So, I defretted a bass a few weeks ago. It is an ESP LTD B-50. The defret went well and looks great, but I am having trouble intonating it properly. At the 12th fret, the harmonic and fretted notes are very close. However, notes at the 5th fret are all noticeably flat. Tuning this bass with the 5th fret and next open string method is impossible. I have a feeling that it has something to do with the nut. I filed the slots down during the defret process, but I don't know if I went far enough. Also, the neck is almost completely straight and I am using 40-100 DR Hi-Beams, if that matters. The notes around the 5th fret ARE between the lines, they are just very close to the next, higher fret. It appears to me as though the strings are having to travel too far to reach the fretboard, thus making them flat. I thought I would consult the ever-helpful TB before digging into the nut again, just to be certain. Does anyone know if I am on the right track? All opinions and advice are welcome. Thanks.