You also need to solder the additional 4 pin header to access all 7 PB i/o pins. D7 has PWM! (other not connected pins with a timer as well). The 16u2 pinout is the same for Arduino Uno/Mega. Keep in ...

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 ISP header of the 16u2 is flipped 180 ...