There are two things your son needs right now; Love and Validation. Love – The first step is to show him (not just tell) that your love for him is unconditional. You must show him that even if he chooses this path in life he always has a warm home to come to.
Validation – Somewhere in the last couple of years your son must have felt very little self worth living a Torah life-style. If he was happy with himself this usually does not happen. Therefore, before he takes any further steps down this road try to validate parts of his life right now. Example: if he listens to certain music, instead of asking “why are you listening to such shmutz?” surprise him by picking up the headphones and saying “this song is pretty good”… eventually that feeling of validation often leads to positive improvements in the future.
As for you… PLEASE have patience, I happen to be a highschool Rebbe and have seen this scenario many times before. 16 is a very immature age. As long as he can see the positive in Yiddishkeit then he has a very good chance of coming back in a couple of years.
In conclusion: It will be extremely tough for you to watch your son doing certain things, yet, if you stay calm, just show him love, validate anything you can of his newly acquired lifestyle(obviously nothing that is clearly against the Torah) and have patience, things should eventually work out.
Hatzlocha Rabbah!