! Module file: siterefine
!
! CNS module
! **********
!
! Author: Axel T. Brunger
!
! copyright Yale University
!
! Function: 
!   Refines (heavy) atom sites for mir/sir/miras/siras/mad
!   Determines phase probability distribution for "native"

{ We assume that heavy atoms are stored in residues.  Each residue
  will be treated as a rigid body.  Residues can belong to the same
  lack-of-closure expression class or can belong to different classes.  Atom types
  must match standard form factor library specifications.  

 It is important to put the data on an quasi-absolute scale
 before refining the heavy atom parameters.  Otherwise the occupancies
 may be ill-behaved.  Also the data has to be relatively scaled to each
 other.

  Prior to running this module the following items must be defined

  1. Molecular structure file with heavy atoms.
  2. Initial heavy atom coordinates
  3. form factor library (normal and anomalous if required)
  4. diffraction data (native and derivatives)
  
 }

module {siterefine}
(

{LIST}  { Specify which lack-of-closure expressions should be included in phasing or refinement.   }
{====}  { This also specifies the order with which phasing and refinement proceeds.}
&list= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19;   
       { default: all lack-of-closure expressions with specified fph_<i> }

&scatter="" ; { scattering library, if empty 
                                    existing library will be used. }

{NATIVE DATA}
{===========}
&fp;     {native amplitudes stored in complex array -
          on output returns the centroid phases - required}
&sp;     {native sigma - required}

{PRIOR PHASE PROBABILITY DISTRIBUTION INDEPENDENT OF lack-of-closure expressions}
{===============================================================================}
&priora;  {prior probability Hendrickson and Lattman A array}
&priorb;  {prior probability Hendrickson and Lattman B array}
&priorc;  {prior probability Hendrickson and Lattman C array}
&priord;  {prior probability Hendrickson and Lattman D array}

{OUTPUT PHASE PROBABILITY DISTRIBUTION AND FOM}
{=============================================}
&pa;   {output probability Hendrickson and Lattman A array}  
&pb;   {output probability Hendrickson and Lattman B array}
&pc;   {output probability Hendrickson and Lattman C array}
&pd;   {output probability Hendrickson and Lattman D array}
&fom; {FOM array}


{SUMMARY FILE NAME}
{=================}
&summary;

{ FOR MORE lack-of-closure expressions simply add more entries. }
{ ------------------------------------------------------------  }
{PARAMETERS FOR lack-of-closure expression 0}
{===========================================}
&on_off_0="on"; {on/off flag for this lack-of-closure expression}
&fph_0=NULL;         {name of 0th lack-of-closure expression data array}
&sph_0=NULL;    {name of 0th lack-of-closure expression's sigma array}
&target_set_0=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_0=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_0=(none) ; {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_0=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_0=20;   {number of coordinate minimization steps}
&qstep_0=20;   {number of occupancy factor minimization steps}
&bstep_0=20;   {number of B-factor minimization steps}
&bindgroup_0=false; {refine individual B-values for each atom in a group}
&fpstep_0=0;   {number of fp minimization steps}
&fdpstep_0=0;  {number of fdp minimization steps}
&kstep_0=20;     {number of scaling minimization steps}                
&kscale_0="yes";       {"yes" | "no" k-scaling}
&bscale_0="no";        {"no" | "isotropic" | "anisotropic"  B }
&xstep_ano_0=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_0=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_0=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_0=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_0=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_0=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_0="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_0="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_0="";

{PARAMETERS FOR lack-of-closure expression 1}
{===========================================}
&on_off_1="on"; {on/off flag for this lack-of-closure expression}
&fph_1=NULL;         {name of 1st lack-of-closure expression data array}
&sph_1=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_1=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_1=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_1=(none) ; {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_1=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_1=20;   {number of coordinate minimization steps}
&qstep_1=20;   {number of occupancy factor minimization steps}
&bstep_1=20;   {number of B-factor minimization steps}
&bindgroup_1=false; {refine individual B-values for each atom in a group}
&fpstep_1=0;   {number of fp minimization steps}
&fdpstep_1=0;  {number of fdp minimization steps}                
&kstep_1=20;     {number of scaling minimization steps}        
&kscale_1="yes";       {"yes" | "no" k-scaling}
&bscale_1="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_1=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_1=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_1=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_1=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_1=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_1=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_1="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_1="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_1="";

{PARAMETERS FOR lack-of-closure expression _2}
{============================================}
&on_off_2="on"; {on/off flag for this lack-of-closure expression}
&fph_2=NULL;         {name of 1st lack-of-closure expression data array}
&sph_2=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_2=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_2=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_2=(none) ; {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_2=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_2=20;   {number of coordinate minimization steps}
&qstep_2=20;   {number of occupancy factor minimization steps}
&bstep_2=20;   {number of B-factor minimization steps}                
&bindgroup_2=false; {refine individual B-values for each atom in a group}
&fpstep_2=0;   {number of fp minimization steps}
&fdpstep_2=0;  {number of fdp minimization steps}                
&kstep_2=20;     {number of scaling minimization steps}        
&kscale_2="yes";       {"yes" | "no" k-scaling}
&bscale_2="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_2=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_2=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_2=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_2=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_2=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_2=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_2="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_2="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_2="";

{PARAMETERS FOR lack-of-closure expression _3}
{============================================}
&on_off_3="on"; {on/off flag for this lack-of-closure expression}
&fph_3=NULL;         {name of 1st lack-of-closure expression data array}
&sph_3=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_3=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_3=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_3=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_3=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_3=20;   {number of coordinate minimization steps}
&qstep_3=20;   {number of occupancy factor minimization steps}
&bstep_3=20;   {number of B-factor minimization steps}                
&bindgroup_3=false; {refine individual B-values for each atom in a group}
&fpstep_3=0;   {number of fp minimization steps}
&fdpstep_3=0;  {number of fdp minimization steps}                
&kstep_3=20;     {number of scaling minimization steps}        
&kscale_3="yes";       {"yes" | "no" k-scaling}
&bscale_3="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_3=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_3=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_3=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_3=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_3=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_3=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_3="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_3="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_3="";

{PARAMETERS FOR lack-of-closure expression _4}
{============================================}
&on_off_4="on"; {on/off flag for this lack-of-closure expression}
&fph_4=NULL;         {name of 1st lack-of-closure expression data array}
&sph_4=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_4=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_4=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_4=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_4=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_4=20;   {number of coordinate minimization steps}
&qstep_4=20;   {number of occupancy factor minimization steps}
&bstep_4=20;   {number of B-factor minimization steps}                
&bindgroup_4=false; {refine individual B-values for each atom in a group}
&fpstep_4=0;   {number of fp minimization steps}
&fdpstep_4=0;  {number of fdp minimization steps}                
&kstep_4=20;     {number of scaling minimization steps}        
&kscale_4="yes";       {"yes" | "no" k-scaling}
&bscale_4="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_4=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_4=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_4=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_4=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_4=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_4=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_4="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_4="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_4="";

