is_continue == false
Output rootname: == Refine3D/good1
Continue from here:  == Refine3D/run1_it012_optimiser.star
Input images STAR file: == particles_subtomo_good.star
Use parallel disc I/O? == Yes
Reference map: == Refine3D/run1_class001.mrc
Ref. map is on absolute greyscale? == Yes
Initial low-pass filter (A): == 40
Symmetry: == C1
Do CTF-correction? == Yes
Has reference been CTF-corrected? == Yes
Have data been phase-flipped? == No
Ignore CTFs until first peak? == No
Mask individual particles with zeros? == Yes
Reference mask (optional): == 
Initial angular sampling: == 15 degrees
Initial offset range (pix): == 8
Initial offset step (pix): == 2
Local searches from auto-sampling: == 3.7 degrees
Realign movie frames? == No
Input movie frames STAR file: == 
Running average window: == 5
Stddev on the translations (pix): == 1
Also include rotational searches? == No
Stddev on the rotations (deg): == 1
Number of MPI procs: == 24
Number of threads: == 6
Available RAM (in Gb) per thread: == 3
Submit to queue? == Yes
Queue name:  == openmpi
Queue submit command: == qsub
Standard submission script: == /public/EM/RELION/relion-prerelease/bin/qsub.csh
Additional arguments: ==