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We are checking intonation now.

Place your finger on the 12th fret and repluck the string.
I actually prefer a petersons tuner when doing intonation as its very sensitive.
As the fretted note is flatter than the open string, the distance between the 12th fret and the saddle needs to be reduced, this will make the fretted note sharper.
Here the saddle has been wound forward
Check the open string and the fretted 12th again and repeat adjustments until we have a correctly intonated string.
Like so.
Repeat for all string positions.
Then we test play the instrument and check every fretted position for buz..
Check all strings
Recheck open string tune
The note is flat as per the tuner.
P3
With our radius gauge of 12, which we identified earlier as the radius of the fretboard, we use our paper and check for drag of each string.

If drag does not exist then you willl need to file the string slots so the saddle shape match's the fingerboard shape
"How To" Basic Guitar Setup
After playing every fretted position we play a few tunes / chords / songs and so forth

It is from here we then tweak our height / relief to suit how the guitar responds under our fingers.