NOTE: The program Gctf-v1.18_b2 is a branched version of GCTF-1.18. It is essentially the same as version 1.18, a simplified version without several advanced features, such as local/movie CTF refinement, CTF validation etc. It works on micrograph-level CTF estimation, EquiPhase Averaging (EPA) and Phase plate data in general cases. Use this as a starting command for further optimization: Gctf-v1.18_sm_30_cu7.5_x86_64 --apix 1.04 --cosearch_refine_ps --refine_2d_T 1 --overlap 0.8 --do_EPA --smooth_resL 20 --phase_shift_S 3