I personally like to shoot a five shot group. Many shoot only a three, but a five gives me a chance to flinch or throw one for any number of reasons. I like to see where that one might go. Then I look at the group and measure center to center the two furthest apart holes.
for instance, when I was sighting in my Sightron Scope, the final group had a couple fliers. But I still measure the overall group from the two furthest shots. This tells me that although the rifle will shoot where it should I can flinch a few out of the main group.