Hi Lu,

The serine contains no H atoms and the ligand has H atoms in the PDB file. How do Phenix refine deal with this two kind of H atoms at nearly the same place?

phenix.refine is a refinement program, not model building. It will attempt to refine whatever you give it, good or garbage, and, in case of garbage in, expect garbage out, typically.

So if you have that H that given the new bond should go, then you should delete it. Perhaps we should detect such cases automatically and deal with them seamlessly (thoughts, Nigel?) but at present it appears to me as the next level of sophistication that we haven't gotten to yet.

I have deleted the H atoms of the ligand, and refined again. The coordinate is reasonable without H atoms being seen.
So, I think the simplest way is to delete all H atom in such resolution.

Yes, this is true.

Best wishes!

Likewise!

Pavel