Forgive me for saying this but the object of refinement is to build the most accurate model, not to obtain the lowest Rvalue, which will vary with weights applied to diffraction data versus constraints. There have been multiple posts about this on crystallographic BBs in the last few months ... -----Original Message----- From: Jianghai Zhu [mailto:[email protected]] Sent: Sat 8/4/2007 9:19 PM To: PHENIX user mailing list Subject: [phenixbb] R, Rfree, and wxu_scale Hi, Just finished a round of refinement. Rfree went up about 1% and R went down a bit. I am wondering what happened here. Also Rfree always went down after TLS refinement but always went up a lot more after the individual ADP refinement. Is there anything I can do here? Should I use weaker B restraints? I tried to assign a wxu_scale value. But phenix.refine automatically adjust it to 1.81 every time. ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3982 0.5701 6.156859e+00 6.238509e+00 1_bss: 0.2008 0.2494 5.949117e+00 6.088855e+00 1_xyz: 0.2030 0.2497 5.953829e+00 6.091696e+00 1_adp: 0.1998 0.2559 5.952833e+00 6.099340e+00 2_bss: 0.1996 0.2557 5.952517e+00 6.099196e+00 2_xyz: 0.1984 0.2576 5.953246e+00 6.104085e+00 2_adp: 0.1974 0.2578 5.950434e+00 6.102336e+00 3_bss: 0.1972 0.2574 5.950333e+00 6.102222e+00 3_xyz: 0.1997 0.2576 5.956524e+00 6.103647e+00 3_adp: 0.1987 0.2590 5.955554e+00 6.104434e+00 3_bss: 0.1986 0.2588 5.955445e+00 6.104227e+00 ------------------------------------------------------------------------ Weights for target T = Exray * wxc * wxc_scale + Echem * wc and angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/d_sites) stage wxc wxu wxc_sc wxu_sc /_gxc,gc /_gxu,gu 0 : 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_bss: 5.5611e-01 7.2249e-01 0.050 1.810 96.334 101.736 1_xyz: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 1_adp: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_bss: 4.5001e-01 6.1023e-01 0.050 1.810 96.591 102.016 2_xyz: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 2_adp: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_bss: 5.1326e-01 6.5356e-01 0.050 1.810 112.802 141.393 3_xyz: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_adp: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 3_bss: 3.3568e-01 7.0695e-01 0.050 1.810 111.975 135.760 ------------------------------------------------------------------------ Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

Hi Jianghai,

Just finished a round of refinement. Rfree went up about 1% and R went down a bit. I am wondering what happened here.

You may want to play with wxc_scale and wxu_scale, that define relative contribution of X-ray term in coordinate and ADP refinement, correspondingly. The corresponding weights, wxc and wxu, are determined automatically and are good for most of the cases, but as always, there are some deviations (rarely significant). Try different values for wxc_scale: just an array of values differing from default by say 0.25, 0.5, 1.5, 2 times and choose the one that gives you the best Rfree, gap Rfree-Rwork and geometry statistics. Same for wxu_scale. This always almost helps to resolve this kinds of issues.

Also Rfree always went down after TLS refinement but always went up a lot more after the individual ADP refinement. Is there anything I can do here?

Here you must be careful. There are two potential traps to be aware of (these are not bugs but features that people have to be aware of): 1) If you do TLS first, the atoms in output file have ANISOU records. If you then take that output file and refine individual ADP (without using TLS), by default they will be refined as anisotropic (since input file has ANISOU records and those atoms are considered as anisotropic). This is most likely not what you want and also in this case Rfree may go up drastically. 2) If you force them to be refined isotropically, then the anisotropic atoms got converted to isotropic and hence both R and Rfree will go up. This is also you may not want to do. So, the best, if you used TLS refinement once, keep using it in next refinements, otherwise you will fall into one of two traps above.

Should I use weaker B restraints? I tried to assign a wxu_scale value. But phenix.refine automatically adjust it to 1.81 every time.

This is intentional and always happens for TLS+ADP individual refinement. We found this the best by re-refining 350 models from PDB. All these questions are explained in depth in phenix.refine documentation in the next upcoming PHENIX release. Pavel.