It's probably something unique to me, but proline certainly makes me feel more 'unrefreshed' when I wake up. I tried some wheat-based (fairly high proline) foods yesterday, and definitely felt groggier than usual, and it was really hard to pry myself out of bed. Proline might not be causing the 'unrefreshing sleep' symptoms, but for me it seems to increase or at least mimic them.
This is the reason I recommend going on a temporary 'safe' (empty calories) diet once in a while: if you have a certain food or nutrient in your diet every day, how can you know that it isn't causing problems?