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-----
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
+++++++++++++++++++++++++++++++
<winmail.dat>
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