No problem. The nut slot should be "U" not "V" in shape. The string should fit comfortably in the bottom of the slot and tune smoothly without binding or grabbing.
Witness points: The string needs a clean break as it passes over the nut and bridge saddle. This is pretty much what sets / delineates the true speaking path of the vibrating string. Strings, especially the larger diameter E & B, are particularly resistant to this notion and, left to themselves, have the tendency to form a "lazy loop" as they pass over the nut and bridge saddle...not good. Here's what you do:
*Once tuned to pitch, take your thumb and
forcibly depress the string downward just on the fretboard side of the nut. This will create a clean bend or break as the string leaves the nut en route to the bridge.
*Repeat the procedure with each string at the bridge, pushing down on the fretboard side of each saddle.
If done properly, 3 things will occur: (1) tuning will probably be flat, (2) string height will be lower, (3) intonation will be off. Re-adjust as necessary to bring back into spec. Of course, we're also hoping the rattle is gone.
Edit: just saw the nut slot / string reference. Once you've set your witness points as above, check the nut slot depth. Here's a quick "cheater" method:
*Depress the string directly onto the 3rd fret with your left hand thumb.
*Now, with your right hand index finger, tap the string quickly directly above the 1st fret.
*You should hear a distinctive "ping" as the string hits the 1st fret and bounces back. If all you get is a "thud", you've got a problem.
Riis