On my SRAM road brakes, if the throw of the lever is more than the adjustment can handle, I’ll remove the wheel and keep squeezing the levers until the pads almost touch. Then I use the SRAM spacing tool to spread them back out to the proper gap. This is straight out of the SRAM manual. I assume Shimano would be the same. You may have to spread the pads a bit more than the spacer spreads them if you have brake rub.