Yes, unfortunately the database file is damaged.
Jun 04, 2018 10:21:27.119 [0x700001177000] ERROR - SQLITE3:0x7000006b7590, 11, database corruption at line 59739 of [fc49f556e4]
Jun 04, 2018 10:21:27.119 [0x700001177000] ERROR - SQLITE3:0x7000006b7590, 11, statement aborts at 83: [select distinct media_items.id as 'media_items_id', media_items.library_section_id as 'media_items_library_section_id', media_items.section_location_id as 'media_items_section_location
Jun 04, 2018 10:21:27.123 [0x700001177000] ERROR - Soci Exception handled: sqlite3_statement_backend::loadRS: database disk image is malformed
Are you comfortable with the terminal?
The repair procedure involves copy&paste’ing several commands.
Make sure you quit/exit your Plex Media Server so that it is not running. The following commands are run in the Terminal application. When running the commands, you need to escape any spaces in paths.
##1) First, simply switch over to the directory containing the database.
cd ~/Library/Application Support/Plex Media Server/Plug-in Support/Databases/
##2) Remove a certain index table which will otherwise cause the integrity check to abort.
sqlite3 com.plexapp.plugins.library.db "DROP index 'index_title_sort_naturalsort'"
sqlite3 com.plexapp.plugins.library.db "DELETE from schema_migrations where version='20180501000000'"
It is of utmost importance, that the above commands are copied exactly as written, because they alter the database directly.
##3) Now run the integrity check
sqlite3 com.plexapp.plugins.library.db "PRAGMA integrity_check"
And then attempt repair
##4) export the DB to SQL file:
sqlite3 com.plexapp.plugins.library.db .dump > dump.sql
##5) Now rename the original, corrupted DB file
mv com.plexapp.plugins.library.db com.plexapp.plugins.library.db.original
##6) reimport the SQL dump back into a new DB file:
sqlite3 com.plexapp.plugins.library.db < dump.sql
##7) Run another check to establish if repair was successful
sqlite3 com.plexapp.plugins.library.db "PRAGMA integrity_check"
If the last check was successful, you can now start Plex Server again.