Intellij get frozen after create a new gradle project in Intellij 3.3

Our plugin provide a wizard to create a prepared gradle project which has one thousand dependencies. After finished the wizard and during the indexing all the libraries intellij will get hang about 2min or more (depends on hardware) and take 50% cpu resources. 

https://drive.google.com/open?id=17UDd6_Gp2clBwkNyK9ZzIHLDC4FMqp8T   ---thread dump

This problems exist in our plugin after updating build version to 2018 3.3, but it was good at 2018 2.2.