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This page contains the input and output files of MDFF for each of the test targets.

Steps to run MDFF:

1. 1. Generate the "*.psf", "*.dx", "*grid.pdb" and other files and assign the domain definition to the starting model using VMD based on the starting model and the cryo-EM density map (see MDFF tutorial )
   

2. 2. Run the following command to perform the MDFF domain rigid-body assembly:
   
   mdff setup -o domain -psf xxx.psf
      -pdb xxx.pdb
      -griddx xxx.dx
      -gridpdb xxx-grid.pdb
      -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
      -gscale 1.0
      -minsteps 2000
      -numsteps 200000
   

3. 3. After the rigid-body assembly, run the following command to perform the MDFF flexible refinement:
   
   mdff setup -o adk -psf xxx_autopsf.psf
      -pdb xxx_autopsf.pdb
      -griddx xxx_autopsf-grid.dx
      -gridpdb xxx_autopsf-grid.pdb
      -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
      -gscale 1.0
      -minsteps 2000
      -numsteps 500000
   

   mdff setup -o adk -psf xxx_autopsf.psf
      -pdb xxx_autopsf.pdb
      -griddx xxx_autopsf-grid.dx
      -gridpdb xxx_autopsf-grid.pdb
      -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
      -gscale 0.3
      -minsteps 2000
      -numsteps 500000
      -step 2
   

   mdff setup -o adk -psf xxx_autopsf.psf     ← last step for the final energy minimization
      -pdb xxx_autopsf.pdb
      -griddx xxx_autopsf-grid.dx
      -gridpdb xxx_autopsf-grid.pdb
      -extrab {xxx-extrabonds.txt xxx-extrabonds-cispt.txt xxx-extrabonds-chaira.txt}
      -gscale 10     ← ξ in following tables is set for here
      -minsteps 2000
      -numsteps 0
      -step 3
   

   where "-numsteps" of the first two steps of the flexible fitting should set to 200000 in cMDFF (cases with map resolution < 5 Å).
   

1. Initial model-----------------the starting model created through Situs by superposing each domain model into the density map.
   
2. Domain definition-----------the predicted domain definition, which should be assigned into the initial model before running the domain rigid-body assembly. In the definition, domains are separated by semicolons, while segments of a discontinuous domain are separated by commas. For example, the domain definition of 4crnX (1-13,273-421;14-139;140-272;) means that the first domain is a discontinuous domain, where residue 1 to residue 13 belong to the first segment and residue 273 to residue 421 belong to the second segment. "14-139" indicates that the second domain is a continuous domain which covers residues from 14 to 139.
   
3. MDFF final model-----------the final model refined by MDFF.
   
4. Molprobity of final model--the Molprobity score of the MDFF final model calculated by "phenix.molprobity", which includes the following terms:
   
   1. Ramachandran outliers--------the percentage of residues with Ramachandran outlier.
      
   2. Ramachandran favored--------the percentage Ramachandran favored residues.
      
   3. Rotamer outliers---------------the percentage of residues with rotamer outliers.
      
   4. Clash score----------------------the number of serious steric overlaps (>0.4Å) per 1000 atoms.
      
   5. RMS(bonds)--------------------the root-mean-square deviations from standard bond lengths.
      
   6. RMS(angles)--------------------the root-mean-square deviations from standard bond angles.
      
   7. MolProbity score---------------the weighted sum of clashes, Ramachandran not-favored and rotamer outliers.
      
5. MDFF log file----------------compressed file of MDFF logs which contains the following files:
   1. domain-step1_new.namd.log--the log file of the MDFF domain rigid-body assembly.
      
   2. adk-step1.namd.log------------the log file of the first step of the MDFF flexible refinement using the original density map.
      
   3. adk-step2.namd.log------------the log file of the second step of the MDFF flexible refinement using the original density map.
      
   4. 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:
   1. adk-step1.namd.logN----------the log file of the first step of the MDFF flexible refinement using the N-th Gaussian blurred density map.
      
   2. adk-step2.namd.logN----------the log file of the second step of the MDFF flexible refinement using the N-th Gaussian blurred density map.
      
   3. 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.
   
6. MDFF intermediate file----------all intermediate files generated by MDFF.
7. ξ ------------ the weight (scaling factor, set by "-gscale" in MDFF) of the cryo-EM data restraint for the final energy minimization.
8. MD_only---------- MDFF without the final energy minimization, which only performs the MD simulation.

1. Please remember to run the domain rigid-body assembly and flexible refinement in order using the above commands. Otherwise, you may fail to run the MD simulation of MDFF due to the poor quality of initial models.
   
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 assign the domain can be found in the MDFF tutorial.
   
3. Please read README.txt if you download the tarball file of each case.
   
   

• Click here to download data for all cases (~7.7GB) or click the following link to download each case independently
  
  
• ξ in the following tables is the weight of the cryo-EM density restraint for the final energy minimization rather than for the MD simulation of MDFF.
• MD_only represents MDFF without the final energy minimization, which only performs the MD simulation.
  
  
• 4crnX:
  

  Input data
  Initial model	Domain definition: 1-13,273-421;14-139;140-272;	Cryo-EM density map	Map resolution: 9.15Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 13.13 12.89 13.13 12.17 13.13 13.13 14.32 15.99 17.42 Ramachandran favored(%) 77.57 76.61 77.09 76.37 73.51 70.88 70.41 69.69 68.26 Rotamer outliers(%) 12.50 8.63 11.90 15.48 21.13 22.92 25.60 31.25 33.93 Clash score 1.99 0.15 0.61 5.52 20.24 29.90 38.95 59.83 84.52 RMS(bonds) 0.0354 0.0188 0.0191 0.0203 0.0237 0.0257 0.0278 0.0322 0.0366 RMS(angles) 4.11 2.91 3.07 3.36 3.88 4.14 4.42 4.97 5.48 MolProbity score 2.57 2.05 2.29 2.98 3.62 3.83 3.98 4.23 4.41 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4crnX

  
  

• 6c54A:
  

  Input data
  Initial model	Domain definition: 1-107;108-201;202-347;	Cryo-EM density map	Map resolution: 5.8Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 9.28 9.28 9.57 8.41 10.43 10.72 10.14 11.30 11.59 Ramachandran favored(%) 84.35 84.35 83.77 82.32 82.61 82.32 81.74 80.29 79.13 Rotamer outliers(%) 13.14 10.22 11.31 14.60 19.71 21.90 25.55 30.66 32.12 Clash score 2.03 0.18 0.18 1.85 7.94 10.15 14.03 26.77 40.27 RMS(bonds) 0.0344 0.0186 0.0189 0.0203 0.0252 0.0281 0.0309 0.0371 0.0435 RMS(angles) 4.04 2.79 2.85 2.97 3.26 3.40 3.57 3.93 4.23 MolProbity score 2.49 2.01 2.05 2.53 3.12 3.25 3.44 3.78 3.98 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6c54A

