You need to parse the file tab delimited file named .proteinortho or .poff (if you used syteny). Per the manual, you'll see that the first column is the number of species that the orthologous group is found in. So lets say you had 4 species (i.e. you ran with 4 proteome fasta files), you could then filter the tab-delimited .proteinortho or .poff output as follows:

#this will show orthologous groups containing proteins from each species
grep '^4' output.proteinortho

However, since it seems like you are maybe looking for single copy orthologs, you could filter those like:

#this will get orthologs containing all 4 species and no duplications in each genome
grep '^4\t4' output.proteinortho