How to repair the system disk:

Choose Volumes > Repair Disk.
If your disk is reporting any problems about its volumes or data, or if any of your applications aren’t working or exhibiting problems, try repairing the disk.
The repairs include, among others, the partition map layout, the EFI System Partition, Core Storage Physical Volume partitions and the boot loaders.
Choose Volumes > Repair Disk.
Note: Repair Disk is also called “First Aid” on Mac OS X 10.11 El Capitan and later.