Keep in mind that I rarely go into third-fourth phase of the diet.
Before I ever started Atkins: (About 198lbs 34in waist/44reg suit jacket/bench 225lb 5 sets/5 reps) I got on the diet and went exactly how the website said to do the diet. I had 20g of carbs and I didn't think about the other calories or protein. I had no energy and didn't go to the gym the whole two weeks
After the two week period: (181lbs/32in waist/42reg/bench 180lbs 5 sets/5 reps) I lost weight yes, but my muscle suffered tremendously. I was lean though. Not magazine quality but when I lifted you could see the difference.
Layed off dieting. Got back up to 190 again.
For the past month I've been doing Atkins. Start
195lbs/34in waist/44reg/225lbs 5 sets/5 reps) Did it the websites way again but this time I lifted. No energy but, I pushed through it. Did that for two weeks. Got down to (189lbs/34in waist/44reg/same bench)
For the past two weeks, I've just been making sure to keep my carb intake at a mininum with complex carbs, but I included lots of protein from shakes and food about 150-190 daily, plus creatine. I lift in moderation everyday. By moderation I mean i lift with 75% of my max for reps. Just yesterday I'm now (193/33waist/44reg/225lbs 3 sets of 10 reps)
I'm pretty happy. I think I've found what works for me. I keep it low carb but, when I need an energy boost or I just get sick of eggs and bacon. I grab some whole wheat toast. I make sure I get my cardio (not much at all but, I get it) Last week I did some sprints in the field, that was hard! But for the most part I like treating my workouts with Aerobic and anaerobic excercises together, that's why I do reps with 225lbs.