The most common cause of the kind of pain you are describing (if you know he's not constipated) is anal gland problems. Cats naturally strain when they poop and this empties the glands (as long as there is not a problem). If your cat is having soft stools, he might not be straining enough to empty the glands so they could be overly full. This will cause pain. They can also get infected and need antibiotics.
I would also be concerned that he has a urinary disorder (crystals or a UTI) and you are hearing him complain because the litter box is a source of pain.
Be sure that he is passing urine through the weekend and then see your vet as soon as you are able.