From: Yuri <[email protected]>
To: phenix forum <[email protected]>
Sent: Saturday, May 21, 2011 7:55 PM
Subject: [phenixbb] Weird R-free discrepancy.
I was working on a model for at 1.9 A using the previous phenix release (650). I was almost finished r-free was 0.197. I installed the newest release and refined again and my r-free went up to 0.228!!.
The values for bsol and ksol look significantly different. I do not understand where the biggest difference is coming from...
Below I pasted part of the .log files. Old and new, respectively.
=============================== refinement start ==============================
----------structure factors based statistics (before refinement)----------
----------X-ray data----------
|--(resolution: 1.90 - 28.74 A; n_refl. = 32203)------------------------------|
|
|
| r_work= 0.1747 r_free= 0.1967 ksol= 0.40 Bsol= 39.70 scale= 0.064 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.65,-1.65,3.31,-0.00,0.00,0.00); trace/3= -0.00 |
|
|
| maximum likelihood estimate for coordinate error: 0.21 A |
| x-ray target function (ml) for work reflections: 2.567485 |
=============================== refinement start ==============================
----------structure factors based statistics (before refinement)----------
----------X-ray data----------
|--(resolution: 1.90 - 28.74 A; n_refl. = 34277)------------------------------|
| |
| r_work= 0.1911
r_free= 0.2279 ksol= 0.40 Bsol= 59.62 scale= 0.063 |
| |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.73,-1.73,3.47,0.00,0.00,-0.00); trace/3= 0.00 |
| |
| maximum likelihood estimate for coordinate error: 0.55 A
|
| x-ray target function (ml) for work reflections: 2.591014 |
|-----------------------------------------------------------------------------|
-- Yuri Pompeu
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