Cleaning:
Run a wet (CLP) patch down the barrel, let it soak while you clean and relube the lower.
Run the brush (with a little CLP dripped on it) through from the chamber end, not the muzzle, when the brush emerges from the muzzle, unscrew the brush and pull the rod back out. Repeat 5 or 6 times.
DO clean the chamber and locking lugs with the M16 brush. I mount the brush on a few rod sections, chuck up in my cordless Black and Decker, and hit each chamber a few seconds.
Let sit while you clean the bolt carrier.
Hose out the chamber/barrel extension with Gun scrubber.
Run 4 dry patches through the barrel.
That's enough.
Trying to get a barrel perfectly clean, patches come out perfectly clean, is a waste of time and totally unnecessary. Excessive brushing of the barrel is also unnecessary.
If the rifle is to be put away now, run one oily patch through the bore, wipe it around in the chamber, too. Before you shoot, run a dry patch in the chamber and bore.
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Barrel breakin:
Clean the barrel before going to the range for the first time. In fact, clean the entire rifle, lube it well. You never know what may be in the bore from mfg and shipping.
Shoot 200-300 rounds.
Go home. Clean rifle as per above.
It's broke in.
No, I don't do the shoot, clean shoot clean, shoot 3, clean, etc.