If you want to check, if it is caused by your custom theme, just delete the custom theme folder in atom/plugins and retry.
Reading the log, it seems as if /home/user is your AtoM-folder!?
That differs much from the installation guide where /usr/share/nginx/atom is proposed.
And changing the theme should primarily mean "create a new custom theme" - it is separated as aPlugin and based on the DominionB5ThemePlugin and far better to debug.
And no, you do not need to install developer files from the beginning.
Do a normal installation, test the success and then create your custom plugin from the documented template.
Regards,
-Hans-Arno