The XEM3010 user’s manual does not list connections for JP4 on BRK3010.
I am trying to monitor the PLL clk at 48Mhz. The tables cover JP1, JP2 and JP3.

If the documentation is not clear, perhaps you could look at the schematics which are posted in the Software Downloads Forum. You can also physically trace the wires on the two layers of the BRK3010 to see where they go.