{PARAMETERS FOR lack-of-closure expression _5}
{============================================}
&on_off_5="on"; {on/off flag for this lack-of-closure expression}
&fph_5=NULL;         {name of 1st lack-of-closure expression data array}
&sph_5=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_5=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_5=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_5=(all); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_5=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_5=20;   {number of coordinate minimization steps}
&qstep_5=20;   {number of occupancy factor minimization steps}
&bstep_5=20;   {number of B-factor minimization steps}                
&bindgroup_5=false; {refine individual B-values for each atom in a group}
&fpstep_5=0;   {number of fp minimization steps}
&fdpstep_5=0;  {number of fdp minimization steps}                
&kstep_5=20;     {number of scaling minimization steps}        
&kscale_5="yes";       {"yes" | "no" k-scaling}
&bscale_5="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_5=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_5=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_5=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_5=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_5=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_5=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_5="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_5="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_5="";

{PARAMETERS FOR lack-of-closure expression _6}
{============================================}
&on_off_6="on"; {on/off flag for this lack-of-closure expression}
&fph_6=NULL;         {name of 1st lack-of-closure expression data array}
&sph_6=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_6=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_6=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_6=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_6=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_6=20;   {number of coordinate minimization steps}
&qstep_6=20;   {number of occupancy factor minimization steps}
&bstep_6=20;   {number of B-factor minimization steps}                
&bindgroup_6=false; {refine individual B-values for each atom in a group}
&fpstep_6=0;   {number of fp minimization steps}
&fdpstep_6=0;  {number of fdp minimization steps}                
&kstep_6=20;     {number of scaling minimization steps}        
&kscale_6="yes";       {"yes" | "no" k-scaling}
&bscale_6="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_6=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_6=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_6=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_6=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_6=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_6=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_6="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_6="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_6="";

{PARAMETERS FOR lack-of-closure expression _7}
{============================================}
&on_off_7="on"; {on/off flag for this lack-of-closure expression}
&fph_7=NULL;         {name of 1st lack-of-closure expression data array}
&sph_7=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_7=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_7=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_7=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_7=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_7=20;   {number of coordinate minimization steps}
&qstep_7=20;   {number of occupancy factor minimization steps}
&bstep_7=20;   {number of B-factor minimization steps}                
&bindgroup_7=false; {refine individual B-values for each atom in a group}
&fpstep_7=0;   {number of fp minimization steps}
&fdpstep_7=0;  {number of fdp minimization steps}                
&kstep_7=20;     {number of scaling minimization steps}        
&kscale_7="yes";       {"yes" | "no" k-scaling}
&bscale_7="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_7=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_7=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_7=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_7=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_7=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_7=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_7="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_7="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_7="";

{PARAMETERS FOR lack-of-closure expression _8}
{============================================}
&on_off_8="on"; {on/off flag for this lack-of-closure expression}
&fph_8=NULL;         {name of 1st lack-of-closure expression data array}
&sph_8=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_8=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_8=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_8=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_8=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_8=20;   {number of coordinate minimization steps}
&qstep_8=20;   {number of occupancy factor minimization steps}
&bstep_8=20;   {number of B-factor minimization steps}                
&bindgroup_8=false; {refine individual B-values for each atom in a group}
&fpstep_8=0;   {number of fp minimization steps}
&fdpstep_8=0;  {number of fdp minimization steps}                
&kstep_8=20;     {number of scaling minimization steps}        
&kscale_8="yes";       {"yes" | "no" k-scaling}
&bscale_8="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_8=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_8=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_8=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_8=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_8=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_8=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_8="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_8="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_8="";

{PARAMETERS FOR lack-of-closure expression _9}
{============================================}
&on_off_9="on"; {on/off flag for this lack-of-closure expression}
&fph_9=NULL;         {name of 1st lack-of-closure expression data array}
&sph_9=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_9=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_9=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_9=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_9=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_9=20;   {number of coordinate minimization steps}
&qstep_9=20;   {number of occupancy factor minimization steps}
&bstep_9=20;   {number of B-factor minimization steps}                
&bindgroup_9=false; {refine individual B-values for each atom in a group}
&fpstep_9=0;   {number of fp minimization steps}
&fdpstep_9=0;  {number of fdp minimization steps}                
&kstep_9=20;     {number of scaling minimization steps}        
&kscale_9="yes";       {"yes" | "no" k-scaling}
&bscale_9="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_9=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_9=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_9=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_9=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_9=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_9=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_9="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_9="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_9="";

{PARAMETERS FOR lack-of-closure expression 10}
{============================================}
&on_off_10="on"; {on/off flag for this lack-of-closure expression}
&fph_10=NULL;         {name of 0th lack-of-closure expression data array}
&sph_10=NULL;    {name of 0th lack-of-closure expression's sigma array}
&target_set_10=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_10=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_10=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_10=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_10=20;   {number of coordinate minimization steps}
&qstep_10=20;   {number of occupancy factor minimization steps}
&bstep_10=20;   {number of B-factor minimization steps}
&bindgroup_10=false; {refine individual B-values for each atom in a group}
&fpstep_10=0;   {number of fp minimization steps}
&fdpstep_10=0;  {number of fdp minimization steps}                
&kstep_10=20;     {number of scaling minimization steps}        
&kscale_10="yes";       {"yes" | "no" k-scaling}
&bscale_10="no";        {"no" | "isotropic" | "anisotropic"  B }
&xstep_ano_10=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_10=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_10=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_10=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_10=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_10=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_10="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_10="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_10="";

{PARAMETERS FOR lack-of-closure expression 11}
{============================================}
&on_off_11="on"; {on/off flag for this lack-of-closure expression}
&fph_11=NULL;         {name of 1st lack-of-closure expression data array}
&sph_11=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_11=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_11=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_11=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_11=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_11=20;   {number of coordinate minimization steps}
&qstep_11=20;   {number of occupancy factor minimization steps}
&bstep_11=20;   {number of B-factor minimization steps}
&bindgroup_11=false; {refine individual B-values for each atom in a group}
&fpstep_11=0;   {number of fp minimization steps}
&fdpstep_11=0;  {number of fdp minimization steps}                
&kstep_11=20;     {number of scaling minimization steps}        
&kscale_11="yes";       {"yes" | "no" k-scaling}
&bscale_11="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_11=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_11=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_11=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_11=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_11=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_11=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_11="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_11="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_11="";

{PARAMETERS FOR lack-of-closure expression 12}
{============================================}
&on_off_12="on"; {on/off flag for this lack-of-closure expression}
&fph_12=NULL;         {name of 1st lack-of-closure expression data array}
&sph_12=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_12=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_12=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_12=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_12=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_12=20;   {number of coordinate minimization steps}
&qstep_12=20;   {number of occupancy factor minimization steps}
&bstep_12=20;   {number of B-factor minimization steps}                
&bindgroup_12=false; {refine individual B-values for each atom in a group}
&fpstep_12=0;   {number of fp minimization steps}
&fdpstep_12=0;  {number of fdp minimization steps}                
&kstep_12=20;     {number of scaling minimization steps}        
&kscale_12="yes";       {"yes" | "no" k-scaling}
&bscale_12="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_12=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_12=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_12=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_12=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_12=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_12=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_12="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_12="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_12="";

