[phenixbb] model vs Wilson b-factor

Gino Cingolani Gino.Cingolani at jefferson.edu
Wed Apr 21 10:42:39 PDT 2010

Hi all,

we've solved a large structure (~20,000 residues/asymm unit), with 4-fold ncs and diffraction data to 3.3A.

The Rfree/Rfac is ~28%-24% with OK geometry with no major outliers in the Ramachandran plot.
I would think I'm done (.. after 6 years!). 

However, my refined model b-factor (~130A2) is >> Wilson b-factor (~80A2). Obviously I'm not too happy with it.

Here is what I tried to resolve this discrepancy: 
--> play with wxu_scale 
--> play with B-factor weight in ncs restraint (4-fold ncs)
--> play with number of macrocycles 
--> Redefine tls groups

So far nothing really works, except switching from
individual_adp to group_adp. However, this increases 
my Rfree by almost 3%.

Any ideas?

Thanks in advance,

Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab    (215) 503 4595
Fax    (215) 923 2117
E-mail:   gino.cingolani at jefferson.edu
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge")
Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120) 

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