Programming STM32F407 discovery by the ST-Link V2
I managed to solve that problem. If anybody encounters similar problem, here's what I've done:

According to the ST-LINK V2 User manual , the needed but not enough connections between ST-LINK V2 and MCU is as below:

SWDIO -> PA13

SWDCLK-> PA14

GND   -> GND

VAPP(target VCC) -> MCU VDD

User manual  also recommends to connect all the GND pins on the ST-LINK V2 to the ground and the problem is actaully here. User manual must emphasize that  you must connect all the ST-Link GND pins to the ground for properly connection. And then all the connection frequencies will be available and also target will be detected and could be connected.