how to set phase residue target
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The parameter, phase residue target: according to README, we should set it small, like 15.0. But I check couple data sets in your website, DLP and TMV are set to 82.0, 7RP set to 60.0, and BPV set to 30.0. I wonder what is rule to adjust this parameter? I found those datasets, DLP or 7rp with target residue at 82., their phase residues in par file are around 60 to 70 and dataset BPV with target residue 30, their phase residues are around 80 to 90. I am confused.
The phase residue target
The phase residue target parameter only plays a role when Frealign runs in mode = 4. In mode = 4, Frealign performs a search that stops either until it has exhausted all the parameters it is supposed to search through, or if the phase residual drops below the phase residue target. Therefore, if you happen to know what kind of phase residual is "good", i.e. the particle must be aligned correctly, you can cut the search short.
In the data sets you looked at we did not use mode = 4 to get initial alignments of the parameters and therefore the phase residue target was not used. It was set to something arbitrary.