Can I Erase Macintosh HD partition?
Apple recommends an erase install when you need to start fresh. If you have all data backed up, this happens when you boot to Recovery HD or internet Recovery:


https://support.apple.com/en-us/HT204904


Step 3 covers the erase install to get the latest software possible:


Hold Option-Command-R at start
Release the keys when you see the Apple logo or a spinning globe
Choose to erase: https://support.apple.com/en-us/HT204904#erase


You'll be in the erase since Disk Utility can't fix things. You will lose any partition data, EFI customizations, recovery HD when you erase and the installer will put things right again and drop the OS and an installer log that you can review in case there are still hardware or other errors.