Dear @geng,
How large is the box size relative to the protein? The fact that the curves are all closely spaced indicates to me the box could be a bit too small: applying the mask eliminates a lot of noise from the reconstruction, so the masked FSC scores are significantly higher than unmasked. If the initial box size is less than around 2.5-3 times the max diameter of the protein, could you try re-doing everything post extraction with a larger box size?’
Best,
Michael