{+ file: bgroup_twin.inp +}
{+ directory: xtal_twin +}
{+ description: Grouped, 2-groups per-residue, unrestrained B-factor 
                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 -}

{========================== 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(

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

{* molecular topology file *}
{===>} structure_infile="porin.mtf";

{* parameter files *}
{===>} parameter_infile_1="CNS_TOPPAR:protein_rep.param";
{===>} parameter_infile_2="";
{===>} parameter_infile_3="";
{===>} parameter_infile_4="";
{===>} parameter_infile_5="";

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

{====================== 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="";

{* 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 search *}
{+ choice: true false +}
{===>} sol_auto=true;

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

{* fixed solvent mask parameters if the automatic option is not used *}
{+ table: rows=1 "bulk solvent" cols=2 "probe radius (A)" "shrink radius (A)" +}
{===>} sol_rad=1.0;
{===>} sol_shrink=1.0;

{* fixed solvent parameters if the automatic option is not used *}
{+ table: rows=1 "bulk solvent" cols=2 "e-density level (e/A^3)" "B-factor (A^2)" +}
{===>} sol_k=-1;
{===>} sol_b=-1;

{======================= 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 *}
{===>} atom_select=(known and not hydrogen);

{* select atoms whose B-factor will remain fixed *}
{===>} atom_fixed=(none);

{* B-factor groups *}

{* select atoms in group 1 - protein mainchain example *}
{===>} bg_group_1=((resname ALA or resname ARG or resname ASN or
                  resname ASP or resname CYS or resname GLN or
                  resname GLU or resname GLY or resname HIS or
                  resname ILE or resname LEU or resname LYS or
                  resname MET or resname MSE or resname PHE or
                  resname PRO or resname SER or resname THR or
                  resname TRP or resname TYR or resname VAL or
                  resname HISH or resname HISU or resname M3L or
                  resname CPR) and
                  (name c or name n or name ca or name o or name ot+));

{* select atoms in group 2 - protein sidechain example *}
{===>} bg_group_2=((resname ALA or resname ARG or resname ASN or
                  resname ASP or resname CYS or resname GLN or
                  resname GLU or resname GLY or resname HIS or
                  resname ILE or resname LEU or resname LYS or
                  resname MET or resname MSE or resname PHE or
                  resname PRO or resname SER or resname THR or
                  resname TRP or resname TYR or resname VAL or
                  resname HISH or resname HISU or resname M3L or
                  resname CPR) and
                  not(name c or name n or name ca or name o or name ot+));

{* select atoms in group 3 - nucleic acid backbone example *}
{===>} bg_group_3=((resname THY or resname CYT or resname GUA or
                  resname ADE or resname URI) and
                  (name c+' or name h+' or name op or name o+' or
                  name p or name ht or name ot));

{* select atoms in group 4 - nucleic acid bases example *}
{===>} bg_group_4=((resname THY or resname CYT or resname GUA or
                  resname ADE or resname URI) and
                  not(name c+' or name h+' or name op or name o+' or
                  name p or name ht or name ot));

{* select atoms in group 5 - carbohydrates example *}
{===>} bg_group_5=(resname GLC or resname GAL or resname MAN or
                  resname NAG or resname FUC or resname SIA or
                  resname XYL);

{* select atoms in group 6 *}
{===>} bg_group_6=(none);

{* select atoms in group 7 *}
{===>} bg_group_7=(none);

{* select atoms in group 8 *}
{===>} bg_group_8=(none);

{================= B-factor minimization parameters ==================}

{* reset all atomic B factors to this number if positive *}
{===>} reset_b=-1;

{* number of steps of group B-factor minimization *}
{===>} bfactor_nstep=30;

{* B-factor limits *}
{+ table: rows=1 "B-factor" cols=2 "minimum" "maximum" +}
{===>} bmin=1;
{===>} bmax=200;

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

{* 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="bgroup_twin.pdb";

{* format output coordinates for use in o *}
{* if false then the default CNS output coordinate format will be used *}
{+ choice: true false +}
{===>} pdb_o_format=true;

