ffmpeg -deinterlace -y -i in_movie.mkv -f matroska -acodec ac3 -ac 2 -ar 48000 -ab 128k -vcodec libx264 -level 41 -r 25 -coder 1 -g 250 -b 1024k -bt 1024k -bf 16 -threads 2 out_movie.mkv
There is also a couple of another interesting options like
-aspect : change aspect of movie to i. e. 4:3, 16:9 etc.