R/Rfree from phenix.autobuild
Hi Folks, Quick question about R/Rfree from phenix - I ran the autobuild and it kindly built pretty much all of the visible residues, and it gave me the following output: SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.22 0.23 169 169 2 2 0.21 0.23 170 170 3 4 0.22 0.23 170 170 Now, I'm not one to complain about good results, but I did feel that the Rfree looked a little close to the R factor - usually I would expect a difference of maybe 4-5%. Is there a reason for this that I am missing? The model seemed to fit very nicely, closely corresponded to the PDB entry and the waters were pretty good. There is no NCS (one copy in the ASU) and the phases are from SeMet mad data from Autosol. Resolution is ~1.6A, if that is any help. Just noticed this and thought it was interesting. I am used to Arp/wArp for automated tracing, which typically gives a bigger difference... Many thanks, Graeme
Hi Graeme, the difference between Rwork and Rfree depends on resolution. Here is some R-factor statistics for all PDB structures refined at resolution range between 1.55A and 1.65A: Distribution of R-work at resolution 1.55-1.65 Resolution range Number of structures 9.90 - 11.86: 6 11.86 - 13.82: 28 13.82 - 15.78: 185 15.78 - 17.74: 415 17.74 - 19.70: 562 19.70 - 21.66: 358 21.66 - 23.62: 144 23.62 - 25.58: 27 25.58 - 27.54: 8 27.54 - 29.50: 2 Distribution of R-free 1.55-1.65 Resolution range Number of structures 14.00 - 15.93: 11 15.93 - 17.86: 73 17.86 - 19.79: 293 19.79 - 21.72: 490 21.72 - 23.65: 458 23.65 - 25.58: 244 25.58 - 27.51: 110 27.51 - 29.44: 39 29.44 - 31.37: 11 31.37 - 33.30: 6 Distribution of R-work-Rfree 1.55-1.65 Resolution range Number of structures 0.10 - 1.23: 69 1.23 - 2.36: 426 2.36 - 3.49: 562 3.49 - 4.62: 401 4.62 - 5.75: 163 5.75 - 6.88: 67 6.88 - 8.01: 31 8.01 - 9.14: 11 9.14 - 10.27: 3 10.27 - 11.40: 2 1% difference in your case is suspiciously small indeed. Although Autobuld combines model building with refinement using phenix.refine, its main purpose to build the structure and not produce the best refined possible one. After Autobuld you may want to do some more refinement customized to your particular case (resolution, etc...). At 1.6A you may want to try: - refining anisotropic ADP; - if refinement of anisotropic ADP is prohibitive (Rfree and Rfree-Rwork go too high), try TLS instead; - simply do more refinement macro-cycles to achieve full convergence (by default phenix.refine does 3 macro-cycles), say try 5, for example; - optimize weights using automatic options (use "optimize_wxc=true optimize_wxu=true" - this may take a while to finish), or try a few different values manually (wxc_scale=..., wxu_scale=...). Please let us know if you have any other questions! Pavel. On 11/27/2008 8:54 AM, Graeme Winter wrote:
Hi Folks,
Quick question about R/Rfree from phenix - I ran the autobuild and it kindly built pretty much all of the visible residues, and it gave me the following output:
SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.22 0.23 169 169 2 2 0.21 0.23 170 170 3 4 0.22 0.23 170 170
Now, I'm not one to complain about good results, but I did feel that the Rfree looked a little close to the R factor - usually I would expect a difference of maybe 4-5%. Is there a reason for this that I am missing? The model seemed to fit very nicely, closely corresponded to the PDB entry and the waters were pretty good. There is no NCS (one copy in the ASU) and the phases are from SeMet mad data from Autosol.
Resolution is ~1.6A, if that is any help.
Just noticed this and thought it was interesting. I am used to Arp/wArp for automated tracing, which typically gives a bigger difference...
Many thanks,
Graeme _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Graeme, I agree with everything that Pavel pointed out yesterday. I have added below a tabulation of R/Rfree for a set of 46 structures from the PHENIX library, solved with autosol and then built with autobuild. You will see that your result is not unprecedented (e.g., the p9 structure), but a slightly larger spread of 0.02 to 0.06 is more common: R Rfree Resolution structure 0.17 0.24 1.80 pen 0.17 0.22 2.80 rh-dehalogenase 0.18 0.23 2.52 flr 0.19 0.25 2.40 mev-kinase 0.20 0.21 1.75 p9 0.20 0.24 2.25 gpatase 0.20 0.23 2.50 aep 0.20 0.23 1.90 myoglobin 0.21 0.24 2.80 s-hydrolase 0.21 0.23 2.40 cyanase 0.21 0.26 2.00 tryparedoxin 0.22 0.25 1.80 mbp 0.22 0.26 2.00 cobd-sad 0.22 0.25 1.95 nsf-n 0.22 0.27 2.50 psd-95 0.22 0.25 3.00 1038B 0.22 0.30 2.60 gene-5 0.22 0.25 1.80 epsin 0.23 0.28 2.50 p32 0.23 0.26 2.40 armadillo 0.23 0.27 2.40 nsf-d2 0.23 0.26 1.80 ic-lyase 0.24 0.30 2.80 cp-synthase 0.24 0.29 2.30 vmp 0.24 0.26 1.10 calmodulin 0.24 0.36 3.00 hn-rnp 0.25 0.28 2.00 synapsin 0.26 0.27 1.70 insulin 0.26 0.28 2.80 ut-synthase 0.26 0.29 1.71 1063B 0.26 0.31 2.50 rnase-s 0.26 0.30 2.33 gran-orig 0.28 0.30 1.50 rnase-p 0.28 0.34 3.00 1071B 0.29 0.34 2.50 1102B 0.29 0.36 2.60 rab3a 0.29 0.33 2.00 1167B 0.30 0.35 2.70 gere 0.30 0.33 2.10 pdz 0.30 0.32 1.90 rop 0.34 0.40 3.30 sec17 0.35 0.43 2.50 qaprtase 0.41 0.47 3.20 synaptotagmin 0.41 0.48 3.80 groel 0.43 0.48 2.90 fusion-complex 0.43 0.47 3.50 group2-intron All the best, Tom T
Hi Folks,
Quick question about R/Rfree from phenix - I ran the autobuild and it kindly built pretty much all of the visible residues, and it gave me the following output:
SOLUTION CYCLE R RFREE BUILT PLACED 1 1 0.22 0.23 169 169 2 2 0.21 0.23 170 170 3 4 0.22 0.23 170 170
Now, I'm not one to complain about good results, but I did feel that the Rfree looked a little close to the R factor - usually I would expect a difference of maybe 4-5%. Is there a reason for this that I am missing? The model seemed to fit very nicely, closely corresponded to the PDB entry and the waters were pretty good. There is no NCS (one copy in the ASU) and the phases are from SeMet mad data from Autosol.
Resolution is ~1.6A, if that is any help.
Just noticed this and thought it was interesting. I am used to Arp/wArp for automated tracing, which typically gives a bigger difference...
Many thanks,
Graeme _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Graeme Winter -
Pavel Afonine -
Thomas C. Terwilliger