Dear All,

I did a Phenix refine, and before the refine all the H were added. MolProbity analysis demonstrated that almost everything are acceptable after the refinement.

However when I did the geometry analysis by the COOT validation, I find all the residues having a significant deviation bond involving H. with z score higher than 7.

I am looking forward to  getting an explanation from you on it,including how to avoid it.

Cheers,

Dialing