I think I must learn it again and again. I watched many Youtube videos and understood all the basic upto es6 very well. and built about 5 simple project with tutorials. and know I am in Basic Algorithm Scripting of FCC. also I finished codeacademy javascript course and understood all subjects well. I am following Brad traversy and other best youtube channel and bought brad’s course from Udemy. but STEEL I cant make my simple own app that made with prototype, module, and other javascript subjects.
also I have a backgorund of ton of programming language from university like c++, java, c# , andriod,python. 
What should I do know?
also sorry if I had an English grammatical mistake
To start with, forget about using prototype. Build your simple app in a FOP (Functional Programming). It will simplify things for you.
Start with a simple todo app and move on to a more complex apps using APIs etc.
You only really learn by doing.
Well, I know what you mean its not the problem with your knowledge. Software Engineering is like any other engineering which needs a Blue Print or Plan of Action so that the people can divide the problem/work accordingly in small units.
This is the most basic sample there’s more to it, but you can use this one to your personal projects as well:
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Open Notebook or any Digital Paper
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Sketch your app (optional)
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Write Down All Functionality
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Database (if any)
You can use this simple and powerful approach to divide your work into smaller units so rather than focusing on the bigger problem (whole website) at once you can concentrate much better on one problem at a time. This will also improves your problem solving ability and you can ask more precise questions related to your problem.
I hope it helps you.