{PARAMETERS FOR lack-of-closure expression 13}
{============================================}
&on_off_13="on"; {on/off flag for this lack-of-closure expression}
&fph_13=NULL;         {name of 1st lack-of-closure expression data array}
&sph_13=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_13=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_13=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_13=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_13=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_13=20;   {number of coordinate minimization steps}
&qstep_13=20;   {number of occupancy factor minimization steps}
&bstep_13=20;   {number of B-factor minimization steps}                
&bindgroup_13=false; {refine individual B-values for each atom in a group}
&fpstep_13=0;   {number of fp minimization steps}
&fdpstep_13=0;  {number of fdp minimization steps}                
&kstep_13=20;     {number of scaling minimization steps}        
&kscale_13="yes";       {"yes" | "no" k-scaling}
&bscale_13="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_13=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_13=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_13=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_13=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_13=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_13=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_13="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_13="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_13="";

{PARAMETERS FOR lack-of-closure expression 14}
{============================================}
&on_off_14="on"; {on/off flag for this lack-of-closure expression}
&fph_14=NULL;         {name of 1st lack-of-closure expression data array}
&sph_14=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_14=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_14=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_14=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_14=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_14=20;   {number of coordinate minimization steps}
&qstep_14=20;   {number of occupancy factor minimization steps}
&bstep_14=20;   {number of B-factor minimization steps}                
&bindgroup_14=false; {refine individual B-values for each atom in a group}
&fpstep_14=0;   {number of fp minimization steps}
&fdpstep_14=0;  {number of fdp minimization steps}                
&kstep_14=20;     {number of scaling minimization steps}        
&kscale_14="yes";       {"yes" | "no" k-scaling}
&bscale_14="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_14=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_14=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_14=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_14=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_14=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_14=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_14="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_14="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_14="";

{PARAMETERS FOR lack-of-closure expression 15}
{============================================}
&on_off_15="on"; {on/off flag for this lack-of-closure expression}
&fph_15=NULL;         {name of 1st lack-of-closure expression data array}
&sph_15=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_15=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_15=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_15=(all); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_15=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_15=20;   {number of coordinate minimization steps}
&qstep_15=20;   {number of occupancy factor minimization steps}
&bstep_15=20;   {number of B-factor minimization steps}                
&bindgroup_15=false; {refine individual B-values for each atom in a group}
&fpstep_15=0;   {number of fp minimization steps}
&fdpstep_15=0;  {number of fdp minimization steps}                
&kstep_15=20;     {number of scaling minimization steps}        
&kscale_15="yes";       {"yes" | "no" k-scaling}
&bscale_15="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_15=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_15=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_15=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_15=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_15=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_15=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_15="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_15="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_15="";

{PARAMETERS FOR lack-of-closure expression 16}
{============================================}
&on_off_16="on"; {on/off flag for this lack-of-closure expression}
&fph_16=NULL;         {name of 1st lack-of-closure expression data array}
&sph_16=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_16=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_16=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_16=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_16=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_16=20;   {number of coordinate minimization steps}
&qstep_16=20;   {number of occupancy factor minimization steps}
&bstep_16=20;   {number of B-factor minimization steps}                
&bindgroup_16=false; {refine individual B-values for each atom in a group}
&fpstep_16=0;   {number of fp minimization steps}
&fdpstep_16=0;  {number of fdp minimization steps}                
&kstep_16=20;     {number of scaling minimization steps}        
&kscale_16="yes";       {"yes" | "no" k-scaling}
&bscale_16="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_16=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_16=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_16=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_16=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_16=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_16=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_16="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_16="no";        {"no" | "isotropic" | "anisotropic"  B }
&grad_map_16="";

{PARAMETERS FOR lack-of-closure expression 17}
{============================================}
&on_off_17="on"; {on/off flag for this lack-of-closure expression}
&fph_17=NULL;         {name of 1st lack-of-closure expression data array}
&sph_17=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_17=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_17=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_17=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_17=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_17=20;   {number of coordinate minimization steps}
&qstep_17=20;   {number of occupancy factor minimization steps}
&bstep_17=20;   {number of B-factor minimization steps}                
&bindgroup_17=false; {refine individual B-values for each atom in a group}
&fpstep_17=0;   {number of fp minimization steps}
&fdpstep_17=0;  {number of fdp minimization steps}                
&kstep_17=20;     {number of scaling minimization steps}        
&kscale_17="yes";       {"yes" | "no" k-scaling}
&bscale_17="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_17=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_17=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_17=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_17=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_17=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_17=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_17="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_17="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_17="";

{PARAMETERS FOR lack-of-closure expression 18}
{============================================}
&on_off_18="on"; {on/off flag for this lack-of-closure expression}
&fph_18=NULL;         {name of 1st lack-of-closure expression data array}
&sph_18=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_18=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_18=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_18=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_18=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_18=20;   {number of coordinate minimization steps}
&qstep_18=20;   {number of occupancy factor minimization steps}
&bstep_18=20;   {number of B-factor minimization steps}                
&bindgroup_18=false; {refine individual B-values for each atom in a group}
&fpstep_18=0;   {number of fp minimization steps}
&fdpstep_18=0;  {number of fdp minimization steps}                
&kstep_18=20;     {number of scaling minimization steps}        
&kscale_18="yes";       {"yes" | "no" k-scaling}
&bscale_18="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_18=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_18=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_18=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_18=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_18=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_18=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_18="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_18="no";        {"no" | "isotropic" | "anisotropic"  B } 
&grad_map_18="";

{PARAMETERS FOR lack-of-closure expression 19}
{============================================}
&on_off_19="on"; {on/off flag for this lack-of-closure expression}
&fph_19=NULL;         {name of 1st lack-of-closure expression data array}
&sph_19=NULL;    {name of 1st lack-of-closure expression's sigma array}
&target_set_19=(all);  {selection for Fiso phasing calculation;  set to (not all) if undesired }
&target_set_a_19=(all);  {selection for Fano phasing calculation ; set to (not all) if undesired }
&h_19=(none); {atom selection for all atoms belonging to 1st lack-of-closure expression }
&hfix_19=(none); {heavy atoms whose parameters are kept fixed.}
&xstep_19=20;   {number of coordinate minimization steps}
&qstep_19=20;   {number of occupancy factor minimization steps}
&bstep_19=20;   {number of B-factor minimization steps}                
&bindgroup_19=false; {refine individual B-values for each atom in a group}
&fpstep_19=0;   {number of fp minimization steps}
&fdpstep_19=0;  {number of fdp minimization steps}                
&kstep_19=20;     {number of scaling minimization steps}        
&kscale_19="yes";       {"yes" | "no" k-scaling}
&bscale_19="no";        {"no" | "isotropic" | "anisotropic"  B } 
&xstep_ano_19=20;   {number of coordinate minimization steps for Fano calc.}
&qstep_ano_19=0;   {number of occupancy factor minimization steps for Fano calc.}
&bstep_ano_19=0;   {number of B-factor minimization steps for Fano calc.}                
&fpstep_ano_19=0;   {number of fp minimization steps for Fano calc.}
&fdpstep_ano_19=0;  {number of fdp minimization steps for Fano calc.}                
&kstep_ano_19=20;     {number of scaling minimization steps for Fano calc.}                
&kscale_ano_19="yes";       {"yes" | "no" k-scaling  for Fano calc.}
&bscale_ano_19="no";        {"no" | "isotropic" | "anisotropic"  B } 
&cen360="no"; {"yes" | "no" ; use full 360 range for centric phase prob. distr. for anomalous data}
&grad_map_19="";


