Hi @Izana! Welcome to the forum! Let’s see if we can clear a few things up about CTF refinement.
The standalone Local CTF job
Starting with the most straightforward problem, it looks like your Local CTF job has an empty half-set. This can occur when the particles come straight from an Ab initio reconstruction job. If this is true, first refining the particles (using, e.g., Homogeneous Refinement) or re-splitting them (by, e.g., using Homogeneous Reconstruction Only with Force re-do GS split turned on) should solve this particular problem.
When to do CTF refinement
When you perform CTF refinement, you compare the particle images to projections of your volume and try to adjust any mismatch between the two by adjusting CTF parameters. As we mention in our guide page on CTF Refinement, this generally works best when the particle is rigid and the volume is already of pretty high quality (better than 4 Å for local CTF refinement and even higher resolution for global CTF refinement).
If your volume is still at around 10 Å, CTF refinements will probably not help (and may in fact make things worse)! Generally, we’d recommend trying to improve your map via cleanup (perhaps with Heterogeneous Refinement) and refinement of particle poses (through Homogeneous or Non-Uniform Refinement) before attempting CTF refinement.
I hope that helps! Please let me know if you have any more questions!