Hello Sina--

> In the tutorial there is a command which do the refining for gb1.
> xplor -smp 2 -py -o refine.out refine.py
> What are smp 2 and o here?

-smp 2 specifies that the calculation will run on two cores of the
computer.

-o filename specifies the name of the output (log) filename. If run on
 more than one core, additional output files will be written to
 filename.1,  filename.2 ...

You can get full help by running

   xplor -h

> if I want to refine some other protein what should I do?
> 

Specific a different python input file.

best regards--
Charles
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