I was having some difficulties using sfall to compute pseudo structure factors from a cryo-EM map. The map (in CCP4 format) is currently in a cubic pseudo-cell (P1 space group) with a size of ~500 Å in each dimension and with all three angles being 90 degrees. There was no input mtz file because an EM map was used. However, there was an error message of "Large Difference in CELL DIMENSIONS" after running sfall. Then I tried to cut out part of the EM map using a mask defined by a coordinate file, which corresponds to one of sixty asymmetric units  (due to an icosahedral symmetry).  When the new map (upon cutting the original map) was used, I had the same error message as mentioned above. I was therefore wondering if anyone has any suggestions on how to fix this problem. Thanks.