It seems that the df is indeed showing that the /usr 90% full.
You can run "du -kh --max-depth=1 /usr" to check the directories under it that has taken most space then try this on the directory that has taken more space to indentiy the directory or the files that have taken the most space.
Possibly the apche domlogs have taken away most spaces.
Already did that and none of the directorys or sub directorys are big. There are only 2 domains on this server and the total /usr/local/apache path including domlogs is only 458 meg. Verified also by going to each directory and doing a ls -lah