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Dear Takanori, Hi, thank you for your fast reply, I'm sorry to say that it's not the reason why my refinement job crashed. Every time I reextract my particles, I use relion_reconstruct of extracted particles to directly generate my reference, the low pass filtered to a reasonable value, for instance 30~40 angstroms, and I use the low pass filtered reference to generate my mask, so the coordinates within particle, reference, mask should be consistent. Cheers, Linhua Tai ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1