How can probability cut off value be set for amino acids residues that causes functional divergence by using False Discover Rate (Diverge Software)?

Question

[evo_genomics]

I have used Diverge 3 for type1 analysis. Kindly guide me how can I define probability cut off value for amino acids residues that are causing functional divergence (site profile of type 1divergence) by using False Discover Rate (FDR). What maximum value of FDR can be selected?

Thanks