This error in httpd error_log
[Wed Jul 12 21:39:57.069313 2017] [cgi:error] [pid 16811] [client 127.0.0.1:35330] AH01215: (13)Permission denied: exec of '/home/rupert/Sites/client1-www/cgi-bin/refnum.pl' failed:/home/rupert/Sites/client1-www/cgi-bin/refnum.pl
[Wed Jul 12 21:39:57.070405 2017] [cgi:error] [pid 16811] [client 127.0.0.1:35330] End of script output before headers: refnum.pl
This fix
sudo semanage fcontext -a -t httpd_sys_script_exec_t "/home/rupert/Sites/client1-www/cgi-bin(/.*)?"
sudo restorecon -Rv /home/rupert/Sites/client1-www/cgi-bin
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