I recommend you always activate these three settings:
- Use shift/pose priors
- Recenter poses each iteration
- Recenter shifts each iteration
IMO they should be on by default. Most users are surprised to learn that without “recentering” the same initial input angles are used again and again in each iteration. I also usually find that local refinement is not effective without recentering, but that it tends to diverge without the priors. OTOH if they are made the default I’ll lose the ability to look like a miracle worker when I advise other users…
BTW, to control the search, just change the angle and shift standard deviations but leave the search extents as the default (3 * standard deviations). I use e.g. 7˚ and 4 Å for refinements already around 2-2.5 Å and slightly bigger ones for lower resolutions. Probably the particles are not 10+ pixels off in shift if the resolution is already reasonably good.
The initial resolution is also important to consider. If you can already see secondary structures in the focused region, I would use something like 8-12Å. If the resolution is already ~3Å I tend to use ~6Å.