  
  

• 6iaxA:
  

  Input data
  Initial model	Domain definition: 1-113;114-212;213-355;	Cryo-EM density map	Map resolution: 5.2Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 7.65 7.37 6.80 7.37 9.35 8.22 8.50 10.48 8.50 Ramachandran favored(%) 84.99 85.84 84.70 83.57 82.72 81.59 81.87 81.30 81.87 Rotamer outliers(%) 12.20 4.72 4.72 7.09 14.17 17.72 20.47 26.77 27.17 Clash score 1.12 0.37 0.75 1.12 2.25 3.93 6.74 14.04 22.84 RMS(bonds) 0.0360 0.0188 0.0192 0.0203 0.0239 0.0262 0.0286 0.0340 0.0396 RMS(angles) 4.03 2.82 2.85 2.96 3.29 3.45 3.62 3.95 4.32 MolProbity score 2.31 1.79 1.92 2.15 2.57 2.84 3.08 3.46 3.65 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6iaxA

  
  

• 6enyD:
  

  Input data
  Initial model	Domain definition: 1-106;107-214;215-333;334-461;	Cryo-EM density map	Map resolution: 5.8Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 7.63 6.75 8.71 8.06 10.24 10.24 11.33 10.89 12.20 Ramachandran favored(%) 82.14 82.35 79.30 77.78 76.47 75.82 72.98 71.90 72.33 Rotamer outliers(%) 6.97 4.29 5.90 9.12 14.75 17.16 19.57 23.32 24.93 Clash score 6.87 3.79 6.45 12.34 33.10 45.16 56.94 78.84 108.37 RMS(bonds) 0.0502 0.0397 0.0400 0.0408 0.0443 0.0464 0.0485 0.0539 0.0594 RMS(angles) 3.77 2.39 2.69 3.05 3.90 4.37 4.80 5.57 6.24 MolProbity score 2.73 2.35 2.69 3.10 3.67 3.86 4.03 4.23 4.38 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6enyD

  
  

• 6hwyA:
  

  Input data
  Initial model	Domain definition: 1-133;134-236;	Cryo-EM density map	Map resolution: 8.6Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 14.96 17.09 17.09 17.09 17.52 17.52 18.38 19.23 18.38 Ramachandran favored(%) 75.21 77.35 77.35 75.64 73.93 73.93 71.79 69.66 69.23 Rotamer outliers(%) 15.35 8.91 12.38 15.84 21.78 22.77 28.71 36.14 41.58 Clash score 2.66 0.80 1.86 8.78 24.22 35.40 46.58 77.72 117.38 RMS(bonds) 0.0361 0.0191 0.0193 0.0203 0.0237 0.0258 0.0279 0.0327 0.0377 RMS(angles) 4.22 3.01 3.13 3.34 3.78 4.04 4.28 4.68 5.13 MolProbity score 2.75 2.24 2.55 3.17 3.70 3.87 4.08 4.39 4.61 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6hwyA

  
  

• 6uc0A:
  

  Input data
  Initial model	Domain definition: 1-143,333-370;144-332;	Cryo-EM density map	Map resolution: 7.5Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 11.68 10.60 12.77 13.86 14.67 14.95 15.22 14.13 16.58 Ramachandran favored(%) 74.46 76.63 75.54 75.00 73.91 73.10 73.91 72.01 72.01 Rotamer outliers(%) 13.07 8.83 11.66 13.78 18.73 21.91 23.32 25.09 27.56 Clash score 1.78 0.00 1.25 3.03 7.14 11.42 16.24 31.59 39.09 RMS(bonds) 0.0353 0.0187 0.0189 0.0201 0.0236 0.0257 0.0278 0.0326 0.0367 RMS(angles) 4.02 2.87 2.97 3.14 3.47 3.63 3.81 4.14 4.48 MolProbity score 2.58 2.00 2.44 2.75 3.17 3.41 3.56 3.87 3.99 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6uc0A

  
  

• 6sjeD:
  

  Input data
  Initial model	Domain definition: 1-115,587-597;116-352;353-586;	Cryo-EM density map	Map resolution: 4.1Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 12.44 14.29 14.79 14.12 14.29 15.29 16.47 16.47 17.48 Ramachandran favored(%) 76.13 74.62 73.95 73.95 72.27 70.92 71.43 70.92 70.08 Rotamer outliers(%) 13.47 9.93 11.48 13.69 19.21 21.63 21.19 27.15 28.04 Clash score 1.54 0.44 2.09 10.89 32.79 38.95 54.68 80.98 105.18 RMS(bonds) 0.0358 0.0191 0.0194 0.0204 0.0231 0.0245 0.0259 0.0293 0.0326 RMS(angles) 3.79 3.01 3.21 3.44 3.90 4.08 4.26 4.63 4.89 MolProbity score 2.54 2.21 2.59 3.22 3.80 3.92 4.05 4.30 4.43 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6sjeD

  
  

• 6bf9A:
  

  Input data
  Initial model	Domain definition: 1-242;243-487;488-966;	Cryo-EM density map	Map resolution: 7.2Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 18.76 18.76 18.98 19.20 21.26 22.02 22.56 22.78 23.32 Ramachandran favored(%) 67.90 68.66 68.44 67.90 67.35 67.35 66.49 65.40 64.75 Rotamer outliers(%) 15.77 11.03 12.18 14.36 19.23 21.28 21.54 25.13 27.31 Clash score 8.76 6.57 7.76 10.68 21.09 27.86 35.75 57.97 78.54 RMS(bonds) 0.0467 0.0356 0.0357 0.0360 0.0374 0.0385 0.0396 0.0424 0.0453 RMS(angles) 4.59 3.53 3.62 3.75 4.10 4.30 4.50 4.92 5.31 MolProbity score 3.24 3.01 3.10 3.29 3.66 3.81 3.92 4.18 4.34 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6bf9A

  
  

• 6ce7A:
  

  Input data
  Initial model	Domain definition: 1-155;156-203;204-264;265-420;421-528;	Cryo-EM density map	Map resolution: 7.4Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 34.38 33.98 33.59 33.79 35.55 38.09 37.50 37.50 37.89 Ramachandran favored(%) 47.85 48.05 47.46 46.88 42.58 40.82 41.80 41.80 38.87 Rotamer outliers(%) 17.08 13.03 17.30 20.67 24.72 25.84 29.21 33.26 32.36 Clash score 20.35 16.48 20.96 31.98 61.06 77.91 96.21 131.41 167.86 RMS(bonds) 0.0614 0.0537 0.0539 0.0546 0.0570 0.0584 0.0603 0.0645 0.0683 RMS(angles) 4.63 3.55 3.75 4.05 4.72 5.08 5.39 6.11 6.80 MolProbity score 3.72 3.55 3.74 3.98 4.33 4.45 4.58 4.75 4.86 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6ce7A

  
  

• 6kspA:
  

