[phenixbb] X-ray/Neutron joint refinement

Hi All, I have a couple of questions about X-ray/neutron joint refinement in phenix. Is it possible to use the neutron data only for refining hydrogen atom positions and the X-ray data for all other atoms? I used the option to add hydrogen atoms to model and refine H/D at exchangable sites and H elsewhere. This worked for many of the exchangeable hydrogen atoms. However, for some side chains, especially Lysine, the program has placed a hydrogen and deuterium atom (with refined occupancies) in the same position as the atom it is supposed to be bonded to. Does anybody know why this is happening and what I may be able to do about it. Or will I need to manually move each misplaced H/D in Coot? Thank you for your help. Emily