Notice CP141R tell you that the IRS has "Removed your penalty charge" and that you don't need to do anything.
Notice CP210 (pictured above) shows how much the penalty was and how much the decrease in the penalty was. Generally the IRS only has the authority to completely remove a late-filing penalty for Form 990. It does not technically have the authority to reduce the penalty, unless you can show that it was calculated incorrectly.
If your nonprofit organization is facing an IRS penalty, contact me. I can help.