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It's common with high calorie/high protein diets. Keep your fiber HIGH. It is very important to get 20-25 grams of fiber in daily. The easiest way for me is oats. 1 cup of oats = 8 grams of fiber.
Also eat tons of green veggies like green beans and broccoli. Drink tons of water as well. After that you can start looking into stuff like probiotics or digestive enzymes to help out. I'm a huge fan of probiotics.