I tried Homogeneous refinement (Legacy) to refine one of my maps obtained from ab initio reconstruction (~78k particles), and I kept getting strange FSC curves with super low resolution (please see below)
The box size I use is relatively large - 420 pix because I’m expecting to see particles of different sizes (up to 300 pix). But for this particular map, the maximum dimension is about 120 pix. After first attempt of Homo refi without a mask, I saw similar FSC curves as above, and I thought adding a circular mask might help. So I used relion_mask_create to create a sphere mask with a diameter of 250 pix and ran the homo ref again, but I got similar FSC curve as without mask (see above).
I did see the real space slices (please see below) look very noisy although the circular mask is pretty close to the map already.
I’m not sure what could be causing the refined map to have such a low resolution (worse than the ab initio map). I would really appreciate any suggestion on what I should try from here. Thank you so much.