Have seen this a few times in the past. My data when refining will go to 2.1A very easily (pixel size 1.05). Dataset is small (10k particles), somewhat noisy, and definitely not 2.1A resolution limit. The data itself is fine I think, since I got to 8A ab initio which looks nice. The problem is when I then try to refine the data against the ab initio model.
See attached screenshot, things seem to refine alright up to a certain point then the next round it just maxes out to nyquist. I don't think this is a small # of particles problem because I have seen it with larger datasets. The output map for the penultimate step looks reasonable, then the final map is way jacked up with noise and clearly over-refined/sharpened.
Have tried doing a global manual refine and limiting resolution but it takes ages to make any progress, which makes no sense since it shoul drun quicker. I've tried with just doing local refine and the nyquist problem occurs again. Haven't yet ruled out that manual refining is the solution and I am just setting it up incorrectly.