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My KitProg is from CY8CKIT-043 but at least pins used were same with the KitProg of CY8CKIT-059.
The last 2 pins are optional, but if you connect them, you can use USB-SERIAL function of the KitProg, too.
After connecting these pins, you (or I?) can just create a project for CY8C4245AXI-483 (the PSoC on CY8CKIT-049)
and build/debug via KitProg.