I am definitely on my way to becoming crazy!!! I took the pdb created by Greg and I prepared my own .cif file in CCP4  as well as used the .cif file prepared by Greg but once i merge the molecule after placing it in the density. it somehow doesnot refine. I merge the restraints into one cif file and still it does not let me refine even in COOT when I am using Calculate>Model/fit/refine>Real space refine zone, right after I place the molecule. I am deleting the hydrogens though before I place the molecule into the density (before refinement image). After running Refmac5 I lose most of the density as you see in the image and the molecule is misplaced.

Another problem is that this molecule is basically placed at the N-terminal of residue 1 of chainA so it also has the number 1. I do not know if this is creating the problem. I chnaged the chain name into Chain A, as this is a residue in chain A and renumbered it to the last residue of the peptide instead of renumbering all the aminoacids and still no luck.

What should I do, I am running out of ideas. 

Am I doing the steps right?

1) I generate or get a pdb of the ligand molecule (basically it is not ligand in that sense!!)

2) Generate restraints by ProDrg

3) Open the pdb of the molecule, and import cif file and then open the PDB protein molecule and the corresponding map

4) Fiting the ligand molecule into the protein Map

5) Merge molecule in COOT

I can't explain how much I would appreciate your help and suggestions.

Thanks,

Ivan