This file contains the input and output files of MDFF for each case
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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
dom_definition.txt---------the domain definition, which should be assigned into the initial model
                           before running the domain rigid-body assembly
map.mrc--------------------cryo-EM density map
						   
output_X-------------------includes the following data generated by using the weight(scaling
fator) X of the potential derived from the cryo-EM density map for the final energy minimization, 
where X=0,1,2,4,5,6,8,10:		   
	MDFF_final.pdb-------------the final model refined by MDFF
	molprobity.score-----------the Molprobity score of the final model refined by MDFF  
	adk-step3.namd.log---------the log file of the third step of the final energy minimization of
							   the MDFF flexible refinement

output_MD_only-------------includes the model generated by MDFF without using the final energy
						   minimization
	
record---------------------includes all intermediate files and lof files generated by MDFF:
	domain_seg.pdb-------------the initial model with domain definition assigned in PDB
	domain.pdb-----------------the domain information for TMD
	domain*--------------------the files for the MDFF domain rigid-body assembly
	initial_model_MD_rig.pdb---the model generated by the MDFF domain rigid-body assembly
	initial_model_MD_rig*------the files for the MDFF flexible rigid-body assembly
	adk*-----------------------the files generated by NAMD during the MDFF flexible rigid-body assembly
	*.mdff---------------------the VMD commands for the file preparation
	*.namd---------------------the NAMD commands to run MDFF
	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
							   
	The following log files are included in the folder for cases with resolution <5A 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 following
   the NAMD commands at https://zhanggroup.org/DEMO-EM/data_set/benchmark51/MDFF/.
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 to define the domain 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, "1-190,375-524;191-374;" in the 
   domain definition of 2c7cC means that the first domain is a discontinuous domain, where residue
   1 to residue 190 belong to the first segment and residue 375 to residue 524 belong to the 
   second segment. "191-374" indicates that the second domain is a continuous domain which covers
   residues from 191 to 374.
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