There can be different reasons for this issue. The best way to figure out the issue is "check your webserver log" which will be "/var/logs/[apache or nginx]/[the log file name configured in virtual host]".
In this case, the error message is:
FastCGI sent in stderr: "PHP message: PHP Fatal error: Call to undefined function apc_clear_cache() in /path/app/code/community/Buric/Apc/Model/Observer.php on line 13" while reading response header from upstream, client: 93.106.222.157, server: www.mydomain.com, request: "GET /index.php/admin/cache/flushSystem/key/a2a654d657aafaa937e8acdfba5540af/ HTTP/1.1", upstream: "fastcgi://127.0.0.1:9000", host: "mydomain", referrer:
Means, the magento plugin Buric_Apc is unable to perform the apc cache flush which is because, the APC module is not enabled in php or not installed on server
index.php
file will be there, take backup of that file & uncommnet this lineini_set('display_errors', 1);
and check what error its showing after that..... also please check var/logs folder errors