Hi Meranda,
Are you using signal-subtracted particles (from the Particle subtraction job) for local refinement, or are you using the particles directly from a consensus refinement? Subtracted particles will (ideally) only contain signal outside of the mask that was used for subtraction, thus if there are large chunks of volume missing that are within the mask used for local refinement, that likely indicates something went awry somewhere in the signal subtraction. In that case, you may want to try running a local refinement first using the raw unsubtracted particles from the consensus refinement, then run a second local refinement using the signal subtracted particles, and compare the resulting output maps to make sure that density within the mask looks similar and no chunks are missing – this can help validate how successful the signal subtraction was.
Per the mask size issue, generally local refinements need a reasonably sized mask in order to produce optimal results. A commonly cited metric is that the masked domain of the protein should be at least ~150 kDa in mass. The reason for this is that only signal within the mask is used to align particles to the volume, and with a diminishing amount of signal, alignments can get less accurate. The main protection against this in local refinement is the rotation and shift search extents, which constrain the alignments to lie within the specified magnitude around the original poses and shifts. If using a larger mask is not an option, the main way to prevent overfitting / poor alignments is to make the search extents very tight (e.g. a few degrees and 1-2 pixels of shift).
Best,
Michael