You may already have good .pdb format coordinates for your ligand, inhibitor, ion, etc.  If not, start out by searching the HIC-Up site for your molecule.  Once you've gotten the .pdb format coordinates, run it through Shelxpro using option [J]:

You'll be asked to enter the unit cell parameters if they are not present in the header information of your .pdb file.  Shelxpro will output a .dfx file that contains the appropriate restraints.  Below, is an example output for a 'TRIS' molecule obtained from the HIC-Up website:
 

Cut and paste this into your .ins file.

NOTE:    You likely have a line in your .ins file that reads:

CONN 0 O_??? > LAST

where ??? is the residue number of your first water molecule.

If you have anything with a residue number greater than ??? other than water, this CONN command will tell Shelx that all the atoms in that residue have a connectivity of ZERO!

Therefore, make certain that the residue numbers of the water molecules are higher than those of all other residues!
 

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