Remove all partitions and reinstall MacOS
You have shown no evidence the internal drive is 3 TB in size. Assuming you are correct, then proceed as follows. 


Boot to the USB Sierra installer.
From the menu bar select to open a Terminal Window.
Enter the command given below.

diskutil partitiondisk disk0 1 gpt jhfs+ "Macintosh HD" R

Quit the Terminal application.
Install Sierra.



  Note: The drives shown as disk images are just temporary drives created when you booted from the USB installer. This also occurs when you boot to a recovery volume or from internet recovery. The disk images are not stored on your internal drive.