{+ file: deposit_mmcif.inp +}
{+ directory: xtal_mmcif +}
{+ description: Produces an mmCIF file for deposition +}
{+ comment: This input file populates the mmCIF categories describing
            the structure, reflection data and refinement. +}
{+ author: John Westbrook, Paul Adams and Ralf Grosse-Kunstleve +}
{+ copyright: Yale University +}

{- 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 xxx through xxx are available for general use -} 
 
{- begin block parameter definition -} define( 
 
{========================= name of structure =========================}

{* mmCIF entry identifier *}
{===>} entry_id="eg1";

{* A title for this structure *}
{===>} title="Endogluconase-1";

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

{* coordinate file *}
{===>} coordinate_infile="eg1_dimer.pdb";

{* optional final coordinate file refined without cross-validation *} 
{* leave blank if not available *} 
{===>} nocv_coordinate_infile="";

{==================== 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="eg1_dimer.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="P4(1)2(1)2";

{* unit cell parameters in Angstroms and degrees *}
{+ table: rows=1 "cell" cols=6 "a" "b" "c" "alpha" "beta" "gamma" +}
{===>} a=101.4;
{===>} b=101.4;
{===>} c=199.5;
{===>} 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, include test array for cross-validation *} 
{===>} reflection_infile_1="eg1_abcd.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 *}
{===>} 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 *} 
{* 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="";

{* reciprocal space array containing partial structure factors: optional *} 
{* this will default to a constant value of 0 if array is not present *} 
{===>} mod_fpart="";
 
{* cross-validation method *} 
{+ choice: "none" "throughout" "a posteriori" +} 
{===>} cv_method="throughout";
 
{* test set selection *} 
{+ choice: "random" "shells" "spheres" "everynth" "other" +} 
{===>} cv_select="random";
 
{* resolution limits *} 
{* 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=4.0;
 
{* Fobs/sigma amplitude cutoff *} 
{* reflections with |Fobs|/sigma_Fobs < cutoff will be rejected. *} 
{===>} sigma_cut=0.0;
 
{* rms outlier cutoff *} 
{* reflections with |Fobs| > cutoff*rms(Fobs) will be rejected *} 
{===>} obs_rms=10000;
 
{* low resolution cutoff for coordinate error estimates *} 
{* this should be less than or equal to the low resolution limit *} 
{===>} low_res_cut=5;
 
{* low resolution cutoff for Wilson plot *} 
{* this should be less than or equal to low resolution limit *} 
{===>} low_res_wilson=3;
 
{* number of equal volume reciprocal space bins *} 
{===>} mbins=8;
 
{* memory allocation for FFT calculation *} 
{* this will be determined automatically if a negative value is given 
   otherwise $fft_memory words of space will be allocated *} 
{===>} fft_memory=-1;
 
{=================== 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;

{======================= atomic B-factor model =======================} 
 
{* isotropic atomic B-factor refinement model *} 
{+ choice: "overall" "group" "restrained" +} 
{===>} bfactor_model="overall";
 
{* select mainchain atoms - atoms outside this selection are considered 
   to be side chain *} 
{===>} atom_main=(name ca or name n or name c or name o or name ot+);
 
{* restrained B-sigmas (only used for restrained mode) *} 
 
{* mainchain bonds *} 
{===>} bsig_main=1.5;
{* mainchain angles *} 
{===>} asig_main=2.0;
 
{* sidechain bonds *} 
{===>} bsig_side=2.0;
{* sidechain angles *} 
{===>} asig_side=2.5;

{========================= refinement target =========================}

{* 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;

{========================== atom selection =========================}
 
{* select atoms that were included in the refinement *} 
{* this should include all conformations if multiple conformations are used *} 
{===>} atom_select=(known and not hydrogen);
 
{* select polymer atoms *} 
{===>} atom_poly=(segid AAAA or segid CCCC);
 
{* select nonpolymer atoms *} 
{===>} atom_nonpoly=(segid BBBB or segid DDDD);
 
{* select water atoms *} 
{===>} atom_water=(none);
 
{================== contents of asymmetric unit =====================} 
 
{* Define the contents of the asymmetric unit *} 
{* each independent item must be identified *}
{* note: selections must be non-overlapping 
         chain names will be converted to uppercase *} 
 
{* select atoms in chain 1 *} 
{===>} chain_sele_1=(segid AAAA);
{* chain name for these atoms *}
{===>} chain_name_1="MOL_A";

