The following data for each target is included in an independent folder:

initial_model.pdb----------the starting model created through Situs by superposing each domain
                           into the density map
MDFF_final.pdb-------------the final model refined by MDFF
dom_definition.txt---------the domain definition, which should be assigned into the initial model
                           before running the domain rigid-body assembly
map.mrc--------------------the cryo-EM density map
map_resolution.txt---------the resolution of the density map
domain-step1_new.namd.log--the log file of the MDFF domain rigid-body assembly
adk-step1.namd.log---------the log file of the first step of the MDFF flexible refinement using 
						   the original density map
adk-step2.namd.log---------the log file of the second step of the MDFF flexible refinement using
                           the original density map
adk-step3.namd.log---------the log file of the third step of the MDFF flexible refinement using
                           the original density map


The following log files are included in the folder for cases with resolution <5Å because cMDFF
is employed:

adk-step1.namd.logN--------the log file of the first step of the MDFF flexible refinement using 
                           the N-th Gaussian blurred density map
adk-step2.namd.logN--------the log file of the second step of the MDFF flexible refinement using
                           the N-th Gaussian blurred density map
adk-step3.namd.logN--------the log file of the third step of the MDFF flexible refinement using
                           the N-th Gaussian blurred density map
Here, N=1,2,3,4,5, which corresponds to the half-width of 5, 4, 3, 2, 1, respectively.


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NOTE: 
1. Please remember to run the domain rigid-body assembly and flexible refinement in order.
2. The domain definition should be assigned to the starting model "initial_model.pdb" before
   running the domain rigid-body assembly of MDFF. The method for the domain assignment can be 
   found in the MDFF tutorial.
3. In the domain definition file, domains are separated by semicolons, while segments of a 
   discontinuous domain are separated by commas. For example, "1-104" in the domain definition
   of 2piaA means that residue 1 to residue 104 belong to the first domain. "1-100,496-521" 
   in the domain definition of 6nr9A means that the first domain is a discontinuous domain, 
   where residue 1 to residue 100 belong to the first segment, and residue 496 to residue 521 
   belong to the second segment.
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