SMA ports

what is connected to ports pss, clk, gnss?

I connected a GPS antenna to the gnss. Can I also connect a GPS antenna to the pss and clk?

It would help if you said what hardware you were using.

You could, but it wouldn’t do any good. PPS is “Pulse Per Second”, and is used to synchronize the internal timing to a disciplined timing source like a rubidium standard. CLK is Clock, and is used to provide an external clock to ensure frequency and phase sync with other devices.

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LimeSDR XTRX Pcie. what is recommended to connect to these connectors to receive signals from the air?

If you mean the ports you mentioned, you do not connect anything to these to receive signals. Please see the documentation for details: