The ZIF socket on STK503 takes AVRs in 100-pin TQFP packages.
To use STK500 and 100-pin AVR devices with LCD controller such as the ATmega3290 and ATmega6490, you must use the STK504 top module, not the STK503.
Make sure the STK500 power is switched off.
Make sure that the STK503 is properly mounted on the STK500. See Mounting the STK503 for more details.
Place the AVR in the ZIF socket. Pay attention to the pin 1 marking on the device and on the ZIF socket and PCB.