usage:  New single particle refinement routine. Still under construction. For simple usage,
	e2spa_refine.py --ptcl <particle list file> --ref <reference map> --res <inital resoution>

Option Type Description
--version None show program's version number and exit
--ptcl str Input particle stack.
--ref str Reference map. This will be scaled/clipped to match the particles automatically.
--path str Path for refinement output files. default is r3d_xx
--parallel str Run in parallel, specify type:<option>=<value>:<option>=<value>.
--sym str sym
--res float The resolution that reference map is lowpass filtered to (with phase randomization) at the begining of the refinement.
--keep float Fraction of best particles to keep in each iteration.
--niter int Number of iterations. Default is 10.
--startiter int Start from a specified iteration in an existing refinement
--setsf str Text file containing structure factor for map sharpening. Can be produced during CTF estimation, or from an existing high resolution map.
--tophat str Options for filtering maps. Run 'e2help.py tophat' for more information. Default=local.
--threads int Threads to use during postprocessing of 3d volumes
--mask str Specify a mask file for each iteration of refinement. Otherwise will generate mask automatically.
--compressbits int Bits to keep when writing images. 4 generally safe for raw data. 0-> true lossless (floating point). Default 6
--localsize float Override the automatic local region size (in A) used for local resolution calculation and filtration.
--m3dthread None do make3d in threading mode with shared memory. safer for large boxes
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness