Index.php无法访问私有文件

Question

I developed a php MVC framework from scratch and my index.php cannot access some files when I change the permissions. I use fillezilla and the only file permissions I can set are read, write and execute checkboxes for each group (owner, group and public). If I uncheck all the public ones then I get an error, but if I leave the public->execute box checked, index.php finds the files. I don't have public/private folder setting so is this setting ok or what should I do??