rmsd bonds= $rmsd_bond[f8.6]  rmsd angles= $rmsd_angle[f8.5]
 xray wa=? end
 evaluate ($wa_print=$result)
 display REMARK wa= $wa_print
 display REMARK target= &STRIP%reftarget cycles= &num_cycles steps= &minimize_nstep
 display REMARK sg= &STRIP%sg a= &a b= &b c= &c alpha= &alpha beta= &beta gamma= &gamma

 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
      display REMARK parameter file $counter  : &STRIP%parameter_infile_$counter
    end if
  else
   evaluate ($done=true)
  end if
  evaluate ($counter=$counter+1)
 end loop read
 
 if ( &BLANK%structure_infile = true ) then
   display REMARK molecular structure file: automatic

   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
        display REMARK topology file $counter  : &STRIP%topology_infile_$counter
      end if
    else
     evaluate ($done=true)
    end if
    evaluate ($counter=$counter+1)
   end loop read

   evaluate ($counter=1)
   evaluate ($done=false)
   while ( $done = false ) loop read
    if ( &exist_link_infile_$counter = true ) then
      if ( &BLANK%link_infile_$counter = false ) then
        display REMARK linkage file $counter  : &STRIP%link_infile_$counter
      end if
    else
     evaluate ($done=true)
    end if
    evaluate ($counter=$counter+1)
   end loop read

   if ( &BLANK%patch_infile = false ) then
      display REMARK custom patch file = &STRIP%patch_infile
   end if

 else
   display REMARK molecular structure file: &STRIP%structure_infile
 end if

 display REMARK input coordinates: &STRIP%coordinate_infile
 if ( &BLANK%anom_library = false ) then
   display REMARK anomalous f' f'' library: &STRIP%anom_library
 end if

 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
         display REMARK reflection file $counter : &STRIP%reflection_infile_$counter       
      end if
   else
     evaluate ($done=true)
   end if
   evaluate ($counter=$counter+1)
 end loop read

 if ( &BLANK%restraints_infile = false ) then
    display REMARK additional restraints file: &STRIP%restraints_infile
 end if
 if ( &BLANK%ncs_infile = false ) then
   display REMARK ncs= &STRIP%ncs_type  ncs file= &STRIP%ncs_infile
 else
   display REMARK ncs= none
 end if
 
 if ( &bscale # "no" ) then
   if ( $low_b_flag = true ) then
     display REMARK warning: B-correction gave atomic B-values less than zero
     display REMARK          they have been reset to zero
   end if
 end if
 
 ! 
 ! Begin modification (8/01/06)
 if ( &bscale = "anisotropic" ) then
   display REMARK Anisotropic B-factor tensor Ucart of atomic model without isotropic component :
   display REMARK   B11=$Baniso_11[f8.3] B22=$Baniso_22[f8.3] B33=$Baniso_33[f8.3]
   display REMARK   B12=$Baniso_12[f8.3] B13=$Baniso_13[f8.3] B23=$Baniso_23[f8.3]
   display REMARK Isotropic component added to coordinate array B: $Biso_model[f8.3]
 elseif ( &bscale = "isotropic" ) then
   display REMARK B-factor applied to coordinate array B: $Biso_model[f8.3]
 else
   display REMARK initial B-factor correction: none
 end if

 if ( &bulk_sol = true ) then 
   display REMARK bulk solvent: probe radius=$solrad_best, shrink value=$solrad_best
   display REMARK bulk solvent: density level= $sol_k_ref e/A^3, B-factor= $sol_b_ref A^2
 else
   display REMARK bulk solvent: false
 end if
 {- END MODIFICATION -}

 if ( &obs_type = "intensity" ) then 
   display REMARK reflections with Iobs/sigma_I < &sigma_cut rejected
   display REMARK reflections with Iobs > &obs_rms * rms(Iobs) rejected
   display REMARK reflections with Iobs[&STRIP%twin_oper] = 0 rejected
 else
   display REMARK reflections with |Fobs|/sigma_F < &sigma_cut rejected
   display REMARK reflections with |Fobs| > &obs_rms * rms(Fobs) rejected
   display REMARK reflections with |Fobs|[&STRIP%twin_oper] = 0 rejected
 end if
 xray anomalous=? end
 if ( $result = true ) then
   display REMARK anomalous diffraction data was input
 end if
 
 {- MODIFIED 8/01/06 -}
 display REMARK fft gridding factor = $fft_grid, B factor offset = $fft_b_add A^2, Elimit = $fft_elim
 {- END MODIFICATION -}

 display REMARK theoretical total number of refl. in resol. range:    $total_theor[I6] ( 100.0 % )
 display REMARK number of unobserved reflections (no entry):          $unobserved[I6] ( $per_unobs[f5.1] % )
 display REMARK number of reflections rejected:                       $rejected[I6] ( $per_reject[f5.1] % )
 display REMARK total number of reflections used:                     $total_used[I6] ( $per_used[f5.1] % )
 display REMARK number of reflections in working set:                 $total_work[I6] ( $per_work[f5.1] % )
 display REMARK number of reflections in test set:                    $total_test[I6] ( $per_test[f5.1] % )

 remark

 @CNS_XTALMODULE:write_pdb (pdb_o_format=true;
                            coordinate_outfile=&coordinate_outfile;
                            sgparam=$sgparam;)

 stop