Until there is more glucose available than is utilized over a particular via glycolysis, at which point the excess glucose is converted to fat and stored as fat for later use as an energy source.
There really is no ambiguity on this. There's nothing magical in physiology. A calorie is a measure of energy, specifically a measure of heat energy in relation to water.
Should more calories be ingested than are burned over any particular time period, the body will store the excess energy for later use.
There is a law in physics called the conservation of energy.
When you ingest a calorie, the energy of that calorie (the energy required to raise 1g of water 1 degree celsius) must be maintained. The energy can take other forms, but its absolute magnitude is constant.
That calorie is either utilized in some form of energy release (in the exact same energy amount as was ingested) or is stored in the body as an energy source that can be used later.
If you ingest 5,000 Calories from protein and the net caloric expenditure over that same time period is 4,000 Calories, 1,000 calories will be stored as defined by the law of conservation of energy. This 1,000 calories can be stored as protein, glycogen, or fat depending on the needs of the body at that time.
Unless you re-write the laws of physics, this is an unarguable point.
Although none of us care to challenge the laws of physics, I think many of us would choose to question your point.
Of course the law of conservation of energy applies in all ordinary processes, such as the case of food metabolism. Energy stored in food is neither created nor destroyed, but MAY change form. To say it another way, the food-energy does not magically disappear into oblivion, nor will energy magically appear from nowhere. To put it in even simpler terms--the FOOD and its associated energy HAS TO GO SOMEWHERE (which is obvious to us all).
Is every food calorie ingested which is not "burned for fuel" definitely stored as either protein, glycogen, or fat? Has this been proven? What if you ingest so much food that your body doesn't need it all for fuel, and also doesn't need to add to its protein, glycogen, or fat storage? Can't some of the food simply not be used for anything (which does not violate conservation of energy--your food energy just didn't change form)?
I've trained very thin guys who have desperately tried to gain weight. They'll pack in as many super-high-density meals as possible to achieve ridiculously high caloric intakes, and still not gain weight--fat or muscle. Not everybody gets big and/or fat from eating a lot. Are they really expending that large a number of calories, burning them all up for fuel? Are that large a number of extra calories really being stored somewhere somehow as something? Maybe not? When force-fed large quantities of food, can some of the food simply pass through a bit undigested, unused (it sure LOOKS that way!)?
The laws of physics are exact, and in the study of metabolism would apply exactly. The law of conservation of energy applies exactly. But when and under what circumstances the starting food-energy converts to other forms doesn't seem to be 100 percent predictable. If we could handle food metabolism as an exact science, we could simply compare food intake to calorie expenditure and hope to make some fairly accurate predictions about what one should lose or gain--this is very hard to do.
Of course there's nothing magical in physiology. None of us here believe in magic. But sometimes things do seem ambiguous--not because they truly are ambiguous, but because it's proved so difficult to know the fine details of how one individual's body really handles the food that's put in it.
