Hints for improving a refinement
Ok, you did your average and you are not yet satisfied. Looks like you should be able to get better results?
Do you have a single class? If you are aligning two or more classes together, the alignment would get stuck at some point (funnily enough, in this circumstances the FSC can easily lie about the attained resolution, even when using a golden standard procedure!). A first approach to diagnose this is to check the cross correlation of the alignment (in column 10 of the table). A simple inspection of the histogram can be very revealing, especially if you detect different behaviours when considering particles stemming from different tomograms (column 20) or models (column 21).