  Input data
  Initial model	Domain definition: 1-126,264-371;127-263,372-404;	Cryo-EM density map	Map resolution: 8.1Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 24.63 23.88 24.13 25.37 25.87 25.87 28.11 27.36 29.35 Ramachandran favored(%) 62.44 63.68 63.18 61.69 59.70 58.46 58.46 56.22 54.98 Rotamer outliers(%) 14.03 8.66 10.15 11.34 15.22 17.31 21.49 24.48 27.16 Clash score 9.26 4.47 7.03 9.42 19.48 25.87 34.97 55.26 80.49 RMS(bonds) 0.0506 0.0405 0.0406 0.0410 0.0422 0.0429 0.0439 0.0462 0.0495 RMS(angles) 4.39 3.25 3.34 3.45 3.82 3.98 4.16 4.59 5.15 MolProbity score 3.26 2.83 3.05 3.20 3.60 3.77 3.96 4.21 4.41 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6kspA

  
  

• 6njnJ:
  

  Input data
  Initial model	Domain definition: 1-107;108-211;	Cryo-EM density map	Map resolution: 6.7Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 24.76 23.79 24.27 24.27 25.24 26.70 26.70 26.70 28.64 Ramachandran favored(%) 60.19 63.11 63.11 62.62 59.71 59.22 58.74 56.31 55.34 Rotamer outliers(%) 16.29 9.55 10.67 10.67 12.92 14.04 14.61 18.54 20.79 Clash score 2.22 0.32 0.64 3.49 10.48 20.96 28.90 54.30 80.42 RMS(bonds) 0.0355 0.0192 0.0194 0.0206 0.0247 0.0276 0.0302 0.0365 0.0424 RMS(angles) 4.37 3.27 3.37 3.51 3.90 4.15 4.36 4.99 5.50 MolProbity score 2.83 2.26 2.39 2.82 3.30 3.61 3.76 4.11 4.32 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6njnJ

  
  

• 6uzhA:
  

  Input data
  Initial model	Domain definition: 1-66;67-154;155-254;	Cryo-EM density map	Map resolution: 3.3Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 17.06 15.48 15.48 15.48 16.27 16.27 15.87 16.67 16.67 Ramachandran favored(%) 72.62 72.62 71.83 72.62 72.62 72.22 72.22 72.22 72.22 Rotamer outliers(%) 14.86 14.86 14.86 14.86 16.57 16.00 16.00 16.00 16.00 Clash score 12.57 19.15 20.20 19.93 19.67 20.20 20.98 22.83 22.04 RMS(bonds) 0.0535 0.0470 0.0471 0.0470 0.0469 0.0468 0.0473 0.0473 0.0473 RMS(angles) 3.85 5.75 5.72 5.72 5.66 5.71 5.65 5.63 5.70 MolProbity score 3.32 3.49 3.52 3.50 3.54 3.54 3.55 3.59 3.57 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6uzhA

  
  

• 6kxsA:
  

  Input data
  Initial model	Domain definition: 1-102;103-232;	Cryo-EM density map	Map resolution: 3.4Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 12.67 14.48 14.48 15.38 14.93 14.93 14.48 14.93 14.48 Ramachandran favored(%) 67.87 69.68 69.68 70.14 70.14 70.14 69.68 70.14 69.68 Rotamer outliers(%) 8.76 9.79 9.79 10.31 10.31 10.31 9.79 10.82 10.82 Clash score 1.44 13.00 13.29 10.41 9.83 12.14 11.56 8.09 10.98 RMS(bonds) 0.0361 0.0356 0.0348 0.0326 0.0323 0.0330 0.0339 0.0313 0.0334 RMS(angles) 3.91 6.10 6.09 6.10 6.11 6.14 6.15 6.10 6.10 MolProbity score 2.46 3.22 3.23 3.15 3.13 3.21 3.18 3.07 3.19 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6kxsA

  
  

• 6uiaC:
  

  Input data
  Initial model	Domain definition: 1-25,113-242;26-112;243-424;425-563;564-757;758-1021;	Cryo-EM density map	Map resolution: 4.3Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 16.63 17.52 17.92 17.72 17.92 18.71 18.02 17.92 18.81 Ramachandran favored(%) 71.39 70.69 69.80 69.11 67.62 66.14 67.82 66.14 64.85 Rotamer outliers(%) 11.23 10.18 11.36 14.49 19.84 22.19 20.63 22.98 24.93 Clash score 2.98 0.65 4.20 11.90 35.19 55.05 56.41 85.00 114.69 RMS(bonds) 0.0355 0.0188 0.0191 0.0201 0.0234 0.0257 0.0267 0.0302 0.0339 RMS(angles) 3.70 3.04 3.22 3.39 3.76 4.02 4.04 4.33 4.64 MolProbity score 2.72 2.31 2.85 3.32 3.88 4.11 4.08 4.30 4.47 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6uiaC

  
  

• 2c7cC:
  

  Input data
  Initial model	Domain definition: 1-190,375-524;191-374;	Cryo-EM density map	Map resolution: 7.7Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 15.52 15.33 15.90 16.48 20.31 19.54 20.31 20.88 21.26 Ramachandran favored(%) 72.41 74.14 73.37 72.80 69.92 68.39 67.62 67.05 67.24 Rotamer outliers(%) 15.86 10.22 11.02 15.32 23.92 25.00 25.54 30.11 33.33 Clash score 6.64 3.26 6.38 12.90 33.62 41.04 48.21 72.70 103.19 RMS(bonds) 0.0357 0.0191 0.0192 0.0201 0.0234 0.0252 0.0272 0.0319 0.0367 RMS(angles) 4.45 3.36 3.46 3.66 4.08 4.27 4.51 4.95 5.43 MolProbity score 3.10 2.69 2.95 3.34 3.90 4.01 4.09 4.32 4.50 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 2c7cC

  
  

• 6vsjA:
  

  Input data
  Initial model	Domain definition: 1-269;270-297,609-708;298-311,545-608;312-544;709-1122;	Cryo-EM density map	Map resolution: 3.94Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 15.76 15.22 15.49 15.40 15.04 15.58 15.67 15.13 15.22 Ramachandran favored(%) 70.01 70.10 69.65 70.10 69.65 69.74 69.20 69.83 70.28 Rotamer outliers(%) 4.43 5.54 5.21 5.21 5.21 4.99 4.99 5.21 5.43 Clash score 3.98 7.32 7.32 5.29 6.19 6.60 6.37 5.89 6.48 RMS(bonds) 0.0412 0.0332 0.0325 0.0310 0.0312 0.0314 0.0319 0.0310 0.0309 RMS(angles) 3.75 4.41 4.38 4.27 4.43 4.44 4.55 4.19 4.04 MolProbity score 2.52 2.81 2.79 2.67 2.73 2.74 2.73 2.71 2.76 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6vsjA

  
  

• 3iziA:
  

