Short answer: Burn more calories than you take in and you will lose weight. Do it right and you will burn fat. Do it wrong and you will burn muscle and store fat.
EDIT: It's great to watch what you eat when trying to lose weight. But, don't forget to watch what you drink.
EDIT #2: D'Oh! I forgot to mention the highly rated guide that is the ONLY sticky at the top of this forum:
http://forums.anandtech.com/showthread.php?t=162171
Many a thanks to Socially Challenged for writing an excellent guide. I haven't used it yet (I still want to lose a little more weight), but I haven't heard anyone say something bad about it. And, I tremendously respect SC for his contributions in this forum!
Long answer:
While what you eat sounds reasonably healthy (assuming you meant 'looks' like an in and out burger, and not is an in and out burger), you don't mention how much you eat. Until you start running a calorie deficit, you won't lose weight. Running 3 miles is great, but it isn't clear if you are doing it twice a week or the situps, pullups, and pushups twice a week.
For me, I run 2 miles Tuesday - Friday mornings before work and run longer distances on Saturday and Sunday (from 5.4 to 13.2 miles). Now that the warmer weather is here, I'll likely cut out one run day on the weekend and ride or paddle instead. Doing all of that while eating decently had me looking decent. Now that I really started watching how much I eat, I'm starting to lose weight.
BTW: I don't know why you'd stop halfway in the middle of 3 miles to stretch / etc... Take a drink, sure. But, why stop for anything else? Stretch and 'work out' before or after. For me, running is running. Also, have you considered what your heart rate is? Simply put, for a male, take 220 and subtracting your age will give your maximum heart rate. There are a zones that correspond with what percentage of max your heart rate is. If you are running, you can track your HR and determine if the zone you are in meets your goals. Take a look at what these two websites have to say about what zones do what:
http://www.polar.com/us-en/training...ormance/running/polar_sport_zones_for_running
http://www.runningforfitness.org/calc/heart-rate-calculators/hrzone
You'll see some big differences in explanations, but my point is if you aren't elevating your heart to the right rate, you won't see the results that you want. Running while at %50-%59 is great for a warm up or cool down, but it won't get you the results that you are looking for. I'm going to add a link to what the AMA has to say about heart rates. Not the greatest for what we are talking about, but perhaps it is a good baseline to compare what others have to say:
http://www.heart.org/HEARTORG/Getti...ics/Target-Heart-Rates_UCM_434341_Article.jsp
I started checking my HR with my fingers on my neck. Then, I got a HR monitor watch (around $30 at Amazon). Now, I use my smartphone and an app called 'Sports-Tracker' along with a (Sports-Tracker) HR chest strap that I got from Radio Shack for $80. Certainly, it is easier for me to review post workout now. But, I also typically 'have-a-feel' of where I'm at now. So, don't be afraid to start with the cheapest method and work up to where you are comfortable.
Of course,
these are my opinions. Also, please consider, that what works well for me might not be the best for others. I read about a lot of people going to the gym here, people who run or ride don't seem to be as well represented. Be sure to check out the: 100,000 miles for AT thread. Sometimes it's just a posting of how many miles a person does in a day or week, but if you ask a question there, you are likely to get it answered by a runner.
I'm not saying that one type of person is better than another. But, I am saying sometimes one type of persons answer is better suited to a similar type of person.