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The intonation on the 6th (E) string is too sharp across all frets including the 12 fret.
However, I can't flatten the string by adjusting the intonation screw as that screw is stopped out. What can I do?
https://i.ibb.co/K5td0XK/IMG20230627101622.jpg
Fix the nut. Lower the pickups too, they're way up there.
Is this a new build?
Has the intonation always been good, but suddenly it's out now.
What happened?
Have you changed tuners? Nut? Neck? Bridge?
More info needed...
If this is a new issue with a new set of strings and nothing else has been changed, it could be a bad string. They happen.
If it's an ongoing issue and everything the previous posters recommended all check out, then I'd cut that spring shorter.
Cut the spring in half
Dead Thread...
This could even be a case of using the neck pickup. Many Strats and Teles are far more difficult to tune because the neck pickup sits right on the harmonic node.
Switch to the bridge pickup and it all becomes easier.