  Input data
  Initial model	Domain definition: 1-135,393-513;136-203,359-392;204-358;	Cryo-EM density map	Map resolution: 6.7Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 11.84 11.22 11.22 12.24 13.47 14.69 14.90 17.55 17.76 Ramachandran favored(%) 77.35 78.98 77.76 76.53 75.92 72.86 70.61 71.02 68.78 Rotamer outliers(%) 7.97 3.30 6.04 8.52 14.29 16.21 19.23 23.35 24.18 Clash score 4.67 0.80 4.54 7.60 23.21 36.28 48.95 73.76 100.04 RMS(bonds) 0.0352 0.0191 0.0193 0.0202 0.0236 0.0256 0.0279 0.0326 0.0374 RMS(angles) 3.90 2.54 2.70 2.93 3.45 3.72 3.99 4.56 5.06 MolProbity score 2.69 1.89 2.59 2.90 3.52 3.78 3.98 4.21 4.37 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3iziA

  
  

• 3j15A:
  

  Input data
  Initial model	Domain definition: 1-131;132-259;260-357;	Cryo-EM density map	Map resolution: 6.6Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 22.73 21.88 22.44 22.44 23.86 25.28 26.42 26.42 26.99 Ramachandran favored(%) 62.50 63.35 62.50 63.07 60.23 57.95 57.39 56.53 55.11 Rotamer outliers(%) 13.68 8.42 9.47 12.63 19.30 20.70 19.65 25.61 24.91 Clash score 4.03 1.23 2.63 5.79 18.07 26.31 33.68 47.18 67.37 RMS(bonds) 0.0357 0.0190 0.0191 0.0197 0.0221 0.0239 0.0256 0.0293 0.0339 RMS(angles) 4.38 3.18 3.27 3.42 3.80 3.97 4.16 4.63 5.11 MolProbity score 2.95 2.44 2.69 3.05 3.65 3.84 3.93 4.16 4.31 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j15A

  
  

• 6ue7C:
  

  Input data
  Initial model	Domain definition: 1-113;114-220;221-332;333-442;443-534;	Cryo-EM density map	Map resolution: 2.9Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 14.66 12.03 12.22 11.65 14.66 14.29 13.35 12.22 14.29 Ramachandran favored(%) 76.69 75.56 75.75 76.50 76.50 76.13 73.87 73.87 76.32 Rotamer outliers(%) 8.29 4.84 5.07 6.22 8.06 8.29 15.21 9.91 7.83 Clash score 1.74 0.99 0.87 2.60 1.49 1.61 40.53 42.01 1.74 RMS(bonds) 0.0357 0.0192 0.0193 0.0202 0.0219 0.0212 0.0274 0.0295 0.0214 RMS(angles) 3.84 3.08 3.17 3.22 3.70 3.64 4.41 4.49 3.66 MolProbity score 2.40 2.10 2.09 2.43 2.36 2.39 3.79 3.67 2.39 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6ue7C

  
  

• 3j15B:
  

  Input data
  Initial model	Domain definition: 1-77;78-328;329-593;	Cryo-EM density map	Map resolution: 6.6Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 22.74 22.39 22.22 21.88 23.08 25.13 26.50 28.55 28.72 Ramachandran favored(%) 62.91 64.10 63.59 62.56 58.97 57.09 55.73 54.19 51.97 Rotamer outliers(%) 14.80 8.25 9.30 12.90 18.60 21.56 24.10 28.33 29.60 Clash score 1.83 0.43 1.40 2.80 9.25 14.19 17.96 31.29 43.34 RMS(bonds) 0.0359 0.0191 0.0191 0.0196 0.0217 0.0231 0.0247 0.0282 0.0319 RMS(angles) 4.19 2.96 3.04 3.19 3.59 3.76 3.96 4.38 4.81 MolProbity score 2.73 2.24 2.50 2.81 3.38 3.61 3.75 4.03 4.20 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j15B

  
  

• 3j1fA:
  

  Input data
  Initial model	Domain definition: 1-123,386-505;124-385;	Cryo-EM density map	Map resolution: 6.2Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 22.54 20.93 20.93 23.34 23.74 25.15 24.35 25.15 25.75 Ramachandran favored(%) 65.39 67.20 66.00 64.59 64.59 63.18 63.18 61.97 61.17 Rotamer outliers(%) 14.21 10.93 12.84 14.75 20.22 21.58 23.22 25.68 30.05 Clash score 2.63 0.92 2.11 5.79 17.76 26.71 35.66 54.34 78.42 RMS(bonds) 0.0357 0.0184 0.0186 0.0192 0.0215 0.0232 0.0249 0.0288 0.0322 RMS(angles) 4.25 3.14 3.24 3.40 3.87 4.11 4.33 4.77 5.17 MolProbity score 2.80 2.43 2.70 3.09 3.63 3.82 3.97 4.18 4.39 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j1fA

  
  

• 3j25A:
  

  Input data
  Initial model	Domain definition: 1-341;342-416;417-536,611-638;537-610;	Cryo-EM density map	Map resolution: 7.2Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 17.85 18.33 17.38 18.48 21.17 22.27 22.43 24.17 25.75 Ramachandran favored(%) 69.04 69.19 68.88 66.82 63.51 61.93 61.93 60.19 59.24 Rotamer outliers(%) 12.07 8.24 8.62 11.30 15.71 18.58 19.16 22.61 24.52 Clash score 2.61 0.80 1.10 2.91 10.34 17.77 27.51 44.88 65.46 RMS(bonds) 0.0357 0.0190 0.0191 0.0199 0.0226 0.0246 0.0266 0.0313 0.0364 RMS(angles) 4.36 3.19 3.24 3.37 3.72 3.88 4.03 4.38 4.76 MolProbity score 2.72 2.30 2.38 2.75 3.34 3.62 3.80 4.07 4.26 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j25A

  
  

• 3j5sD:
  

  Input data
  Initial model	Domain definition: 1-91,141-309;92-140;310-395,462-554;396-461;	Cryo-EM density map	Map resolution: 7.5Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 23.26 21.12 20.35 23.64 27.91 28.68 30.81 32.17 31.78 Ramachandran favored(%) 64.34 64.73 64.15 61.63 56.20 55.43 54.84 53.10 53.10 Rotamer outliers(%) 17.81 11.88 14.49 17.10 25.18 26.84 28.27 32.54 35.39 Clash score 3.92 0.59 3.21 10.34 28.65 39.71 55.76 86.44 116.88 RMS(bonds) 0.0357 0.0193 0.0194 0.0201 0.0231 0.0249 0.0269 0.0312 0.0361 RMS(angles) 4.53 3.45 3.54 3.71 4.13 4.33 4.57 5.07 5.54 MolProbity score 3.02 2.40 2.88 3.38 3.95 4.11 4.27 4.51 4.67 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j5sD

  
  

• 3j82B:
  

