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Recently, a lot of pages from our website have moved from page one or ranking number one, to page ten or something. We got a manual penalty message from Google Team, we removed a lot of unnatural links pointing to our pages and disavowed the rest. This got the penalty removed and we got a message from Google confirming the same. Before the manual penalty we were getting about 140,000 visits per day, after the penalty about 80,000. However, after Hummingbird or Penguin 2.1 all our ranks have vanished. We are nowhere in Google for our primary keywords and we getting like 40,000 visits per day. Most are direct or from sources other than Google. We had another look at the links we disavowed, a list of about 11000 domains, we found about 3000 domains to be good. We fixed the disavow file about one week back, but no changes in traffic since. We checking the domains again to see if we have missed more good domains in there; yes, we have. There are still a very few good domains in there. But we are not touching the disavow list; waiting to see the change for the last submitted. We have a dedicated user base, good liking on Facebook, all the stats in Analytics speak good, about 40% repeat visits about 30% direct. About 3000 people search for the site using our brand name as reported in Analytics. I doubt the on-page optimization, the pages could be over-optimized. But the on-page factors for other pages ranking for the keywords are similar. The keyword density is similar, so are the usage of headings and stuff. We have not made any recent changes to these on-page patterns. Our team is not able to figure out what could have gone wrong.