OK, given that it is OS 10.11.1, you do have a couple of more choices regarding a more robust disk maintenance/repair programs.
First, again I ask if you have been making any backups at all, to an external device?
Secondly, there should be a Recovery Partition on your internal hard drive. This link tells how to boot to that partition, and what software it contains:
https://support.apple.com/en-us/HT201314
Note that one of the "pieces" it has is "
- Verify and repair connected drives using Disk Utility.
Hopefully, you can use that to verify and repair your primary partition on your internal drive containing the OS, applications, etc.
If that does not work, then you'll need to invest in something like TechTool Pro (
http://www.micromat.com), or Disk Warrior (
http://www.alsoft.com/DiskWarrior/). Either one can help you. I actually have both of them, and they do help me keep my drives "mean and clean". There is some instances where Disk Warrior is "better".