  Input data
  Initial model	Domain definition: 1-145,335-373;146-334;	Cryo-EM density map	Map resolution: 7.7Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 16.44 16.71 15.63 18.06 21.02 21.56 22.64 22.91 23.45 Ramachandran favored(%) 69.00 70.08 69.00 66.85 63.88 61.46 61.19 58.76 57.95 Rotamer outliers(%) 15.62 9.03 10.76 15.28 21.18 23.61 25.69 30.21 35.07 Clash score 2.48 0.71 1.42 4.08 19.14 26.41 35.45 55.30 77.84 RMS(bonds) 0.0358 0.0187 0.0188 0.0198 0.0232 0.0249 0.0271 0.0316 0.0364 RMS(angles) 4.15 2.99 3.05 3.22 3.67 3.87 4.13 4.51 5.02 MolProbity score 2.79 2.30 2.51 2.96 3.68 3.86 4.01 4.27 4.46 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j82B

  
  

• 3jaqC:
  

  Input data
  Initial model	Domain definition: 1-106;107-217;	Cryo-EM density map	Map resolution: 6.0Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 13.49 14.42 13.02 12.09 18.14 18.60 17.67 20.93 24.19 Ramachandran favored(%) 73.02 74.88 74.42 73.02 69.77 69.30 67.44 65.58 61.40 Rotamer outliers(%) 11.25 8.12 10.62 11.88 12.50 17.50 26.25 25.62 31.87 Clash score 3.68 2.45 4.60 9.50 26.05 34.63 50.57 71.10 98.74 RMS(bonds) 0.0363 0.0199 0.0200 0.0207 0.0239 0.0258 0.0283 0.0325 0.0376 RMS(angles) 4.05 2.77 2.88 3.07 3.65 3.94 4.32 4.88 5.60 MolProbity score 2.77 2.51 2.81 3.13 3.58 3.81 4.12 4.27 4.51 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3jaqC

  
  

• 3jb9B:
  

  Input data
  Initial model	Domain definition: 1-342;343-483;484-566;567-862;	Cryo-EM density map	Map resolution: 4.28Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 20.55 19.60 19.24 19.71 19.12 19.71 19.83 20.78 21.85 Ramachandran favored(%) 66.03 67.58 67.46 67.81 67.70 67.70 67.22 66.27 63.54 Rotamer outliers(%) 12.75 10.48 9.63 9.77 10.34 11.76 12.61 15.72 24.22 Clash score 3.58 3.13 3.96 5.08 6.05 11.42 20.15 48.44 124.42 RMS(bonds) 0.0360 0.0198 0.0197 0.0195 0.0197 0.0207 0.0216 0.0260 0.0329 RMS(angles) 3.87 3.57 3.56 3.55 3.67 3.81 3.84 4.22 4.76 MolProbity score 2.86 2.74 2.79 2.88 2.96 3.25 3.50 3.94 4.50 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3jb9B

  
  

• 4aarA:
  

  Input data
  Initial model	Domain definition: 1-136,413-523;137-189,374-412;190-373;	Cryo-EM density map	Map resolution: 8.0Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 18.15 17.76 18.73 17.95 18.73 18.73 19.11 18.92 20.27 Ramachandran favored(%) 69.11 69.69 69.31 69.31 68.15 67.37 67.18 65.64 64.09 Rotamer outliers(%) 14.91 9.49 10.57 11.11 13.01 14.63 14.91 18.16 18.43 Clash score 6.55 4.45 5.37 9.56 19.90 33.12 34.95 53.02 94.51 RMS(bonds) 0.0462 0.0353 0.0353 0.0356 0.0369 0.0380 0.0390 0.0417 0.0458 RMS(angles) 4.38 3.25 3.28 3.35 3.55 3.73 3.81 4.15 4.61 MolProbity score 3.10 2.81 2.91 3.15 3.50 3.75 3.78 4.03 4.29 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4aarA

  
  

• 4cc8J:
  

  Input data
  Initial model	Domain definition: 1-102;103-208;	Cryo-EM density map	Map resolution: 6.0Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 12.50 14.00 13.00 12.50 16.50 18.00 17.50 23.00 22.50 Ramachandran favored(%) 71.00 73.00 71.00 70.50 63.50 63.00 60.50 55.50 57.50 Rotamer outliers(%) 12.07 7.47 10.92 15.52 19.54 22.99 23.56 24.71 27.59 Clash score 25.22 18.52 24.27 35.76 75.99 100.89 132.82 181.35 236.27 RMS(bonds) 0.0767 0.0708 0.0707 0.0711 0.0722 0.0729 0.0739 0.0759 0.0780 RMS(angles) 4.10 2.87 3.06 3.29 3.82 4.08 4.37 4.89 5.36 MolProbity score 3.55 3.24 3.50 3.78 4.22 4.40 4.54 4.72 4.86 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4cc8J

  
  

• 4crmP:
  

  Input data
  Initial model	Domain definition: 1-79;80-333;334-608;	Cryo-EM density map	Map resolution: 8.75Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 14.50 12.00 14.00 15.00 17.83 19.67 20.17 20.83 22.67 Ramachandran favored(%) 69.67 70.67 70.00 68.33 64.17 63.17 61.67 59.50 58.17 Rotamer outliers(%) 5.62 3.12 3.75 6.67 11.25 15.00 16.25 20.21 25.21 Clash score 2.54 0.74 2.44 4.24 10.91 16.41 21.39 37.06 58.45 RMS(bonds) 0.0361 0.0195 0.0195 0.0200 0.0218 0.0229 0.0242 0.0270 0.0303 RMS(angles) 3.91 2.44 2.52 2.69 3.12 3.30 3.51 3.90 4.28 MolProbity score 2.45 1.95 2.30 2.69 3.24 3.51 3.65 3.96 4.23 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4crmP

  
  

• 4uerC:
  

  Input data
  Initial model	Domain definition: 1-91;92-189;	Cryo-EM density map	Map resolution: 6.47Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 10.16 10.16 11.23 12.83 13.37 13.90 15.51 16.04 17.11 Ramachandran favored(%) 76.47 79.14 78.07 77.01 73.80 73.80 72.19 71.66 71.66 Rotamer outliers(%) 16.08 11.89 13.29 13.99 18.18 21.68 27.97 32.17 35.66 Clash score 2.01 1.34 3.69 7.05 26.85 40.60 42.95 63.76 90.27 RMS(bonds) 0.0358 0.0201 0.0198 0.0202 0.0222 0.0236 0.0249 0.0282 0.0316 RMS(angles) 3.97 2.68 2.80 3.01 3.51 3.85 4.08 4.54 5.02 MolProbity score 2.67 2.43 2.77 3.03 3.68 3.91 4.03 4.25 4.43 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4uerC

  
  

• 4v1mC:
  

