Site Down for few minutes after clearing cache My site is going down every time whenever I am clearing the cache. Site will works again in 5-10 minutes after refreshing web page 2-3 times.
Also I am getting 500 internal server error after clearing the cache. 
After refreshing web page 2-3 times site is working fine as before. 
Additional information as follow.


Drupal 7 
Boost
APC
Apache web server


Can any one put some light on above issue.

Edited

Apache error logs
[Tue Jul 07 08:51:12 2015] [warn] mod_fcgid: read data timeout in 40 seconds, referer: xxxxxxxxx.com 

[Tue Jul 07 08:51:12 2015] [error] [client xx.xx.xx.xx] Premature end of script headers: index.php, referer: xxxxxxxxx.com PHP Warning: Module 'apc' already loaded in Unknown on line 0 

[Tue Jul 07 08:51:18 2015] [warn] mod_fcgid: process 26541 graceful kill fail, sending SIGKILL PHP Warning: Module 'apc' already loaded in Unknown on line 0 PHP Warning: Module 'apc' already loaded in Unknown on line 0
Have you installed "Memcache" module ? If no then : 

First of all, check mysql slow query log. Also install "Memcache" module which will help you to reduce mysql server load.

Please refer this link for Drupal Memcache installation.