You need to add extra nginx directive (for ngx_http_proxy_module) in nginx.conf, e.g.:
proxy_read_timeout 300;
Basically the nginx proxy_read_timeout directive changes the proxy timeout, the FcgidIOTimeout is for scripts that are quiet too long, and FcgidBusyTimeout is for scripts that take too long to execute.
Also if you're using FastCGI application, increase these options as well:
FcgidBusyTimeout 300
FcgidIOTimeout 250
Then reload nginx and PHP5-FPM.
Plesk
In Plesk, you can add it in Web Server Settings under Additional nginx directives.
For FastCGI check in Web Server Settings under Additional directives for HTTP.
See: How to fix FastCGI timeout issues in Plesk?