I am working on a 4MDa ~400x230x230Angstrom, D5 virus which is elongated and mostly hollow. The map generated after CTF correction looks good (nucleotides, and aromatics are clearly distinguished), but the FSC plot appears to have high resolution artifact (attached as FSC_plot.png). If I continue local refinement the high resolution noise appears to get worse, then nonsensible.
I found an old forum post where somebody had a simmilar issue and used calculate_fsc with a mask to improve the FSC quality. I tried to do the same but found minimal improvement in the FSC plots. The calculate_fsc output is provided in the attached my_statistics.txt
I wrote out my half-maps and used the FSC validation server https://www.ebi.ac.uk/pdbe/emdb/validation/fsc/results/ and got a reasonably believable unmasked resolution of 3.6 Angstroms (attached as FSC_plot_pdb_server.png).
Any thoughts on if some measures can be taken to avoid this behavior by cisTEM?