Hi Dialing,

H geometry should be ideal after phenix.refine. If it is not the case then please send me the PDB and I will have a look.

Pavel

On 12/6/11 3:49 AM, Dialing Pretty wrote:

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
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