[phenixbb] cif file for internal bond with one of two alternative conformations

Hi, I have a structure of drug bound to a protein. The drug has two alternative conformations, in which one of them has an internal bond making it a cyclic compound. How do I refine a structure like this? What modification should I do to its cif file, which I generated using elbow without the internal bond. Thank you. Daqi Tu (sorry if I have double posted.)