[phenixbb] ambiguous ligand density

[Pompeu,Yuri Alexey Andreiw]

Hello everyone,
I have this strucuture I solved by Molecular replacement. It is a 
single mutant of previously solved enzyme. I started refining it and 
fit the ligand in a way that gives me the experimental stereochemistry.
 The final map 2mFo-2DFc looks great. After further examination I 
noticed, I have a carbonyl that does not seem to be bound to anything 
!!!
I started looking at my average kick and SA composit omit-map prior to 
modeling in the ligand and now I am really lost.
Could anyone help?
Thank you