Problem with making model of ligand-enzyme complex

[nui2897]

I am new to structural biology.

I have a question regarding adding a ligand/substrate to enzyme by coot and Refmac. I want to make -O- bond between Ser residue and the ligand molecule.

I start Coot, and read in your cif file plus a coordinate file containing
the ligand. Read in structure and read in mtz file as Auto,
then I end up with two maps FWTxPHWT and DELFWTxPHDELWT.
Next go to Calculate / Other Modelling Tools and select Fit Ligand.
merge ligand and coordinate file by coot and run refmac.
After refinement by Refmac, ligand and Serine residue are displayed separately,uncombined.

Please give me instructions how to make combined model of ligand and Ser residue in enzume..