What to check first
Fret the problem string at the third fret and inspect the clearance above the first fret. Also make sure the string is seated correctly and that nothing at the tuner or nut is rattling.
What the result tells you
A nut slot that is too low usually needs repair or replacement rather than more filing. Filing a nut slot is one of those jobs where removing material is much easier than putting it back.
Write down the current measurement before changing anything.
Small, reversible adjustments are easier to understand and undo.
Stuck, stripped, lifted or structural parts are not routine setup territory.
Bench questions
Do I need to chase a factory number exactly?
No. Factory specs are useful baselines, but playing attack, string gauge, fret condition, radius and preference affect the setup that actually works.
Should I change more than one thing at once?
No. Make one measured change, retune, and test again so you know what caused the result.
When should I stop?
Stop if an adjustment is stuck, requires unusual force, hardware is stripped, a fret is visibly lifting, or the problem looks structural rather than setup-related.
Related setup guide
Guitar Fret Buzz Guide gives you the broader context for this problem.
Where to go next
If this check does not explain the symptom, don’t compensate by randomly changing another adjustment. Go back through the symptom diagnostician and follow the next branch.