How to use more particles via Flex reconstruct

I am trying the 3D flex for our dynamic protein and I am satisfied with the model which it generated. The refinement is also working fine, but I want to do it with more particles (currently 100000) to improve resolution even better. I prepared the particles (300000) but the 3D flex reconstruct gives the “Job is unresponsive - no heartbeat received in 30 seconds.” error. Are there any solutions for this issue?
Thanks for the help in advance