21.3.3.4.5 Port Override for Waveform Generation
To make the waveform generation available on the port pins, the corresponding port pin direction must be set as output (PORTx.DIR[n]=1). The TCA will override the port pin values when the compare channel is enabled (CMPnEN=1 in TCAn.CTRLB) and a Waveform Generation mode is selected.
The figure below shows the port override for TCA. The timer/counter compare channel will override the port pin output value (OUT) on the corresponding port pin. Enabling inverted I/O on the port pin (INVEN=1 in PORT.PINn) inverts the corresponding WG output.