I’ve was playing with EasyApache in a WHM install recently and after the upgrade I came across a strange error:

SoftException in Application.cpp:357: UID of script "/home/mysite/public_html/index.php" is smaller than min_uid
Premature end of script headers: index.php

Turns out this error is caused by apache being unable to read files added by root to a users public_html folder. A simple fix for this problem is to

chown -R mysite:mysite /home/mysite/public_html

If you’re still having permissions issues aver doing the above, try chmod:

chmod -R 755 /home/mysite/public_html

Thanks to user ronniev of eukhost forums for his solution here.