I ran the same commands with the build dev-833. Below are the results. These parameters are obtained by running phenix.ramalyze, cbetdev, and clashscore. I am almost done repeating fix-rotamers run. First time it gave a way worse validation results then before running phenix without fix_rotamers=true. I don't understand what I am doing wrong in the runs and would appreciate your help! Thanks, Tanya I used phenix-dev-833 to test the riding hydrogens refinement at 3.6A. I ran two indentical commands: Command line arguments: "model.pdb" "data.mtz" "main.ncs=true" "ncs.find_automatically=false" "ncs_groups.params" "refinement.input.xray_data.high_resolution=3.6" "mgadpbef.cif" "refinement.ncs.excessive_distance_limit=None" "strategy=individual_sites+individual_sites_real_space+group_adp+occupancies" with the only difference in the input files – ncs.params and model.pdb Model pdb contained the model identical to the control run but with added H atoms. I have not add H to the ADP molecules since I did not know how to write a correct CIF file for it. NCS definitions were changed by addition of “and not (element H)” to each line. It was done to exclude H from the NCS groups. *no hydrogens* *with hydrogens* # Date 2011-07-29 Time 19:09:58 EDT -0400 (1311980998.46 s) wall clock time: 2646.75 s Start R-work = 0.2891, R-free = 0.3267 Final R-work = 0.2868, R-free = 0.3304 # Date 2011-07-29 Time 20:14:20 EDT -0400 (1311984860.16 s) wall clock time: 6517.60 s Start R-work = 0.2910, R-free = 0.3273 Final R-work = 0.2720, R-free = 0.3353 clashscore 31.77 clashscore 96.12 cbeta 0 cbeta 151 rama 12.62% outliers rama 19.67% outliers Interestingly in previous release version the same refinement runs produced: without H clashscore = 77.580195/cbeta =8 with H clashscore = 119.729960/cbeta=330