Hello everyone, I have fine electron density 2Fo-Fc around a small ligand (~20 atoms) binding to my protein (at 1sigma level, all of the ligand atoms are surround by electron density, resolution=3 angstrom). However, I also see some negative electron density Fo-Fc surrounding some of the ligand atoms. My question is should I care about these negative electron density? If I should, what should I do in order to decrease or eliminate these negative electron density? I have tried occupancy refinement. It does help to decrease the negative density. However, it also makes 2Fo-Fc weaker. Another method I tried is to use tls refinement only for the ligand. It also helped to decrease the negative electron density. But since the data resolution is only 3 angstrom, I do not know if I am even allowed to do tls refinement? Thank you all in advance. Jason University of Pittsburgh