You can't accurately measure "calorie" intake. Calories are units of heat, and don't represent how the human body utilizes energy from food. The number of calories you'll find attributed to a given food are determined by how much heat is emitted by the available macronutrients if they were set on fire in a bomb calorimeter. Humans don't work like bomb calorimeters. This is why calories as a measure of nutrition are nearly useless.

I'm not exactly speaking as an armchair scientist, though I don't have a Phd. I spent over 9 months this last year developing my own tech to measure human metabolic activity and did extensive research into the broader subject, and quit my job in part to focus on it.

Whether you were overeating or not hardly has anything to do exclusively with eating a couple of extra grams. What you were eating and your individual physiology is primarily what dictates how your body will ultimately respond to your food. The vast majority of people in our industrial societies are eating diets that our species barely or never adapted to, and the prevalent macronutrients of said eating creates this illusion that the problem is calories. Our bodies are actually extremely good at self regulating. Problems enter when we get the fuel mix wrong, which is what we're doing when we're eating carbohydrates 3+ times every day.

A good (though imperfect) analogy is the fuel you put in your car. Modern fuel injected cars can actually start on different fuels. You can, for instance, put E85 ethanol fuel in a non flex-fuel car and it will probably start, and there's a chance it will be able to continuously run on it, albeit poorly. The reason for this is a standard car isn't configured to run on ethanol. While it probably can run on it, it's specialized for one particular fuel, which is gasoline. Maybe you can run your gasoline car on E85, but you'll have to step hard on the gas pedal and you will eventually suffer the consequences of poor engine performance. (Ironically, many modern cars can run fine on E85 with a mere software update, but that's a different story)

I would challenge you to gain any meaningful amount of fat mass on a diet of pure animal protein, let alone hold on to existing fat. It's a lot more difficult than most people believe. The satiety signal that follows eating meat, which is a hormonal response, is more powerful and sustaining than a diet based on carbohydrates. Glucose, what most carbs ultimately become, is poisonous to cells, while protein isn't. A diet based on protein means the body doesn't need to use or store the supply of glucose because the necessary glucose can be generated from protein on demand. The way your body responds to these different macronutrients is very different. People counterintuitively lose a lot of weight eating lots of fat because, unlike carbohydrates, fat has little to no insulin response on its own.

Things also get messier when fat and carbs are eaten simultaneously, but I feel like I've mentioned this on HN a bajillion times already.

All this to say that the calorie model for human nutrition should no longer be taken seriously.

Calories might only mean anything as a measure of energy expenditure, but even that measure has little utility to anyone who isn't in the process of dying. Some people succeed in losing weight by restricting the amount of "calories" they are consuming and offsetting the "calories" they eat by performing exercise. Where this falls apart is taking the same exact energy intake and activity level, replicate it in another person, and fail to see the same fat loss results. Below a certain point, yes, you'll see every participant lose weight, but you may also find them to be wasting muscle. Eventually, the effects of "calorie" restriction and carbohydrate intake will catch up with a person and they will suffer for it because neither "calorie" restriction or frequent carbohydrate intake are things that humans are adapted for.