{GLOBAL PARAMETERS}
{=================}
&anomalous_mode="fano"; { "fano" | "deltaf", anomalous options.  fano mode means
                          that we compute the averages of F+ and F- for the FISO term.
                          deltaf means that we keep the Bijvoet pairs always separate and
                          only compute F lack-of-closures.  
                          The latter option is useful when strong anomalous signals 
                          are present.  It can also be used when the native data 
                          has an anomalous signal. }
&ref_wavelength=1; { reference wavelength for deltaf anomalous option }
&ref_fp=0; {f' at reference}
&test_array;   { global test array cross-validation }
&test_flag=1;
&phase_set=(all);     { global phasing set }
&text="this is a test";
&messages="normal"; {set verbosity "normal" | "all" | "off"}
&method="chisquare";        {"maxlike" or "chisquare" }
&integration="analytic";  {integration for probabilities: numerical | analytic }
&sum_method="direct"; {summation method for structure factor calculation: direct | fft }
&fft_grid=0.2;        {fft grid spacing for fft summation method (normally 0.2) }
&fft_memory=-1;       { memory allocation for FFT calculation; negative value -> automatic }
&macrocycle=10;       {number of macro-cycles for everything.  Must be greater than 1. }
&tolerance=0.001;     {lack-of-closure tolerance (relative) for initial phase prob. iterations}  
                      {also specifies tolerance for conjugate gradient minimizations} 
&iteration=4;        {max. number of initial phase prob. iterations}
&cutoff=4;            {sigma cutoff level for discarding outliers }

&epsilon="no";        {"yes" | "no", use epsilon weighting in summing variances}
&resetzero=0.001;     {reset zero variances to &resetzero, to avoid division
                        by zero}
&zerovar=0.001;      {smallest significant value. For example, the smallest
                        digit defined by the diffraction data.}
&phistep=5;          {integration step size}
&workbin=8;          {select number of bins used in calculations}
&bmin=1;             {minimum B-factor (Ang^2); truncation only applied 
                      to B-factors that are being refined}
&bmax=300;            {maximum B-factor (Ang^2); truncation only applied 
                      to B-factors that are being refined}
&qmin=0.01;          {minimum occupancy factor; truncation only applied 
                      to occupancy factors that are being refined}
&qmax=10.;           {maximum occupancy factor; truncation only applied 
                      to occupancy factors that are being refined}
&fpmin=-300;
&fpmax=+300;         {minimum and maximum fprime; truncation only applied
                        to fprime factors that are being refined}
&fdpmin=-300;
&fdpmax=+300;        {minimum and maximum fdprime; truncation only applied
                        to fprime factors that are being refined}
&qmaxshift=1.;        {maximum q-shift}
&fpmaxshift=20.;      {maximum fp-shift}
&fdpmaxshift=20.;     {maximum fdp-shift}
&bmaxshift=100.;      {maximum b-shift}
)

checkversion 1.3

{--------------------------------------------------------------------------------}
{---------------------procedure-definitions--------------------------------------}
{--------------------------------------------------------------------------------}

procedure getprobs(exclude; exclude_ano; prior)

   {- combines probabilibies except as specified -}

   {- prior probability -}
   if (&prior=true) then
      do (ppa=&priora) ( all )
      do (ppb=&priorb) ( all )
      do (ppc=&priorc) ( all )
      do (ppd=&priord) ( all )
   else
      do (ppa=0) ( all )
      do (ppb=0) ( all )
      do (ppc=0) ( all )
      do (ppd=0) ( all )
   end if

   {- loc probabilities -}   
   for $index in ( &list ) loop comb
    if ($active.$index=true) then
      if ($index # &exclude ) then
	 @CNS_XTALMODULE:combineprobability (
	    messages=&messages;
	    sel=(all);
	    &name="zero";
	    &addname="prior";
	    pa=ppa;
	    pb=ppb;
	    pc=ppc;
	    pd=ppd;
	    adda=$strip%pa.$index;
	    addb=$strip%pb.$index;
	    addc=$strip%pc.$index;
	    addd=$strip%pd.$index;)
       end if
     end if
   end loop comb
  
   {- fano probabilities -} 
   for $index in ( &list ) loop com2
    if ($active_ano.$index=true) then
     if ($index # &exclude_ano) then
      @CNS_XTALMODULE:combineprobability (
	 messages=&messages;
	 sel=(all);
	 &name="zero";
	 &addname="prior";
	 pa=ppa;
	 pb=ppb;
	 pc=ppc;
	 pd=ppd;
	 adda=$strip%pa_ano.$index;
	 addb=$strip%pb_ano.$index;
	 addc=$strip%pc_ano.$index;
	 addd=$strip%pd_ano.$index;)
     end if
    end if
   end loop com2
endprocedure

{----------------------------------------------------------------------}
{-----------------------begin-module-----------------------------------}
{----------------------------------------------------------------------}

xray
   if (&scatter # "") then
      { Read scattering library. }
      { ------------------------ }
   
      set message ? end eval ($master_mess=$result)
      set echo ? end    eval ($master_echo=$result)
      scatter reset  
      @@&scatter 
      set message=$master_mess end
      set echo=$master_echo end
   end if

   show min (d) (&phase_set)
   eval ($minq_min=$result-0.01)
   show max (d) (&phase_set)
   eval ($minq_max=$result+0.01)
   binresolution $minq_min $minq_max

end

{- Copy current coordinates to comparison set -}
do (xcomp=x) ( all )
do (ycomp=y) ( all )
do (zcomp=z) ( all )
do (bcomp=b) ( all )
do (qcomp=q) ( all )
do (fbeta=scatter_fp) ( all )
do (harm=scatter_fdp) ( all )

{- Set the energy flag for positional refinement -- only X-ray term used -}
flags exclude * include xref end

xray

   bins=&workbin
   
   { select direct summation method or FFT method}
   if (&sum_method="direct") then
      method=direct  
   else
      method=fft
      mapresolution $minq_min
      fft 
        grid=&fft_grid 
        if ( &fft_memory < 0 ) then
          automemory=true
        else
          memory=&fft_memory
        end if
     end                 
   end if
   
   lookup=false 
   tolerance=0.0

   
   {- Do we have anomalous (F+,F-) data? -}
   anomalous  ?
   evaluate ($master_anomalous=$result)

   { If "deltaf" mode is used and anomalous data is present we set the flag      }
   { to use a full 0...360 degree phase probability distribution for all centric }
   { structure factors.  Otherwise, the distribution is reduced to two or one    }
   { possible phases which has implications for statistical treatments in        }
   { various places.                                                             }
   evaluate ($master_cen360=FALSE)
   if (&cen360="yes") then
      if (&anomalous_mode # "fano") then
         if ($master_anomalous=TRUE) then
               evaluate ($master_cen360=TRUE) 
         end if
      end if
   end if
   if (&method="maxlike") then
      evaluate ($master_method_ano="anomaxlike")
   else
      evaluate ($master_method_ano="anochisquare")
   end if 
   