  Input data
  Initial model	Domain definition: 1-38,168-266;39-167;	Cryo-EM density map	Map resolution: 6.6Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 25.10 23.14 26.27 25.10 26.27 29.02 29.41 30.20 32.55 Ramachandran favored(%) 56.08 58.82 58.43 56.86 58.82 56.08 53.73 52.16 50.20 Rotamer outliers(%) 12.56 8.84 11.16 12.56 17.67 21.40 22.33 24.65 29.77 Clash score 11.93 9.19 10.43 14.41 30.06 43.98 57.39 80.99 110.09 RMS(bonds) 0.0520 0.0435 0.0436 0.0440 0.0454 0.0463 0.0476 0.0503 0.0527 RMS(angles) 4.29 3.23 3.32 3.47 3.89 4.13 4.41 4.89 5.31 MolProbity score 3.37 3.13 3.26 3.44 3.83 4.07 4.21 4.40 4.60 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4v1mC

  
  

• 5fj6:
  

  Input data
  Initial model	Domain definition: 1-40,67-138,173-515;39-66,516-633;139-172,632-664;	Cryo-EM density map	Map resolution: 7.9Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 17.37 17.22 17.98 18.58 20.39 20.85 21.15 22.51 22.96 Ramachandran favored(%) 68.43 69.34 68.73 68.43 65.86 65.56 65.71 62.08 61.78 Rotamer outliers(%) 10.53 5.08 7.14 9.02 16.73 19.74 22.56 26.69 31.20 Clash score 6.31 3.69 5.63 8.35 20.48 28.53 35.03 52.21 76.48 RMS(bonds) 0.0435 0.0311 0.0311 0.0315 0.0331 0.0343 0.0355 0.0381 0.0412 RMS(angles) 4.23 3.04 3.11 3.25 3.58 3.75 3.89 4.22 4.59 MolProbity score 2.98 2.54 2.81 3.03 3.61 3.80 3.93 4.18 4.39 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 5fj6

  
  

• 5fkwA:
  

  Input data
  Initial model	Domain definition: 1-279,404-436,503-557;280-403;437-502;558-927;	Cryo-EM density map	Map resolution: 7.3Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 15.10 13.68 14.66 15.21 16.85 16.85 18.49 19.69 20.68 Ramachandran favored(%) 75.16 75.93 74.95 74.40 71.23 69.80 68.60 66.74 66.19 Rotamer outliers(%) 12.98 8.74 11.00 13.68 20.87 23.27 25.11 28.77 30.89 Clash score 3.67 0.85 1.62 5.16 17.31 26.56 32.99 52.35 77.66 RMS(bonds) 0.0354 0.0188 0.0190 0.0199 0.0231 0.0251 0.0271 0.0317 0.0363 RMS(angles) 4.26 3.04 3.12 3.26 3.63 3.83 3.99 4.38 4.69 MolProbity score 2.80 2.26 2.50 2.94 3.57 3.79 3.92 4.17 4.36 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 5fkwA

  
  

• 5gafD:
  

  Input data
  Initial model	Domain definition: 1-30,98-209;31-97;	Cryo-EM density map	Map resolution: 4.3Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 8.70 10.14 11.59 11.11 14.49 13.04 15.46 15.94 16.91 Ramachandran favored(%) 76.81 76.81 76.33 74.40 72.95 70.53 68.12 64.25 65.70 Rotamer outliers(%) 8.33 4.49 6.41 6.41 12.18 12.82 17.95 19.87 26.92 Clash score 1.59 0.32 2.23 7.64 23.24 34.38 47.44 66.22 84.37 RMS(bonds) 0.0362 0.0196 0.0203 0.0216 0.0245 0.0263 0.0282 0.0311 0.0343 RMS(angles) 3.78 2.44 2.67 2.97 3.51 3.72 3.97 4.32 4.71 MolProbity score 2.38 1.89 2.39 2.83 3.50 3.70 3.96 4.17 4.36 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 5gafD

  
  

• 6fczH:
  

  Input data
  Initial model	Domain definition: 1-109;110-216;	Cryo-EM density map	Map resolution: 10Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 19.43 18.01 17.54 19.91 24.64 25.59 27.96 28.91 31.75 Ramachandran favored(%) 65.40 65.40 66.82 63.51 61.14 60.19 58.77 57.82 56.40 Rotamer outliers(%) 9.74 7.69 9.74 13.33 16.92 19.49 24.62 28.21 35.38 Clash score 12.72 10.94 16.27 32.83 67.44 86.39 103.85 152.96 207.34 RMS(bonds) 0.0569 0.0485 0.0486 0.0491 0.0509 0.0521 0.0534 0.0563 0.0594 RMS(angles) 4.16 2.88 3.12 3.42 4.06 4.42 4.68 5.39 5.87 MolProbity score 3.25 3.11 3.33 3.75 4.14 4.30 4.46 4.68 4.89 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6fczH

  
  

• 6lfgA:
  

  Input data
  Initial model	Domain definition: 1-151;152-294;295-562;	Cryo-EM density map	Map resolution: 9.58Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 13.46 13.11 13.64 13.11 12.93 13.29 14.54 15.26 16.88 Ramachandran favored(%) 75.76 75.40 75.40 75.22 73.79 73.61 71.81 71.27 69.48 Rotamer outliers(%) 13.47 8.39 9.49 12.58 17.22 20.53 22.08 25.61 28.70 Clash score 2.64 0.80 1.95 4.59 14.35 22.16 30.08 42.94 61.42 RMS(bonds) 0.0355 0.0188 0.0189 0.0194 0.0211 0.0221 0.0234 0.0257 0.0286 RMS(angles) 4.09 2.89 3.00 3.14 3.42 3.60 3.76 4.02 4.32 MolProbity score 2.69 2.24 2.49 2.86 3.41 3.64 3.81 4.01 4.22 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6lfgA

  
  

• 6metA:
  

  Input data
  Initial model	Domain definition: 1-96;97-180;181-296;297-363;	Cryo-EM density map	Map resolution: 4.5Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 13.41 11.17 11.17 11.73 13.13 13.13 16.20 17.88 19.55 Ramachandran favored(%) 76.26 75.70 76.54 75.98 73.18 71.23 69.55 66.76 63.97 Rotamer outliers(%) 11.29 6.77 10.32 13.23 17.10 17.74 21.61 22.90 25.48 Clash score 1.23 0.00 1.06 6.16 26.20 41.68 55.93 80.72 108.34 RMS(bonds) 0.0361 0.0187 0.0195 0.0209 0.0241 0.0257 0.0280 0.0314 0.0348 RMS(angles) 3.87 3.03 3.32 3.58 4.07 4.26 4.49 4.80 5.12 MolProbity score 2.42 1.92 2.36 2.97 3.66 3.88 4.08 4.28 4.46 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6metA

  
  

• 6mmvA:
  

