Note: Some pins are not connected on a standard Arduino Uno R3 but still listed so you can use them if you had a custom board. It might also be possible that your ICSP header of the 16u2 is flipped ...

The 16u2 pinout is the same for Arduino Uno/Mega. Keep in mind that the Leds have inverted logic. Writing LOW means turn them on. 16u2 Pinout [NC] = Not connected on an Arduino Uno/Mega R3 D0 - [NC] ...