Hi rpat,
I can’t explain the difference in the cFSC score between the reconstruction and the refinement, but it’s important to visually inspect the actual maps. Does the refinement show more evidence of preferred orientation than the reconstruction? How does it compare to the actual map output by heterogeneous refinement? If you do a 2D classification on these particles, do you see an assortment of views? I wonder if some of the other heterogeneous refinement classes are soaking up rarer views.
In my experience, an orientation distribution plot that looks that homogeneous usually means that there’s still a lot of junk particles in the particle stack, because junk particles don’t typically show a preferred orientation. You may want to do further iterations of hetero refinement to remove more junk and get a cleaner particle stack, which can sometimes help with getting a better-quality reconstruction.
A “decoy classification” strategy for removing junk particles seems to be the preferred approach for several users on the forum. You can find more information about it here:
Best,
cbeck