The best and easy way to install OS Sierra on a 2009 Mac Pro(MacPro4,1) problem-free is to clone any of your machines that is already running OS Sierra on external Hard Drive or SSD using a software called Super Duper.
You can use your MBPro, iMac, MBAir, Mac mini...(they must already running Sierra, mind you)
Then connect your cloned external HD or SSD to your 2009 Mac Pro and boot from it.
To boot from the external HD or SSD without rolling a dice, just press and hold down the OPTION key on your keyboard the moment you fire up your Mac Pro. Few seconds later, your machine will display all bootable Hard Disks, You should select the Hard Disk with yellow color, which is the external HD that you already cloned.
The next step is for you to utilize Disk Utility to format your internal HD you want to clone.
Lastly, you simply clone the HD using Super Duper software( you can download the unregistered copy of Super Duper for free). Watch how to use Super Duper on YouTube, very easy. A 6-yr-old can use it to clone stuff.
When done cloning, just shut down the machine, remove the external HD and restart the machine.
Your 2009 Mac Pro is now ready to run Sierra with no issues.