{* select atoms in chain 2 *} 
{===>} chain_sele_2=(segid CCCC);
{* chain name for these atoms *}
{===>} chain_name_2="MOL_B";

{* select atoms in chain 3 *} 
{===>} chain_sele_3=(segid BBBB and resid 401);
{* chain name for these atoms *}
{===>} chain_name_3="NAG_A";

{* select atoms in chain 4 *} 
{===>} chain_sele_4=(segid BBBB and resid 402);
{* chain name for these atoms *}
{===>} chain_name_4="NAG_B";

{* select atoms in chain 5 *} 
{===>} chain_sele_5=(segid DDDD and resid 401);
{* chain name for these atoms *}
{===>} chain_name_5="NAG_C";

{* select atoms in chain 6 *} 
{===>} chain_sele_6=(segid DDDD and resid 402);
{* chain name for these atoms *}
{===>} chain_name_6="NAG_D";

{========================= molecular entities =======================}
 
{* define the molecular type of polymer chains in the asymmetric unit *}

{* name of molecular entity *}
{===>} entity_name_1="EG-1";
{* list chains which are of this entity type *} 
{===>} entity_chains_1="MOL_A MOL_B";
 
{* name of molecular entity *}
{===>} entity_name_2="n-acetyl-glucosamine";
{* list chains which are of this entity type *} 
{===>} entity_chains_2="NAG_A NAG_B NAG_C NAG_D";
 
{* name of molecular entity *}
{===>} entity_name_3="";
{* list chains which are of this entity type *} 
{===>} entity_chains_3="";
 
{* name of molecular entity *}
{===>} entity_name_4="";
{* list chains which are of this entity type *} 
{===>} entity_chains_4="";
 
{* name of molecular entity *}
{===>} entity_name_5="";
{* list chains which are of this entity type *} 
{===>} entity_chains_5="";
 
{* name of molecular entity *}
{===>} entity_name_6="";
{* list chains which are of this entity type *} 
{===>} entity_chains_6="";
 
{====================== alternate conformations ====================} 
 
{* 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);
 
{=========================== output file =============================} 
 
{* output file for PDB submission *} 
{===>} deposit_outfile="deposit.mmcif";

{============== output file for experimental data ====================} 
 
{* output file for PDB submission (experimental data) *} 
{===>} deposit_outfile_sf="deposit_sf.mmcif";

{* deposit original uncorrected amplitude data *}
{* if false, the data deposited may have corrections applied for 
   anisotropy - if selected above *}
{+ choice: true false +}
{===>} use_orig_ref=true;

{============== output file for mtf data ====================} 
 
{* output file for mtf data *} 
{===>} deposit_outfile_mtf="deposit_mtf.mmcif";
 
{========================================================================} 
{         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
 
evaluate ($cv_method=&cv_method) 
if ( &cv_method = "none" ) then 
  evaluate ($cv_method="NONE") 
elseif ( &cv_method = "throughout" ) then 
  evaluate ($cv_method="THROUGHOUT") 
elseif ( &cv_method = "a posteriori" ) then 
  evaluate ($cv_method="A POSTERIORI") 
end if 
 
evaluate ($cv_select=&cv_select) 
if ( &cv_select = "random" ) then 
  evaluate ($cv_select="RANDOM") 
elseif ( &cv_select = "shells" ) then 
  evaluate ($cv_select="SHELLS") 
elseif ( &cv_select = "spheres" ) then 
  evaluate ($cv_select="SPHERES") 
elseif ( &cv_select = "everynth" ) then 
  evaluate ($cv_select="EVERYnTH") 
elseif ( &cv_select = "other" ) then 
  evaluate ($cv_select="OTHER") 
end if 
 
evaluate ($bfctor_model=&bfactor_model) 
if ( &bfactor_model = "overall" ) then 
  evaluate ($bfactor_model="OVERALL") 
elseif ( &bfactor_model = "group" ) then 
  evaluate ( $bfactor_model="GROUP") 
elseif ( &bfactor_model = "restrained" ) then 
  evaluate ($bfactor_model="RESTRAINED") 
end if 
 
{- read the NCS relations file if any -}

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

 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

 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
   query name=fbulk domain=reciprocal end
   if ( $object_exist = false ) then
      declare name=fbulk domain=reciprocal type=complex end
      do (fbulk=0) ( all )
      if ( &BLANK%mod_fpart = false ) then
        if ( &STRIP%mod_fpart # fbulk ) then
          do (fbulk=&STRIP%mod_fpart) ( all )
        end if
      end if
   end if