  Input data
  Initial model	Domain definition: 1-119,253-325;120-252,326-368;369-658;	Cryo-EM density map	Map resolution: 4.71Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 23.45 14.42 11.62 16.28 18.21 22.17 24.73 24.76 26.63 Ramachandran favored(%) 60.71 72.09 75.51 67.91 63.90 61.09 55.95 56.31 53.10 Rotamer outliers(%) 12.81 2.46 4.56 8.49 13.57 17.58 19.59 20.61 27.92 Clash score 6.00 4.34 5.25 7.68 16.03 22.10 32.72 52.08 64.51 RMS(bonds) 0.0441 0.0320 0.0321 0.0324 0.0345 0.0353 0.0367 0.0399 0.0438 RMS(angles) 3.87 2.41 2.51 2.78 3.24 3.54 3.98 4.40 4.76 MolProbity score 3.08 2.33 2.57 2.99 3.46 3.69 3.92 4.13 4.34 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6mmvA

  
  

• 6n52A:
  

  Input data
  Initial model	Domain definition: 1-155,293-426;156-292,427-472;473-531;532-774;	Cryo-EM density map	Map resolution: 4.0Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 25.93 25.24 24.14 25.24 24.69 24.97 24.28 23.72 24.69 Ramachandran favored(%) 59.45 60.00 60.28 60.28 60.28 60.14 59.72 61.66 60.00 Rotamer outliers(%) 13.00 12.33 12.33 13.00 12.33 12.33 12.83 14.00 12.83 Clash score 3.61 7.83 7.66 7.49 8.18 10.24 10.67 8.94 9.81 RMS(bonds) 0.0357 0.0269 0.0224 0.0260 0.0246 0.0272 0.0272 0.0221 0.0282 RMS(angles) 3.81 5.58 5.11 5.52 5.47 5.45 5.44 4.73 5.58 MolProbity score 2.92 3.17 3.16 3.17 3.19 3.27 3.31 3.25 3.27 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6n52A

  
  

• 6nr9A:
  

  Input data
  Initial model	Domain definition: 1-100,496-521;101-135,394-495;136-393;	Cryo-EM density map	Map resolution: 8.5Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 18.02 16.67 16.47 16.47 18.22 19.77 20.54 20.35 20.35 Ramachandran favored(%) 71.32 72.29 72.48 72.67 69.38 68.02 68.02 66.86 67.25 Rotamer outliers(%) 15.46 8.51 10.57 13.14 17.53 23.20 25.77 28.09 28.87 Clash score 12.50 11.10 12.12 15.18 26.02 36.10 44.13 61.87 83.82 RMS(bonds) 0.0475 0.0357 0.0355 0.0358 0.0369 0.0379 0.0389 0.0410 0.0438 RMS(angles) 4.66 3.71 3.75 3.87 4.15 4.42 4.56 4.94 5.32 MolProbity score 3.34 3.09 3.19 3.35 3.70 3.94 4.05 4.23 4.37 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6nr9A

  
  

• 6qy3I:
  

  Input data
  Initial model	Domain definition: 1-82;83-164;165-287;	Cryo-EM density map	Map resolution: 9.1Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 19.86 18.44 19.15 19.15 21.28 22.34 23.76 25.18 25.53 Ramachandran favored(%) 63.83 65.60 64.54 63.83 64.18 63.83 63.83 63.83 62.06 Rotamer outliers(%) 21.61 14.83 17.80 22.46 25.00 30.08 31.36 34.32 33.90 Clash score 13.98 9.61 17.26 29.28 51.34 62.92 82.15 115.63 145.14 RMS(bonds) 0.0518 0.0419 0.0419 0.0423 0.0439 0.0450 0.0460 0.0485 0.0511 RMS(angles) 4.62 3.52 3.71 3.94 4.45 4.68 4.93 5.45 5.86 MolProbity score 3.56 3.27 3.57 3.87 4.14 4.28 4.41 4.58 4.69 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6qy3I

  
  

• 6s5tB:
  

  Input data
  Initial model	Domain definition: 1-78;79-144;	Cryo-EM density map	Map resolution: 4.15Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 10.29 8.82 9.56 10.29 11.76 13.24 14.71 16.91 18.38 Ramachandran favored(%) 80.88 83.09 83.09 77.94 77.94 77.21 75.74 74.26 72.06 Rotamer outliers(%) 6.14 4.39 9.65 14.04 22.81 32.46 34.21 38.60 39.47 Clash score 1.87 0.00 3.27 12.62 45.79 65.42 103.74 142.06 178.04 RMS(bonds) 0.0347 0.0190 0.0194 0.0208 0.0252 0.0273 0.0296 0.0352 0.0410 RMS(angles) 3.74 2.24 2.54 2.94 3.58 3.91 4.22 4.82 5.56 MolProbity score 2.27 1.68 2.56 3.25 3.93 4.21 4.43 4.62 4.75 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6s5tB

  
  

• 3j97A:
  

  Input data
  Initial model	Domain definition: 1-91;92-213;214-400;401-495;496-671;672-737;	Cryo-EM density map	Map resolution: 7.8Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 14.07 12.98 13.93 14.75 16.26 15.30 16.12 16.39 17.08 Ramachandran favored(%) 75.55 76.37 76.37 76.23 74.59 73.63 72.95 70.77 70.90 Rotamer outliers(%) 10.96 8.00 8.52 11.48 17.04 19.65 23.65 25.91 29.74 Clash score 1.59 0.18 0.97 3.27 9.62 13.15 18.19 29.93 45.11 RMS(bonds) 0.0356 0.0187 0.0189 0.0195 0.0216 0.0228 0.0240 0.0266 0.0294 RMS(angles) 4.14 2.93 3.03 3.17 3.46 3.60 3.77 4.01 4.30 MolProbity score 2.48 2.04 2.28 2.70 3.24 3.42 3.62 3.87 4.09 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3j97A

  
  

• 4uftB:
  

  Input data
  Initial model	Domain definition: 1-113;114-242;243-384;	Cryo-EM density map	Map resolution: 4.3Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 8.97 9.23 8.97 10.03 8.97 9.50 9.23 8.97 8.71 Ramachandran favored(%) 81.00 81.79 81.79 81.27 81.53 79.95 81.53 81.79 81.79 Rotamer outliers(%) 5.86 5.17 4.83 5.52 5.17 11.38 4.83 5.17 5.17 Clash score 1.90 3.10 4.66 11.90 6.38 32.94 5.69 4.31 4.31 RMS(bonds) 0.0354 0.0223 0.0226 0.0208 0.0233 0.0247 0.0225 0.0224 0.0224 RMS(angles) 3.61 3.40 3.46 3.07 3.46 3.56 3.50 3.57 3.58 MolProbity score 2.26 2.36 2.47 2.87 2.61 3.54 2.54 2.46 2.46 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 4uftB

  
  

• 5m54A:
  