{-----------------------------------------------------------------}
{---------------declare local arrays and selections---------------}
{-----------------------------------------------------------------}

   { Copy the fp and sp array into a local arrays - we don't want to operate on them }
   declare name=fp domain=reciprocal type=complex end
   declare name=sp domain=reciprocal type=real    end
   do (fp=&fp) ( all )
   do (sp=&sp) ( all ) 
   
   if (&anomalous_mode="fano") then
      do (fp=combine(amplitude(fp)+amplitude(friedel(fp)),phase(fp))/2.)
             (friedel_pair(amplitude(fp)>0))
      do (sp=sqrt((&sp^2+friedel(&sp)^2)/2)) 
             (friedel_pair(amplitude(fp)>0))
   end if


   declare name=fcalc domain=reciprocal type=complex end
   declare domain=reci type=complex name=m end  
   declare domain=reci type=real name=ppa end
   declare domain=reci type=real name=ppb end
   declare domain=reci type=real name=ppc end
   declare domain=reci type=real name=ppd end
   group type=hl 
      object=ppa 
      object=ppb 
      object=ppc 
      object=ppd
   end

   {Store prior distribution in parent distribution. }
   { ----------------------------------------------- }
   do (&pa=&priora) ( all )
   do (&pb=&priorb) ( all )
   do (&pc=&priorc) ( all )
   do (&pd=&priord) ( all )
      
   for $index in ( &list ) loop inpr
    evaluate ($active.$index=false) 
    evaluate ($active_ano.$index=false) 
    if (&fph_$index # NULL) then
     if (&on_off_$index = "on") then
      evaluate ($pa.$index="PA_"+ encode($index) )
      evaluate ($pb.$index="PB_"+ encode($index) )
      evaluate ($pc.$index="PC_"+ encode($index) )
      evaluate ($pd.$index="PD_"+ encode($index) )

      declare name=$strip%pa.$index type=real domain=reciprocal end
      declare name=$strip%pb.$index type=real domain=reciprocal end
      declare name=$strip%pc.$index type=real domain=reciprocal end
      declare name=$strip%pd.$index type=real domain=reciprocal end
      group type=hl 
         object=$strip%pa.$index 
         object=$strip%pb.$index 
         object=$strip%pc.$index 
         object=$strip%pd.$index
      end
      do ($strip%pa.$index=0) ( all )
      do ($strip%pb.$index=0) ( all )
      do ($strip%pc.$index=0) ( all )
      do ($strip%pd.$index=0) ( all )

      evaluate ($fph.$index="FPH_SAF_"+encode($index) )
      declare name=$strip%fph.$index type=real domain=reciprocal end
      do ($strip%fph.$index=amplitude(&strip%fph_$index)) ( all )
         
      evaluate ($vloc.$index="VLOC_"+encode($index))
      evaluate ($bad.$index="BAD_"+encode($index))
      declare name=$strip%vloc.$index type=real    domain=reciprocal end
      declare name=$strip%bad.$index  type=integer domain=reciprocal end


      if (&anomalous_mode="deltaf") then
         {- simply identify the particular structure factor arrays -}
         evaluate ($fph_iso.$index=&fph_$index)
         evaluate ($sph_iso.$index=&sph_$index)
         evaluate ($fph_apply.$index="")
         evaluate ($sph_apply.$index="")
      elseif (&anomalous_mode="fano") then
         evaluate ($fph_apply.$index=&fph_$index)
         evaluate ($sph_apply.$index=&sph_$index)
         {- compute the Fiso components and their sigmas -}
         evaluate ($fph_iso.$index="FPH_ISO_"+encode($index))
         evaluate ($sph_iso.$index="SPH_ISO_"+encode($index))
         declare name=$strip%fph_iso.$index type=real domain=reciprocal end
         declare name=$strip%sph_iso.$index type=real domain=reciprocal end
         
         do ($strip%fph_iso.$index=(amplitude(        &strip%fph_$index)
                                   +amplitude(friedel(&strip%fph_$index)))/2.) 
                (amplitude(        &strip%fph_$index) >0 
             and amplitude(friedel(&strip%fph_$index))>0)
         do ($strip%sph_iso.$index=sqrt(&strip%sph_$index^2
                               +friedel(&strip%sph_$index)^2)) 
                (amplitude(        &strip%fph_$index) >0 
             and amplitude(friedel(&strip%fph_$index))>0)
      else
         display unknown anomalous_mode: &anomalous_mode
         abort  
      end if

      evaluate ($targ_set.$index="TARG_SET_"+encode($index))
      evaluate ($phss_set.$index="PHSS_SET_"+encode($index))
      evaluate ($free_set.$index="FREE_SET_"+encode($index))
      declare name=$strip%targ_set.$index type=integer domain=reciprocal end
      declare name=$strip%phss_set.$index type=integer domain=reciprocal end
      declare name=$strip%free_set.$index type=integer domain=reciprocal end
      do ($strip%targ_set.$index=0) ( all )
      do ($strip%free_set.$index=0) ( all )
      do ($strip%phss_set.$index=0) ( all ) 
      do ($strip%targ_set.$index=1) (&phase_set 
                                 and &test_array # &test_flag 
                                 and &target_set_$index 
                                 and amplitude(fp)>0 
                                 and amplitude($strip%fph_iso.$index)>0) 
      do ($strip%free_set.$index=1) (&phase_set 
                                 and &test_array= &test_flag 
                                 and &target_set_$index 
                                 and amplitude(fp)>0 
                                 and amplitude($strip%fph_iso.$index)>0)
      do ($strip%phss_set.$index=1) (&phase_set 
                                 and amplitude(fp)>0 
                                 and amplitude($strip%fph_iso.$index)>0)
      

      {- See if we have to compute the Fiso term at all. -}
      show sum ($strip%targ_set.$index) ( all ) 
       if ($result > 0 ) then
          evaluate ($active.$index=true) 
       end if
     end if
    end if           
   end loop inpr

   if (&anomalous_mode="fano") then   
      if ($master_anomalous=TRUE) then
         for $index in ( &list ) loop inpa
          if ($active.$index=true) then
            evaluate ($pa_ano.$index="PA_ANO"+ encode($index) )
            evaluate ($pb_ano.$index="PB_ANO"+ encode($index) )
            evaluate ($pc_ano.$index="PC_ANO"+ encode($index) )
            evaluate ($pd_ano.$index="PD_ANO"+ encode($index) )
            evaluate ($vloc_ano.$index="VLOC_ANO"+encode($index))
            evaluate ($bad_ano.$index="BAD_ANO"+encode($index))