   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)

   bins=&mbins

   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
                    ( &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 2/15/06 -}
 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

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

 {- BEGIN MODIFICATION -}
 @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;
                             
!
! Begin modification (6/28/06)                             
                             Baniso_11=$aniso_11;
                             Baniso_22=$aniso_22;
                             Baniso_33=$aniso_33;
                             Baniso_12=$aniso_12;
                             Baniso_13=$aniso_13;
                             Baniso_23=$aniso_23;
                             Biso=$Biso_model;
! End modification
! 
                             
                             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=$start_r;
                                 test_r=$start_test_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=$b_min;
                             grid=auto;
                             fft_memory=&fft_memory;
                             fft_grid=$fft_grid;   
                             fft_b_add=$fft_b_add; 
                             fft_elim=$fft_elim; 
                                      )
{- END MODIFICATION -}

 evaluate ($aniso.11=$aniso_11)
 evaluate ($aniso.22=$aniso_22)
 evaluate ($aniso.33=$aniso_33)
 evaluate ($aniso.12=$aniso_12)
 evaluate ($aniso.13=$aniso_13)
 evaluate ($aniso.23=$aniso_23)

 { Assemble alternate conformations in  *store7* } 

 do (store7=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 <= $nalt ) loop alt 
    do (store7=$alt) ( &conf_$alt ) 
   evaluate ($alt=$alt+1) 
 end loop alt 
 
 
 { Assemble components of the asymmetric unit in  *store8* } 

  do (store8=0) (all) 
  
  evaluate ($nasym=1) 
  evaluate ($asym=1) 
  evaluate ($done=false) 
  while ( $done = false ) loop nasym 
    if ( &exist_chain_sele_$asym = true ) then 
      show sum(1) ( &chain_sele_$asym ) 
      if ( $result > 0 ) then 
        evaluate ($chainnum.$nasym=$asym)
        evaluate ($chainnum.&STRIP%chain_name_$nasym=$asym)
        evaluate ($nasym=$nasym+1) 
      end if 
   else 
     evaluate ($done=true) 
     evaluate ($nasym=$nasym-1) 
   end if 
   evaluate ($asym=$asym+1) 
  end loop nasym 
 
 evaluate ($asym=1) 
 while ( $asym <= $nasym ) loop asym 
   evaluate ($asympt=$chainnum.$asym)
   do (store8=$asympt) ( &chain_sele_$asympt ) 
   evaluate ($asym=$asym+1) 
 end loop asym 

 { Assemble entities identifiers in  *store9* } 
 do (store9=0) (all) 
 evaluate ($nentity=1) 
 evaluate ($entity=1) 
 evaluate ($done=false) 
 while ( $done = false ) loop nentity 
   if ( &exist_entity_name_$entity = true ) then 
     evaluate ($nentity=$nentity+1) 
   else 
     evaluate ($done=true) 
     evaluate ($nentity=$nentity-1) 
   end if 
   evaluate ($entity=$entity+1) 
 end loop nentity 

 evaluate ($entity=1) 
 while ( $entity <= $nentity ) loop entity 
   for $ent in ( &STRIP%entity_chains_$entity ) loop chain
     if ( $EXIST%chainnum.$ent = true ) then
       do (store9=$entity) ( attr store8 = $chainnum.$ent )
     end if
   end loop chain
   evaluate ($entity=$entity+1) 
 end loop entity 
 
 
 @CNS_XTALMODULE:exportmmcifstruct ( 

 entry_id=&entry_id; 
 title=&title; 
 a=&a; 
 b=&b; 
 c=&c; 
 alpha=&alpha; 
 beta=&beta; 
 gamma=&gamma; 
 sgparam=$sgparam;

 all_select=( &atom_select );          { select all atoms used} 
 polymer_select=( &atom_poly );        { select all polymer atoms} 
 nonpolymer_select=( &atom_nonpoly );  { select all nonpolymer atoms
                                         less solvent} 
 water_select=( &atom_water );         { select all water atoms} 
 
 sel_alt_conf=store7; 
 
 num_asym=$nasym; 
 asym_id=store8; 
 
 num_entity=$nentity; 
 entity_id=store9;  
 
 list=&deposit_outfile; 
) 

