Small particle set spread over more micrographs requires more cache than larger particle set from fewer micrographs.
The “small” particle set may be spread over many mrc files that still contain “rejected” particles. Therefore, many “rejected” particles may have to be stored in cache. Have you already restacked your particles to create mrc files that exclude the rejected/unused particles?
Restack did not work but i reextracted instead. I guess a work around for now.