            declare name=$strip%pa_ano.$index type=real domain=reciprocal end
            declare name=$strip%pb_ano.$index type=real domain=reciprocal end
            declare name=$strip%pc_ano.$index type=real domain=reciprocal end
            declare name=$strip%pd_ano.$index type=real domain=reciprocal end
            group type=hl 
               object=$strip%pa_ano.$index
               object=$strip%pb_ano.$index 
               object=$strip%pc_ano.$index 
               object=$strip%pd_ano.$index 
            end
            do ($strip%pa_ano.$index=0) ( all )
            do ($strip%pb_ano.$index=0) ( all )
            do ($strip%pc_ano.$index=0) ( all )
            do ($strip%pd_ano.$index=0) ( all )
            declare name=$strip%vloc_ano.$index type=real    domain=reciprocal end
            declare name=$strip%bad_ano.$index  type=integer domain=reciprocal end
            
            evaluate ($targ_set_ano.$index="TARG_ANO"+encode($index))
            evaluate ($phss_set_ano.$index="PHSS_ANO"+encode($index))
            evaluate ($free_set_ano.$index="FREE_ANO"+encode($index))
            declare name=$strip%targ_set_ano.$index type=integer domain=reciprocal end
            declare name=$strip%phss_set_ano.$index type=integer domain=reciprocal end
            declare name=$strip%free_set_ano.$index type=integer domain=reciprocal end
            do ($strip%targ_set_ano.$index=0) ( all )
            do ($strip%free_set_ano.$index=0) ( all )
            do ($strip%phss_set_ano.$index=0) ( all ) 
            do ($strip%targ_set_ano.$index=1) (acentric and 
                              friedel_pair(&phase_set 
                                       and &target_set_a_$index
                                       and amplitude(&strip%fph_$index)>0 
                                       and amplitude(fp)>0
                                       and &phase_set 
                                       and &test_array # &test_flag))
            do ($strip%free_set_ano.$index=1) (acentric and 
                              friedel_pair(&phase_set 
                                       and &target_set_a_$index 
                                       and amplitude(&strip%fph_$index)>0 
                                       and amplitude(fp)>0
                                       and &phase_set 
                                       and &test_array = &test_flag))
            do ($strip%phss_set_ano.$index=1)  (acentric and 
                              friedel_pair(&phase_set 
                                       and amplitude(&strip%fph_$index)>0 
                                       and amplitude(fp)>0 ))
            
            {- check if the fano term is active -}                           
            show sum ($strip%targ_set_ano.$index) (all)
            if ($result > 0) then
               evaluate ($active_ano.$index=true) 
            end if

          end if
         end loop inpa
      end if
   end if
end

if (&anomalous_mode="fano") then   
   if ($master_anomalous=TRUE) then
      for $index in ( &list ) loop inp4
        if ($active.$index=true) then
          show ave ( abs(scatter_fdp) ) ( &h_$index and not &hfix_$index ) 
          if ($result<0.0001) then
	     display  ERROR: Anomalous form factors (f'') are zero for all atoms
	     display	 associated with LOC &strip%fph_$index.
	     display 
	     display      -> Check atom selection for LOC &strip%fph_$index
	     display      -> Check form factor library.
	     display      -> Are you using an anomalous form factor library? 
	     abort
          end if  
        end if
      end loop inp4
    end if
end if

{-----------------------------------------------------------------}
{-----------------------begin macrocycle--------------------------}
{-----------------------------------------------------------------}

evaluate ($master_mcycle=&macrocycle)
evaluate ($master_cycle=0)
while ($master_cycle <= $master_mcycle) loop main
  evaluate ($master_cycle=$master_cycle+1)

   for $mid in (&list) loop gen
      evaluate ($master_table.$mid=&fph_$mid+" Fiso maccyc="+encode($master_cycle))
      evaluate ($master_table_ano.$mid=&fph_$mid+" Fano maccyc="+encode($master_cycle))
   end loop gen

   {---------------------------------------------------------------------}
   {- generate LOC, LOI, and individual phase probability distributions -}
   {---------------------------------------------------------------------}
   
   {- on the last cycle also make a summary -}
   if ($master_cycle <= $master_mcycle) then
      evaluate ($summary="")
   else
      evaluate ($summary=&summary)
   end if

   for $mid in ( &list ) loop loc
   
      {- fiso terms -}
      if ($active.$mid = true) then

         xray
            call getprobs(exclude=$mid;exclude_ano=-1; prior=true;)
            if ($master_anomalous=TRUE) then
               if (&anomalous_mode="fano") then
      	          aselection=( not all )
               else
      	          aselection=( all )
               end if
            else
               aselection=( not all ) 
            end if
         end

         @CNS_XTALMODULE:getlocandprob
         ( 
            text="Fiso calculation";
            nameh=&strip%fph_$mid; 
            table=$master_table.$mid;
            messages=&messages;
            method=&method;
            integration=&integration; 
            epsilon=&epsilon;
            tolerance=&tolerance; 
            phistep=&phistep;
            iteration=&iteration;  
            cen360=$master_cen360;
            cutoff=&cutoff;
            fp=fp;
            sp=sp;
            hp=(&h_0);
            h=(&h_$mid);
            hfix=(&hfix_$mid and &h_$mid);
            fph=$strip%fph_iso.$mid;  
            sph=$strip%sph_iso.$mid;  
            target_set= $strip%targ_set.$mid=1 ; 
            free_set= $strip%free_set.$mid=1 ;
            phase_set= $strip%phss_set.$mid=1 ;
            ppa=ppa;ppb=ppb;ppc=ppc;ppd=ppd;   
            pppa=&pa;pppb=&pb;pppc=&pc;pppd=&pd; 
            m=m;  
            pa=$strip%pa.$mid;
            pb=$strip%pb.$mid;
            pc=$strip%pc.$mid;
            pd=$strip%pd.$mid;      
            vloc=$strip%vloc.$mid;
            bad=$strip%bad.$mid;  
            summary=$summary; 
            )
                        

      end if    
         
      {- fano terms -}
      if ($active_ano.$mid = true) then
           xray
              aselection=( all ) 
           end   
            
           xray
              call getprobs(exclude=-1;exclude_ano=$mid; prior=true;)
           end
           
           @CNS_XTALMODULE:getlocandprob
            ( 
              text="Fano calculation";
              nameh=&strip%fph_$mid; 
              table=$master_table_ano.$mid;
              messages=&messages;
              method=$master_method_ano;
              integration=&integration;
              epsilon=&epsilon;
              tolerance=&tolerance;
              phistep=&phistep;
              iteration=&iteration;
              cen360=$master_cen360;
              cutoff=&cutoff;
              fp=fp;
              sp=sp;
              hp=(&h_0);
              h=(&h_$mid);
              hfix=(&hfix_$mid and &h_$mid);
              fph=&strip%fph_$mid;
              sph=&strip%sph_$mid;
              target_set= $strip%targ_set_ano.$mid=1 ; 
              free_set= $strip%free_set_ano.$mid=1 ;
              phase_set= $strip%phss_set_ano.$mid=1 ;
              ppa=ppa;ppb=ppb;ppc=ppc;ppd=ppd;
              pppa=&pa;pppb=&pb;pppc=&pc;pppd=&pd;
              m=m;
              pa=$strip%pa_ano.$mid;
              pb=$strip%pb_ano.$mid;
              pc=$strip%pc_ano.$mid;
              pd=$strip%pd_ano.$mid;
              vloc=$strip%vloc_ano.$mid;
              bad=$strip%bad_ano.$mid;
              summary=$summary;
             )
 
 
      end if
 
      {-----------------------------------}
      {- do more analysis on final cycle -}
      {-----------------------------------}
      if ($master_cycle > $master_mcycle) then
     
         if ($active.$mid = true) then
            set display=&summary end
            display
            display  Scaling from initial lack-of-closure-expression F to final F
            display  ------------------------------------------------------------

