In stock 3.9 code there is no /usr/ directory nor subdir of profile ... and the rest shown. Plugin?
If a plugin, directions for upgrading say to *copy* not only config.php file from the archived (older) code folder, but also any add-on folder ... from it's location in the archive to the same location in new code. That's *copy* not move. Remember to get the folders and all the contents of those folders copied.
Please verify you have done that.
Some additions to config.php you could add:
turns off maintenance mode.
If you needed it back on ... change 0 to 1
or when you don't need it at all, put // in front of that line.
How about your theme? Is it boost?
If not, force to use boost via config.php file:
Same with commenting out, etc. as maint suggestions above.
Unfortunately, there is no tool to list all additional plugins if one cannot login as admin. There is a query of DB you could run showing all plugins, however:
select id,plugin,name from mdl_config_plugins;
will produce a long list of not only core but addon plugins.