  Input data
  Initial model	Domain definition: 1-243;244-381;382-438;	Cryo-EM density map	Map resolution: 8.0Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 18.14 16.74 16.74 18.14 22.56 23.02 22.79 26.05 26.51 Ramachandran favored(%) 69.07 69.07 68.84 67.91 63.26 62.33 61.16 60.00 59.77 Rotamer outliers(%) 12.09 7.08 9.44 11.50 18.29 21.53 24.19 26.25 31.27 Clash score 4.41 1.22 2.89 6.39 19.62 25.70 36.50 59.91 85.01 RMS(bonds) 0.0355 0.0190 0.0190 0.0195 0.0217 0.0232 0.0246 0.0279 0.0315 RMS(angles) 4.31 3.20 3.32 3.47 3.87 4.08 4.29 4.66 4.97 MolProbity score 2.89 2.33 2.67 3.02 3.64 3.81 4.00 4.24 4.45 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 5m54A

  
  

• 6enyF:
  

  Input data
  Initial model	Domain definition: 1-181;182-274;	Cryo-EM density map	Map resolution: 5.8Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 13.24 13.60 13.24 13.24 14.34 14.34 13.97 15.81 16.91 Ramachandran favored(%) 78.31 76.84 77.57 77.21 75.37 75.00 74.26 73.53 72.06 Rotamer outliers(%) 8.97 5.38 9.42 15.25 20.63 27.35 29.15 28.70 30.49 Clash score 2.11 0.23 2.11 8.19 20.84 30.67 40.27 62.98 83.92 RMS(bonds) 0.0358 0.0189 0.0196 0.0220 0.0284 0.0320 0.0352 0.0415 0.0473 RMS(angles) 4.15 2.91 3.15 3.47 4.21 4.65 5.01 5.67 6.38 MolProbity score 2.46 1.92 2.49 3.11 3.60 3.86 4.00 4.19 4.34 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6enyF

  
  

• 6n89A:
  

  Input data
  Initial model	Domain definition: 1-250;251-397;398-524;525-725;726-873;	Cryo-EM density map	Map resolution: 7.5Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 14.38 14.73 14.04 14.50 15.30 15.77 15.77 16.11 16.80 Ramachandran favored(%) 75.95 76.29 76.18 76.52 76.06 75.83 75.60 74.22 74.22 Rotamer outliers(%) 13.57 9.14 10.57 11.57 15.71 18.14 19.71 23.43 24.14 Clash score 9.23 5.78 7.13 10.59 23.28 29.58 39.27 54.90 74.00 RMS(bonds) 0.0371 0.0221 0.0222 0.0231 0.0263 0.0283 0.0308 0.0356 0.0405 RMS(angles) 4.57 3.51 3.59 3.72 4.08 4.28 4.58 4.97 5.43 MolProbity score 3.14 2.83 2.95 3.13 3.55 3.70 3.85 4.06 4.19 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6n89A

  
  

• 3japD:
  

  Input data
  Initial model	Domain definition: 1-90;91-193;	Cryo-EM density map	Map resolution: 4.9Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 6.81 6.81 6.81 6.28 9.42 10.99 10.47 12.57 15.18 Ramachandran favored(%) 82.72 82.20 80.63 78.01 75.92 74.87 73.30 73.30 73.30 Rotamer outliers(%) 6.25 4.86 5.56 9.03 15.97 18.06 18.06 23.61 27.78 Clash score 0.66 0.66 4.92 9.85 29.54 42.01 59.40 85.66 125.70 RMS(bonds) 0.0365 0.0198 0.0204 0.0215 0.0243 0.0263 0.0275 0.0313 0.0343 RMS(angles) 3.69 2.27 2.58 2.91 3.50 3.74 3.93 4.33 4.77 MolProbity score 2.02 1.94 2.55 3.00 3.66 3.85 4.01 4.26 4.47 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 3japD

  
  

• 4bedA:
  

  Input data
  Initial model	Domain definition: 1-300;301-405;406-706;707-830;831-1139;1140-1238;1239-1545;1546-1664;	Cryo-EM density map	Map resolution: 9.1Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 16.21 15.55 15.73 16.94 18.39 19.24 20.45 22.20 22.57 Ramachandran favored(%) 69.75 70.24 70.11 68.97 67.70 66.61 65.15 62.73 61.46 Rotamer outliers(%) 10.66 7.40 8.63 11.02 16.46 18.85 20.81 24.73 28.43 Clash score 3.28 1.74 2.89 5.94 16.44 22.19 30.45 51.64 72.99 RMS(bonds) 0.0386 0.0240 0.0240 0.0244 0.0260 0.0271 0.0284 0.0312 0.0342 RMS(angles) 4.13 2.95 3.02 3.15 3.46 3.62 3.78 4.15 4.45 MolProbity score 2.74 2.43 2.63 2.97 3.50 3.68 3.85 4.14 4.34 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
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• 6sjeC:
  

  Input data
  Initial model	Domain definition: 1-326;327-440,652-813;441-651;814-1121;	Cryo-EM density map	Map resolution: 4.1Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 13.05 12.78 13.76 14.21 15.37 15.82 15.37 16.71 16.00 Ramachandran favored(%) 76.50 76.59 75.78 74.71 73.10 72.21 72.92 72.03 70.96 Rotamer outliers(%) 12.20 7.88 9.40 12.10 18.57 22.14 23.22 26.24 24.73 Clash score 1.52 0.28 2.54 8.70 24.12 41.17 44.79 78.68 93.98 RMS(bonds) 0.0358 0.0188 0.0188 0.0194 0.0214 0.0232 0.0239 0.0274 0.0299 RMS(angles) 3.67 2.85 3.02 3.21 3.53 3.78 3.84 4.18 4.36 MolProbity score 2.50 2.06 2.56 3.09 3.65 3.94 3.98 4.27 4.33 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
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• 6oljC:
  

  Input data
  Initial model	Domain definition: 1-107;108-387;	Cryo-EM density map	Map resolution: 7.8Å
  Output data
  Scaling factor of cryo-EM data restraint for final energy minimization MD_only ξ=0 ξ=1 ξ=2 ξ=4 ξ=5 ξ=6 ξ=8 ξ=10 MDFF final model MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MDFF_final.pdb MolProbity of final model Ramachandran outliers(%) 10.39 10.65 10.91 12.21 14.29 13.77 13.77 15.32 16.10 Ramachandran favored(%) 77.66 78.70 77.14 77.14 74.03 71.69 70.65 70.91 69.35 Rotamer outliers(%) 10.96 9.63 11.63 15.28 18.60 20.27 23.92 29.24 32.23 Clash score 1.84 0.17 1.67 5.02 16.56 21.91 31.27 49.16 70.23 RMS(bonds) 0.0360 0.0190 0.0191 0.0198 0.0227 0.0244 0.0263 0.0302 0.0343 RMS(angles) 4.20 2.98 3.09 3.24 3.57 3.76 3.95 4.32 4.66 MolProbity score 2.50 2.07 2.50 2.94 3.49 3.65 3.86 4.12 4.31 MDFF log file MD_log.tar.gz MDFF intermediate file record.tar.gz
  Click here to download all data of 6oljC