            {- Get scale factor between initial lack-of-closure-expression F and final F -}
            xray
                @CNS_XTALMODULE:scalef(
                text="";
                table="";
                kscale="yes"; 
                bscale="anisotropic"; 
                apply="no";
                messages="all";
                sel=($strip%targ_set.$mid=1);
                f=$strip%fph.$mid;
                &fref=&strip%fph_$mid; )
            end


            set display=&summary end
            display
            display
            display  initial coordinates for heavy atom sites of this lack-of-closure expression
            display  -----------------------------------------------------------------------------

            coor swap end
            do (store9=b) ( all )
            do (b=bcomp) ( all )
            do (bcomp=store9) ( all )
            do (store9=q) ( all )
            do (q=qcomp) ( all )
            do (qcomp=store9) ( all )
            do (store9=scatter_fp) ( all )
            do (scatter_fp=fbeta) ( all )
            do (fbeta=store9) ( all )
            do (store9=scatter_fdp) ( all )
            do (scatter_fdp=harm) ( all )
            do (harm=store9) ( all )

            @CNS_XTALMODULE:printcoordinates
                (
                 text="";
                 sel=(&h_$mid);
                 anomalous_mode=&anomalous_mode;
                 ref_wavelength=&ref_wavelength;                 
                 ref_fp=&ref_fp;
                 output=&summary;
                )

            coor swap end
            do (store9=b) ( all )
            do (b=bcomp) ( all )
            do (bcomp=store9) ( all )
            do (store9=q) ( all )
            do (q=qcomp) ( all )
            do (qcomp=store9) ( all )
            do (store9=scatter_fp) ( all )
            do (scatter_fp=fbeta) ( all )
            do (fbeta=store9) ( all )
            do (store9=scatter_fdp) ( all )
            do (scatter_fdp=harm) ( all )
            do (harm=store9) ( all )

            set display=&summary end
            display
            display  final coordinates for heavy atom sites of this lack-of-closure expression
            display  -------------------------------------------------------------------------
       
            @CNS_XTALMODULE:printcoordinates
             (
              text="";
              sel=(&h_$mid);
              anomalous_mode=&anomalous_mode;
              ref_wavelength=&ref_wavelength;
              ref_fp=&ref_fp;
              output=&summary;
             )
       

            display
            display
            display
       
            set display=OUTPUT end
         end if       
      end if
   
   end loop loc
   

   {---------------------------------------------------------------------}
   {---------------------- carry out refinement  ------------------------}
   {---------------------------------------------------------------------}
   if ($master_cycle <= $master_mcycle) then

      {- refinement cycle -}
      for $mid in ( &list ) loop ref
         if ($active.$mid = true) then

            evaluate ($xstep_id=&xstep_$mid)
            evaluate ($qstep_id=&qstep_$mid)
            evaluate ($bstep_id=&bstep_$mid)
            evaluate ($bindgroup_id=&bindgroup_$mid)
            evaluate ($fpstep_id=&fpstep_$mid)
            evaluate ($fdpstep_id=&fdpstep_$mid)
            evaluate ($fpstep_ano_id=&fpstep_ano_$mid)
            evaluate ($fdpstep_ano_id=&fdpstep_ano_$mid)
            evaluate ($kstep_id=&kstep_$mid)
            evaluate ($kstep_ano_id=&kstep_ano_$mid)
            evaluate ($kscale_id=&kscale_$mid)
            evaluate ($bscale_id=&bscale_$mid)
            evaluate ($xstep_ano_id=&xstep_ano_$mid)
            evaluate ($qstep_ano_id=&qstep_ano_$mid)
            evaluate ($bstep_ano_id=&bstep_ano_$mid)
            evaluate ($kscale_ano_id=&kscale_ano_$mid)
            evaluate ($bscale_ano_id=&bscale_ano_$mid)
         
            {- fiso term -}
            xray
               if ($master_anomalous=TRUE) then
                  if (&anomalous_mode="fano") then
         	     aselection=( not all )
         	     evaluate ($fdpstep_id=0)
                  else
         	     aselection=( all )
                  end if
               else
                  aselection=( not all ) 
                  evaluate ($fdpstep_id=0)
                  evaluate ($fdpstep_ano_id=0)
               end if
            end
            
            @CNS_XTALMODULE:locrefine(
               table=$master_table.$mid;
               method=&method;
               messages=&messages;
               phistep=&phistep;
               cen360=$master_cen360;
               tolerance=&tolerance; 
               kstep=$kstep_id;
               bscale=$bscale_id;
               kscale=$kscale_id;
               xstep=$xstep_id;
               bstep=$bstep_id;
               bindgroup=$bindgroup_id;
               qstep=$qstep_id;
               fpstep=$fpstep_id;
               fdpstep=$fdpstep_id;
               bmin=&bmin;
               bmax=&bmax;
               qmin=&qmin;
               qmax=&qmax;  
               fpmin=&fpmin;
               fpmax=&fpmax;
               fdpmin=&fdpmin;
               fdpmax=&fdpmax;		
               qmaxshift=&qmaxshift;  
               fpmaxshift=&fpmaxshift;  
               fdpmaxshift=&fdpmaxshift; 
               bmaxshift=&bmaxshift;  
               fp=fp;
               sp=sp;
               hp=(&h_0);
               h=(&h_$mid);
               hfix=(&hfix_$mid and &h_$mid);
               fph=$strip%fph_iso.$mid;  
               sph=$strip%sph_iso.$mid;  
               target_set= $strip%targ_set.$mid=1 ; 
               free_set= $strip%free_set.$mid=1 ;
               phase_set= $strip%phss_set.$mid=1 ;
               pppa=&pa;pppb=&pb;pppc=&pc;pppd=&pd; 
               fop=$fph_apply.$mid;  
               fop2=$sph_apply.$mid; 
               gradient_map=&grad_map_$mid;
               vloc=$strip%vloc.$mid;
               bad=$strip%bad.$mid;  
             )

          end if    

          {- fano term -}         
          if ($active_ano.$mid = true) then
             xray
                evaluate ($fpstep_ano_id=0)
                aselection=( all ) 
             end    
           
