remarks  file  xtalrefine/brefinement.inp   
 remarks  Restrained, individual B-factor refinement
               
               
{===>} parameter @TOPPAR:parhcsdx.pro end                {*Read parameters.*}

{===>} structure @../generate/generate.psf end       {*Read structure file.*}

{===>} coor @slowcool.pdb                               {*Read coordinates.*}
                                             

 xrefine                                    {*This invokes the             *}
                                            {*crystallographic data parser.*} 
{===>}
   a=61.76 b=40.73 c=26.74 alpha=90.0 beta=90.0 gamma=90.0     {*Unit cell.*}

{===>}
   symmetry=(x,y,z)                         {*Symmetry operators for space *}
   symmetry=(-x+1/2,-y,z+1/2)               {*group P212121; notation as in*}
   symmetry=(-x,y+1/2,-z+1/2)               {*Int. Tables.                 *}
   symmetry=(x+1/2,-y+1/2,-z)      

   SCATter ( chemical C* ) 
      2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
   SCATter ( chemical N* )
      12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529
   SCATter ( chemical O* )
      3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800
   SCATter ( chemical S* )
      6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900
   SCATter ( chemical P* )
      6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645 1.11490
   SCATter ( chemical FE* )
      11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566 0.97070
 
{===>} 
   nreflections=15000
   reflection @amy.fob end                              {*Read reflections.*}

{===>}   
   resolution  5.0 2.0                                  {*Resolution range.*}

   reduce   
   do amplitude ( fobs = fobs * step(fobs - 2.0*sigma))     {*Sigma cutoff.*}
   fwind=0.1=100000

   method=FFT          
   
   fft 
      memory=1000000   
   end                 
      

   tolerance=0.0 lookup=false             {*This makes the minimizer happy.*}

   wa=10000     

 end                  


 xrefin
   update 
   optimize overall                            {*Optimize overall B-factor.*}
      drop=0.01                     {*This avoids overshooting the minimum.*}
      nstep=15
   end
 end

              {*The following two VECTOR statements make Gaussian          *}
              {*distributions around current B-factors (stored in array B),*}
              {*with width 1.5 for backbone and 2.0 for side chains.       *}

 vector do (b=b + gauss(1.5))  
    ( name ca or name n or name c )   

 vector do (b=b + gauss(2.0))  
    ( not hydrogen and not ( name ca or name n or name c ))
                   
 xrefin
                                                  {*Used during refinement.*}
   
   optimize bfactors                           {*Invoke B-factor optimizer.*}
  
      nstep=20                        {*Twenty steps of conjugate gradient.*}

      drop=10.0                          {*Expected initial drop in energy.*}

        {*By default, the program will automatically determine the relative*}
        {*weight between restraints and crystallographic residual.         *}

                                      {*Target sigma for 1-2 B-factor pairs*}
                                      {*(for backbone and side chain).     *}
      bsigma=( name ca or name n or name c or name o )=1.5 
      bsigma=( not( name ca or name n or name c or name o ))=2.0 

                                             {*Target sigma for 1-3 (angle)*}
                                             {*B-factor pairs.             *}
      asigma=( name ca or name n or name c or name o )=2.0 
      asigma=( not( name ca or name n or name c or name o ))=2.5 
                                             
   end                                            {*Refinement is executed.*}
                                            
 end
                                        
 write coordinates output=brefinement.pdb end     {*Write final coordinates*}
                                                  {*and B-factors.         *}
 
 stop