remarks  file  xtal_free_r/full_refinement.inp 
 remarks  Example of free R test: full refinement, consisting
 remarks  of initial minimization, slow-cooling SA, and restrained
 remarks  B-factor refinement

{===>} parameter @TOPPAR:parhcsdx.pro end                {*Read parameters.*}

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

{===>} coor @../generate/generate.pdb                   {*Read coordinates.*}
                                             
 vector do ( charge=0.0 ) ( resname LYS and 
    ( name ce or name nz or name hz* ) )         {*Turn off charges on LYS.*}
 vector do ( charge=0.0 ) ( resname GLU and
    ( name cg or name cd or name oe* ) )         {*Turn off charges on GLU.*}
 vector do ( charge=0.0 ) ( resname ASP and
    ( name cb or name cg or name od* ) )         {*Turn off charges on ASP.*}
 vector do ( charge=0.0 ) ( resname ARG and
    ( name cd or name *E or name cz or name NH* or name HH* ) )
                                                 {*Turn off charges on ARG.*}

 flags                                       
    include pele pvdw xref                   
    ?                                        
 end                                         
 
 xrefine 

{===>}
   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.cv end         {*Read reflections, including test array.*}

{===>}   
   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=0.2                                  {*Tolerance for dynamics.*}

{===>}
   wa=26000                                  {*Weight from job "check.inp".*}
 end                  

 minimize powell                                    {*Initial minimization.*}
   nstep=40                                 
   drop=40.0
 end

 set seed=432324368 end {*Set the initial random seed for the v-assignment.*}
     
{===>} 
 evaluate ($init_temp=3000. )                       {*Starting temperature.*}         
 vector do (vx=maxwell($init_temp)) ( all )
 vector do (vy=maxwell($init_temp)) ( all )
 vector do (vz=maxwell($init_temp)) ( all )

 vector do (fbeta=100.) ( all )

 evaluate ($1=$init_temp)
 while ($1 > 300.0) loop main     
          
    dynamics  verlet 
      timestep=0.0005            
      nstep=50
      iasvel=current 
      nprint=5  iprfrq=0
      tcoupling=true tbath=$1   
    end                                         
    evaluate ($1=$1-25)
 end loop main


 xrefin
   tolerance=0.0    lookup=false          {*This makes the minimizer happy.*}             
 end
       
 minimize powell                                       {*More minimization.*}
   nstep=120                                         
   drop=10.0
 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 will be executed.*}

   
   update
   print r                                      {*Print R value statistics.*}
                                            
 end

 constraints inter=( not hydrogen ) ( not hydrogen ) end

 print threshold=0.06 bonds          {*Do some simple geometric statistics.*}
 print threshold=10.0 angles  
 print threshold=20.0 impropers 
                                        
 write coordinates output=full_refinement.pdb end {*Write final coordinates*}
                                                  {*and B-factors.         *}
 
 stop