A single ad used for a “big amount of keywords” is the wrong approach for a Search campaign. You need to start with many tightly focused ad groups. Each ad group should have a tightly focused topical theme and contain ads written for that specific topical theme.
To recap, you need many ad groups, and many ads each tailored for the specific keywords within the ad group, for a “big amount of keywords”. Each ad group needs to contain at least 2 ads, each written to test a different selling point for that ad group.
Nothing in your post indicates that you made an attempt to normalize your data. CTR will vary a great deal based on ad position, so you must compare CTR based on a consistent ad position to determine if it is relatively high, or relatively low. Was that done?
One of the most significant influences on CTR is the quality and relevancy of your ad text for the search term that triggered your ad. The method you describe to narrow your keywords seems to indicates this was not tested in any way, therefore I would suggest that your keyword selection decisions were likely flawed. I suspect there are many opportunities to optimize the performance of each keyword by testing various ad text using highly specific ad text and significantly different selling points.
Now, this is crucial to understanding how to manage a PPC campaign, so pay particular attention to what I am about to share. It isn’t keywords that you should be narrowing your focus on, it is search terms.
Search terms are not the same thing as a keyword. a keyword has the capacity to trigger ad impressions for many different search terms. Some of those search terms may be very profitable, while others are not. How you structure your account has a lot to do with which search term will be matched to a particular ad, and it is the relevancy of the ad to the search term (not keyword), and the commercial intent behind that search term that impacts CTR, and conversions. When narrowing your focus, forget keyword data, use search term data instead. The Search terms report is your friend.