I’m refining 50k particles using NU refinement program with default parameters. The final FSC is going around 3.9 A however, there seems to be a big jump in FSC which I can not get rid of. The FSC looks like this:
I read in CS discussion forum that these things can happen in presence of duplicate particles, so I also ran Remove Duplicate Particle job with 20 A separation distance. It only yielded 10 particles. Ran the NU refinement again, but the resulting FSC looks exactly the same.
I checked the map visually, it looks very good. No scaly artifacts or suspicious densities. Alpha helices looks really clear.
Please advise what can cause this kind of issue.