How do I erase/Reformat a disk in a Mac Pro 3.1

Mac Pro 3.1
OS 10.9.4
Four 500 GB drives
Whenever I use iPhoto and File Maker together (Latest versions on both), I encounter starting problems the next day). I usually reboot from the Recovery drive and use First Aid. This is good for a couple of weeks.
This morning I could not start the system located in HD1, so I used the Recovery drive and I tried First Aid with no success.
I downloaded a new system (10.9.4) and installed it on HD4.
I tried again to repair HD1 and I got a message indicating that HD1 could not be repaired.
I can't isolate HD1 to reformat it probably because the older system (10.9.4) still there.
How do erase HD1? I am very grateful for any help you can assist me with.

Any version of Disk Utility will attempt to Repair any disk with any data on it, EXCEPT: You cannot Repair the Volume where the currently-running Mac OS X is located, since the repair might change data Mac OS X is actively using, and cause a loss of integrity or worse yet, a crash.
There is NO restriction of what Volumes can be Repaired based on Mac OS X versions. (Example: the Disk Utility on the 10.6 Installer/Utilities DVD can repair Volumes that have Mac OS X 10.9.4 installed on them.)
If Any version of Disk Utility tells you a Volume cannot be repaired, you should believe that assessment. What you should NOT do, especially on a Mac that supports multiple drives, is follow their recommendation to erase that drive to return it to bootabliity. That advice is based on the old assumption that the Drive (in working condition) is the prize. Today, drives are really cheap, and any of YOUR data (not the 350,000 files of Mac OS X) that can be recovered is much more valuable than a sub-US$100 drive.

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How do I erase/Reformat a disk in a Mac Pro 3.1

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