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

 ) {- end block parameter definition -}

 checkversion 1.2

 evaluate ($log_level=quiet)

 structure @&structure_infile end

 coordinates @&coordinate_infile

 parameter
   if ( &BLANK%parameter_infile_1 = false ) then
      @@&parameter_infile_1
   end if
   if ( &BLANK%parameter_infile_2 = false ) then
      @@&parameter_infile_2
   end if
   if ( &BLANK%parameter_infile_3 = false ) then
      @@&parameter_infile_3
   end if
   if ( &BLANK%parameter_infile_4 = false ) then
      @@&parameter_infile_4
   end if
   if ( &BLANK%parameter_infile_5 = false ) then
      @@&parameter_infile_5
   end if
 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

   if ( &BLANK%reflection_infile_1 = false ) then
     reflection @@&reflection_infile_1 end
   end if
   if ( &BLANK%reflection_infile_2 = false ) then
     reflection @@&reflection_infile_2 end
   end if
   if ( &BLANK%reflection_infile_3 = false ) then
     reflection @@&reflection_infile_3 end
   end if

 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)
     show min (amplitude(&STRIP%obs_i)) (all)
     evaluate ($obs_lower_limit=$result-0.1)
   else
     evaluate ($reject_obs=&obs_f)
     evaluate ($reject_sig=&obs_sigf)
     evaluate ($obs_lower_limit=0)
   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) ( ( amplitude($STRIP%reject_obs) > $obs_lower_limit ) 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

 end                  

 igroup interaction (&atom_select) (&atom_select) end

 flags exclude * include xref end

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

 if ( &reset_b > 0 ) then
    do (b=&reset_b) (&atom_select)
 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 -}

 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

 @@CNS_XTALMODULE:one_term_wa (wa=$wa;)

 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 ($ngroup=1)
 evaluate ($group=1)
 evaluate ($done=false)
 while ( $done = false ) loop group
   if ( &exist_bg_group_$group = true ) then
     show sum(1) ( &bg_group_$group )
     evaluate ($size_$group=$result)
     evaluate ($ngroup=$ngroup+1)
   else
     evaluate ($done=true)
     evaluate ($ngroup=$ngroup-1)
   end if
   evaluate ($group=$group+1)
 end loop group

 xray
   optimize group

     bmin=&bmin
     bmax=&bmax

     evaluate ($counter=1)

     while ( $counter <= $ngroup ) loop group

       if ( $size_$counter > 0 ) then

         for $id in id (tag) loop resid

           b=(((&bg_group_$counter) and byres id $id) and not(&atom_fixed))

         end loop resid

       end if

       evaluate ($counter=$counter+1)

     end loop group

     nstep=&bfactor_nstep
     drop=1.0
     ?
   end
 end

 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

 set display=&coordinate_outfile end

 display REMARK coordinates from twinned data group B-factor 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= $full_r[f6.4]
 end if
 xray wa=? end
 evaluate ($wa_print=$result)
 display REMARK wa= $wa_print
 display REMARK target= &STRIP%reftarget  steps= &bfactor_nstep
 display REMARK sg= &STRIP%sg a= &a b= &b c= &c alpha= &alpha beta= &beta gamma= &gamma

 if ( &BLANK%parameter_infile_1 = false ) then
    display REMARK parameter file 1  : &STRIP%parameter_infile_1
 end if
 if ( &BLANK%parameter_infile_2 = false ) then
    display REMARK parameter file 2  : &STRIP%parameter_infile_2
 end if
 if ( &BLANK%parameter_infile_3 = false ) then
    display REMARK parameter file 3  : &STRIP%parameter_infile_3
 end if
 if ( &BLANK%parameter_infile_4 = false ) then
    display REMARK parameter file 4  : &STRIP%parameter_infile_4
 end if
 if ( &BLANK%parameter_infile_5 = false ) then
    display REMARK parameter file 5  : &STRIP%parameter_infile_5
 end if
 display REMARK molecular structure file: &STRIP%structure_infile
 display REMARK input coordinates: &STRIP%coordinate_infile
 if ( &BLANK%anom_library = false ) then
   display REMARK anomalous f' f'' library: &STRIP%anom_library
 end if
 if ( &BLANK%reflection_infile_1 = false ) then
   display REMARK reflection file= &STRIP%reflection_infile_1
 end if
 if ( &BLANK%reflection_infile_2 = false ) then
   display REMARK reflection file= &STRIP%reflection_infile_2
 end if
 if ( &BLANK%reflection_infile_3 = false ) then
   display REMARK reflection file= &STRIP%reflection_infile_3
 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 or |F|=0): $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=&pdb_o_format;
                            coordinate_outfile=&coordinate_outfile;
                            sgparam=$sgparam;)
 
 stop