I could’t push the resolution further. I suspect the reason is too thick ice. I got CTF fit for my 9000 micrographs in average 5.5 Å, which is quite bad.
I probably also have a mild preferred orientation issue. Before I took @olibclarke suggestion, I got the viewing distribution like below:
After several heterogeneous refinement, I got this:
I assume those views that were discarded are not good quality particles or those views are not even exist in my dataset. But the reconstruction actually looks okay (no elongated artefact). Could anyone provide their experience about viewing distribution, is this bad?