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Normally the NPCS and other lines are multiplexed wit a range of other pins to allow you to connect a custom set of devices to the processor without losing functionality. The three available pins for NPCS3 gives you a choice. Either 2 USARTS and the NPCS3 line or a USART, TWI and NPCS3 pin
Choose a pin that supports the NPCS3 as peripheral B (Note any errata) and the set of devices you want to use, connect your peripheral to the pin. Configure that specific pin, and only that one to be NPCS3 in your code.
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