Hi Tatyana, could you please send me the data and model files (off-list) so I can investigate? I will post the summary on phenixbb once we know what's going on. I see a number of potential issues but I don't want to waste time guessing, since it's much more efficient if you send me the files then I run some tests and tell you how to proceed. I'm pretty confident there is a quick fix. Thanks! Pavel. On 7/30/11 11:35 AM, Tatyana Sysoeva wrote:
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
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