Hello @Vtrai
X2 to be used with HSE
X3 to be used with LSE
In crystal mode SB13 and SB14 must be not fitted because PH0 and PH1 are used as in and out for the oscillator.
Otherwise if PH0 and PH1 are use as GPIO instead of clock, SB13 and SB14 must be closed and R24, R25 and R68 must be removed and you can visualize those signals on connector P2
For more details please refer to the User manual Discovery kit with STM32F407VG MCU UM1472 and the schematic of STM32F407VG Discovery MB997.
Best regards
Bouraoui