@CNS_XTALMODULE:exportmmcifrefine ( 
 
 entry_id=&entry_id; 

 { unit cell dimensions } 
 a=&a; 
 b=&b; 
 c=&c; 
 alpha=&alpha; 
 beta=&beta; 
 gamma=&gamma; 
 
 { space group name } 
 sg=&sg; 
 sgparam = $sgparam; 
 
 { parameter files } 
 par_1=&parameter_infile_1; 
 par_2=&parameter_infile_2; 
 par_3=&parameter_infile_3; 
 par_4=&parameter_infile_4; 
 par_5=&parameter_infile_5; 
 par_6=&parameter_infile_6; 
 par_7=&parameter_infile_7; 
 par_8=&parameter_infile_8; 
 
 { topology files } 
 top_1=&topology_infile_1; 
 top_2=&topology_infile_2; 
 top_3=&topology_infile_3; 
 top_4=&topology_infile_4; 
 top_5=&topology_infile_5; 
 top_6=&topology_infile_6; 
 top_7=&topology_infile_7; 
 top_8=&topology_infile_8; 

 { molecular structure file } 
 structure_file=&structure_infile; 
 
 { coordinate file after the final refinement using cross-validation } 
 coordinate_file=&coordinate_infile; 
 
 { coordinate file after the final refinement without cross-validation } 
 coordinate_file_wo_cv=&nocv_coordinate_infile; 
 
 { NCS information. } 
 strict_ncs_file=&ncs_infile; 
 
 { reciprocal space arrays in reflection file } 
 fobs=&STRIP%obs_f; 
 fcalc=fcalc;
 fpart=fbulk;
 sigma=&STRIP%obs_sigf; 
 test=&STRIP%test_set; 
 test_flag=&test_flag; 
 weight=&STRIP%obs_w; 

 { original structure factors and sigmas - prior to any scaling }

 use_orig_ref=&use_orig_ref;
 fobs_orig=fobs_orig;
 sigma_orig=sigma_orig;

 { reflection and test set selection arrays }

 ref_active=ref_active;
 ref_test=tst_active;
 
 { cross-validation method } 
 cv_method=&cv_method; 
 
 { test set selection } 
 cv_select=&cv_select; 
 
 { resolution range was used in the refinement } 
 high_res=&high_res; 
 low_res=&low_res; 
 
 { low resolution cutoff for coord. err. estimates } 
 low_res_cut=&low_res_cut; 
 
 { low resolution cutoff for Wilson plot } 
 low_res_wilson=&low_res_wilson; 
 
 { number of equal volume reciprocal space bins } 
 mbins=&mbins; 
 
 { memory for FFT calc. } 
 fft_memory=&fft_memory; 
 
 { sigma cutoff } 
 sigcutf=&sigma_cut; 
 
 { outlier cutoff } 
 f_rms=&obs_rms; 

 focut_low=$obs_low;
 focut_high=$obs_high;
 
 { overall anisotropic B-scaling } 
 bscale=&bscale; 
 
 { bulk solvent correction } 
 bulk_sol=&bulk_sol; 
 bulk_mask=&bulk_mask; 
 ksol=$sol_k_ref; 
 bsol=$sol_b_ref; 
 solrad=$solrad_best; {- MODIFIED -}
 shrink=$shrink_best; {- MODIFIED -}
 
 { isotropic B factor refinement model } 
 bfactor=$bfactor_model; 
 aniso=$aniso;
 
 { selection for mainchain atoms } 
 b_main_sel=(&atom_main); 
 
 { restrained B-sigmas } 
 bsig_main=&bsig_main; 
 asig_main=&asig_main; 
 bsig_side=&bsig_side; 
 asig_side=&asig_side; 
 
 { atom selections } 
 all_select=(&atom_select); 
 polymer_select=(&atom_poly); 
 water_select=(&atom_water); 
 nonpolymer_select=(&atom_nonpoly); 

 sel_alt_conf=store7; 

 
 { output file name } 
 list=&deposit_outfile; 
 list_sf=&deposit_outfile_sf; 

) 



evaluate ($display=&deposit_outfile_mtf) 
set display=$display end   

{- output MTF information -}

set remarks=reset end

display
write structure output=&deposit_outfile_mtf end

{- output parameter information -}

display data_cns_parameter

display _cns_parameter.details
display ;

write parameter format=mmcif output=&deposit_outfile_mtf end

display ;

stop