Apache has a default timeout of 60 seconds, you can increase it by creating a custom template in cwp.
Follow this basic steps to increase the php timeout when using php-fpm :

Copy the default templates and save/create it as timeout tpl and stpl:

cd /usr/local/cwpsrv/htdocs/resources/conf/web_servers/vhosts/httpd/php-fpm/
cp default.stpl timeout.stpl
cp default.tpl timeout.tpl

Now you need to edit the both templates "timeout.tpl" and "timeout.stpl" and add this line:

ProxyTimeout 90


<IfModule proxy_fcgi_module>

and save it.

** ProxyTimeout 90 is the limit that allows the script to run for 90 seconds before it gets hit with the timeout threshold.
Increase it according to your needs, please don't use too high numbers to avoid server overloads.

eg :

<IfModule proxy_fcgi_module>
    ProxyTimeout 90
    <FilesMatch \.php$>
        SetHandler "proxy:%backend_fcgi%|fcgi://localhost"

Now all you need is to create a custom configuration under webserver domain config and select the template or choose this template as a default in the webserver main config.

More info about the custom templates can be found here.