After five minutes, you need to purify the mouth and rim of the bottle (which touched the original water source and which will touch your mouth). To do this, you need to "thread" the bottle. Turn the bottle upside down and slowly unscrew the top until you can see a ring of water appear around the inner rim. Once you see that ring of water, you know that the water with the iodine has touched the mouth of the bottle and disinfected it. Screw the top back on and flip the bottle right-side up.
A little water will probably leak out while threading, and that's not bad--it just ensures that you've fully threaded.