Hi @Dmitry,
Homogeneous Reconstruction should replicate the results of standard 3D Refinement. However, it won’t replicate the results of non-uniform refinement if adaptive marginalization is enabled. This is because reconstruction only does not marginalize over alignments. Otherwise, the conditions you outlined in the first post are correct. Which refinement job are you comparing the reconstruction to?
As well, note that you must be careful about which mask is being used: the final refinement iteration shows two plots, one with the static/dynamic mask, and the other with the auto-tightened mask. The auto-tightened mask is output under the result name of mask_fsc_auto, and the static/dynamic mask used for the first FSC calculation is output under mask_fsc. Both of them are output so that the masks used are available for downstream work. To input the specific mask to the Reconstruction Only job, you must use low-level results which are documented in our guide.
Best,
Michael