Dear all,

I am trying to refine an intermolecular disulfide bond in phenix.refine. The disulfide involves Cys 188 in chain A and Cys 188 of chain B of a symmetry related molecule, with symop -X, Y+1/2, Z+1/2. There are two molecules in the AU, SG is P212121. I generated the following SSBOND entry in the pdb header:

SSBOND 2 CYS A   188  CYS B   188                    1555  3555 2.04

Based on this: http://www.wwpdb.org/documentation/file-format/format33/sect6.html the format seems fine, but the disulfide is not being recognized during refinement.

Could someone point out to me how to correctly define this for phenix.refine.

Thanks!
Michael