Your E3DV6 hotend is incorrectly located in the extruder body. It is too low down which means your PINDA is also way too low. This will cause failure to calibrate and at some point it will crash and probably damage your printer. Do not use it until this is corrected.
Strip your extruder down until you can redo the instructions from http://manual.prusa3d.com/Guide/5.+E-ax ... 10?lang=en
Step 17 and pay particular attention to all of the photos in step 17, 18, 19 to get the hotend seated correctly.
You're not the first to have this issue so don't worry, just take your time with the assembly and make 100% sure your work is identical to the photos. Good luck!