I have 5-fluoro-Uracil in my DNA:protein complex.

I modeled 5-F-dU into the map, ran eLBOW for geometry file and did refinement.

After the refinement, 5-F-dU is not connected to the neighboring nucleotides and the phosphate oxygens are rotated to wrong positions.

Can anyone teach me how to refine with non-standard DNA base ?

Any help or advice would be appreciated.

John