             @CNS_XTALMODULE:locrefine(
                table=$master_table_ano.$mid;
                method=$master_method_ano;
                messages=&messages;
                phistep=&phistep;
                cen360=$master_cen360;
                tolerance=&tolerance; 
                kstep=$kstep_ano_id;
                bscale=$bscale_ano_id;
                kscale=$kscale_ano_id;
                xstep=$xstep_ano_id;
                bstep=$bstep_ano_id;
                bindgroup=$bindgroup_id;
                qstep=$qstep_ano_id;
                fpstep=$fpstep_ano_id;
                fdpstep=$fdpstep_ano_id;
                bmin=&bmin;
                bmax=&bmax;
                qmin=&qmin;
                qmax=&qmax;
                fpmin=&fpmin;
                fpmax=&fpmax;
                fdpmin=&fdpmin;
                fdpmax=&fdpmax;
                qmaxshift=&qmaxshift;
                fpmaxshift=&fpmaxshift;
                fdpmaxshift=&fdpmaxshift;
                bmaxshift=&bmaxshift;
                fp=fp;
                sp=sp;
                hp=(&h_0);
                h=(&h_$mid);
                hfix=(&hfix_$mid and &h_$mid);
                fph=&strip%fph_$mid;
                sph=&strip%sph_$mid;
                target_set= $strip%targ_set_ano.$mid=1 ; 
                free_set= $strip%free_set_ano.$mid=1 ;
                phase_set= $strip%phss_set_ano.$mid=1 ;
                pppa=&pa;pppb=&pb;pppc=&pc;pppd=&pd;
                fop="";
                fop2="";
                gradient_map="";
                vloc=$strip%vloc_ano.$mid;
                bad=$strip%bad_ano.$mid;
             	 )
         end if	   
      end loop ref
   end if
end loop main 

{-----------------------------------------------------------------}
{--------- end macrocycle ----------------------------------------}
{-----------------------------------------------------------------}


{-----------------------------------------------------------------}
{-----------------------final figure of merit---------------------}
{-----------------------------------------------------------------}

{- note:  Final probability is in &pa, &pb, &pc &pc. -}
{-        phases are in &fp, fom in &fom             -}

xray
   do (&fp=fp) ( all )
   do (&fom=amplitude(m)) ( all ) 

   set display=&summary end
   display
   display
   display
   display  ======================================================================
   display  ======= figure of merit after final cycle ============================ 
   display  ======================================================================
   set display=OUTPUT end

   @CNS_XTALMODULE:printfom 
      (
      text="Figure of merit for global phase set";
      table="";
      epsilon=&epsilon; 
      m=m;
      sel=&phase_set;
      output=&summary;
      )

   show sum (1) (&test_array = &test_flag and &phase_set)
   if ($select>0) then
   
      display .............................................................. 
      @CNS_XTALMODULE:printfom 
         (
         text="Figure of merit for global test set (for cross-validation)" ;
         table="";
         epsilon=&epsilon; 
         m=m;
         sel=(&test_array = &test_flag and &phase_set);
         output=&summary;
         )
   end if
   display 
   display --------------------------------------------------------------

   if (&priora # NULL ) then
   
     set display=&summary end
     display 
     display --------------------------------------------------------------
     set display=OUTPUT end

     { Combine all probabilities except prior phase probability distribution.    }
     { ------------------------------------------------------------------------- }
     call getprobs(exclude=-1;exclude_ano=-1; prior=false;)
     do (&&pa=ppa) ( all )
     do (&&pb=ppb) ( all )
     do (&&pc=ppc) ( all )
     do (&&pd=ppd) ( all )
!!
!! bug fix 4/3/05, ATB
!!
     do (m=0) ( all )
     
   
     @@CNS_XTALMODULE:getfom 
     (  
        m=m;
        sel=(amplitude(&&pa)>0 or amplitude(&&pb)>0 or amplitude(&&pc)>0 or amplitude(&&pd)>0);
        pa=&&pa;pb=&&pb;pc=&&pc;pd=&&pd;
        phistep=&phistep;
        cen360=$master_cen360;
     )
     
     set display=&summary end
     display
     display
     display
     display  ======================================================================
     display  ======= figure of merit after final cycle without prior phase prob.=== 
     display         (this distribution is written to &&pa &&pb &&pc &&pd ) 
     display  ======================================================================
     set display=OUTPUT end

     @CNS_XTALMODULE:printfom 
        (
        text="Figure of merit for global phase set without prior phase prob.";
        table="";
        epsilon=&epsilon; 
        m=m;
        sel=&phase_set;
        output=&summary;
      )

     show sum (1) (&test_array = &test_flag and &phase_set)
     if ($select>0) then
   
        display .............................................................. 
        @CNS_XTALMODULE:printfom 
           (
           text="Figure of merit for global test set (for cross-validation) without prior phase prob." ;
           table="";
           epsilon=&epsilon; 
           m=m;
           sel=(&test_array = &test_flag and &phase_set);
           output=&summary;
         )
     end if
     set display=&summary end
     display 
     display --------------------------------------------------------------
     set display=OUTPUT end
   end if


{-----------------------------------------------------------------}
{---------------undeclare arrays and cleanup----------------------}
{-----------------------------------------------------------------}
   
   { Undeclare local arrays. }
   { ----------------------- }
   undeclare domain=reci name=fcalc end
   undeclare domain=reci name=m end 

   undeclare domain=reci name=ppa end  
   undeclare domain=reci name=ppb end  
   undeclare domain=reci name=ppc end  
   undeclare domain=reci name=ppd end  

   undeclare domain=reci name=fp end  
   undeclare domain=reci name=sp end  
   
   for $index in ( &list ) loop inpu
    if (&fph_$index # NULL) then
     if (&on_off_$index = "on") then
      undeclare name=$strip%pa.$index domain=reciprocal end
      undeclare name=$strip%pb.$index domain=reciprocal end
      undeclare name=$strip%pc.$index domain=reciprocal end
      undeclare name=$strip%pd.$index domain=reciprocal end

      undeclare name=$strip%fph.$index domain=reciprocal end   
      undeclare name=$strip%vloc.$index domain=reciprocal end
      undeclare name=$strip%bad.$index domain=reciprocal end
      if (&anomalous_mode="fano") then
         undeclare name=$strip%fph_iso.$index domain=reciprocal end
         undeclare name=$strip%sph_iso.$index domain=reciprocal end
      end if
      undeclare name=$strip%targ_set.$index domain=reciprocal end
      undeclare name=$strip%phss_set.$index domain=reciprocal end
      undeclare name=$strip%free_set.$index domain=reciprocal end
   
     end if
    end if
   end loop inpu
   
   if (&anomalous_mode="fano") then   
      if ($master_anomalous=TRUE) thend
         for $index in ( &list ) loop inpp
          if ($active.$index=true) then
            undeclare name=$strip%pa_ano.$index domain=reciprocal end
            undeclare name=$strip%pb_ano.$index domain=reciprocal end
            undeclare name=$strip%pc_ano.$index domain=reciprocal end
            undeclare name=$strip%pd_ano.$index domain=reciprocal end
            undeclare name=$strip%vloc_ano.$index domain=reciprocal end
             undeclare name=$strip%bad_ano.$index domain=reciprocal end
            undeclare name=$strip%targ_set_ano.$index domain=reciprocal end
            undeclare name=$strip%phss_set_ano.$index domain=reciprocal end
            undeclare name=$strip%free_set_ano.$index domain=reciprocal end
          end if
         end loop inpp
      end if
   end if
end