This file contains the input and output files of MDFF for each case ************************************************************** 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. ************************************************************** 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. **************************************************************