I need some help with handling modified DNA bases in phenix refinement.

I am refining a duplex DNA structure (8 bases) that has a modified base (2nd base) . The modification is one of the Oxygen (at position 2) on a thymine is replaced by a Selenium. I used eLBOW of Phenix to create cif file for this modified base and then tried to connect this hetero base to the remaining bases. However I could not manage to get the refinement running.

I was wondering if any body has an example of how to define the connections for DNA that has modified bases for phenix.refine. 

Thank you in advance.

Sincerely

 Venu

======