Dear all, I am refining a crystal structure with two enantiomers of the ligand lying on a two-fold crystallographic axis (making the density an average of 4 orientations/optical identity). The ligand fits pretty well over all in the density, but some atoms stick out of density. While B-factors for the atoms that are within the density, the B-factors are in the range of 20-40. For the ones sticking out, the B-factors are 200-400. Which doesn't make chemical sense, as clearly, one atom isn't jumping around so much more than the others.
Is there any way I can force refmac to make the B-factors more reasonable? I also notice that some side chain atoms that stick out of density have horrendous B-factors. Thanks in advance, Sangeetha.
