[phenixbb] R, Rfree, and wxu_scale

[Mayer, Mark (NIH/NICHD) [E]]

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:jzhu at cbr.med.harvard.edu]
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
+++++++++++++++++++++++++++++++




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