remarks  file  xtalrefine/prepstage.inp 
 remarks  Prepare structure for simulated annealing

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

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

{===>} coor @../generate/generate.pdb                   {*Read coordinates.*}
                                             
{===>}                                     {*If the temperature factors and*}
 vector do (b=15.0) ( all )                {*occupancies are not defined in*}
 vector do (q=1.0) ( all )                 {*the coordinate file,          *}
                                           {*set them now.                 *}
 
 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.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=0.05                            {*Tolerance for the minimizer.*}

{===>}
   wa=26000                                  {*Weight from job "check.inp".*}
 end                  
                                       
 vector do (refx=x) ( all )                   {*The structure is restrained*}
 vector do (refy=y) ( all )                   {*to the main coordinate set *}
 vector do (refz=z) ( all )                   {*(generate.pdb).            *}
 
 vector do (harmonic=0.0) ( all )        {*Set the harmonic energy constant*}
 vector do (harmonic=20.0) ( name ca )   {*to 20.0 kcal/(mole A**2).       *}
 flags include harm end
        
 minimize powell                             {*Invoke the Powell minimizer.*}

   nstep=40                                {*If the initial energy of the  *}
                                           {*structure is large, one should*} 
                                           {*do at least 160 cycles.       *}

   drop=40.0                                {*This is the expected initial *}
                                            {*drop in energy; this value is*}
                                            {*not critical: 40.0 should be *}
                                            {*reasonable in most cases.    *}

 end                                       {*Minimization will be executed.*}

 write coordinates output=prepstage.pdb end            {*Write coordinates.*}

 stop