If you get to the end and reform your government type, I think.

If you dig deep into the files you can see which idea group pairs are needed to get rid of the negative modifiers. Considering how there's literally no other way to find out except reading the files itself, I'd say that that's something of a spoiler so I won't post the needed ones here. Although pro-tip: the celestial reforms get rid of 2 of the 5 maluses so you only have to worry about getting rid of the other 3 with idea groups. Also, reforming your government is not needed, just the idea groups.

The idea groups pairs that are need to get rid of each negative modifier can be found in the triggered modifiers