1000 calories isn't very much. If you're body doesn't have enough calories it goes into starvation & storage mode. This means that by not eating enough you're going to either keep your weight on or even gain weight. I suggest you eat at least another 200 calories, maybe more. What are you eating for lunch? Maybe you can add some nuts, boiled eggs, yogurt, or something else with a good amount of proteins and fats.
you are doing everything right, you are not fat, you are at a healthy weight. because your body is still growing you will have a little extra weight. make sure to drink plenty of water keep hydrated. and you sound perfectly healthy, keep it up!
I havent grown an inch in two three years