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refinement
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Hi
I am having a problem and I would appreciate some help.
I had a reflections file which I processed with denzo using data up to
2.4 A for the 50 images I collected. I then used this reflections file
to refine my structure. I am getting nice maps and my R-factor and Rfree
are going down (21% and 30%).(first dataset)
However, I decided to reprocess my images because during the first half
of my collection the crystal was diffracting to 2.17A (the crystal
decayed).
The first half was processed using data to 2.2 A and the second half
using data to 2.4 A. I then obtained a new reflections file which I was
going to use to continue my refinement.(second data set)
Now comes the problem. When I try to use this new data set, my Rfactor
and Rfree become 51% and 55% and they never go down! Why is this?
For each reflection file I run f2mtz,truncate,cad,freerflag,uniqueify.
Space Group I4.
I have already scaled both data sets and all looks ok.
Thanks,
Paula Kuser
The mtzfiles of both look like:
first dataset:
* Number of Reflections = 26424
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
From MTZUTILS, 9/16/98 11:22:50 after history:
From FREERFLAG, 9/16/98 11:22:49 with fraction 0.050
From FREERFLAG, 9/16/98 11:06:27 with fraction 0.050
From TRUNCATE, 9/16/98 10:00:29
From f2mtz, 9/16/98 10:00:29
data from CAD on 9/16/98
data from CAD on 9/16/98
From FREERFLAG, 9/16/98 11:22:49 with fraction 0.050
From FREERFLAG, 9/16/98 11:06:27 with fraction 0.050
From TRUNCATE, 9/16/98 10:00:29
From f2mtz, 9/16/98 10:00:29
data from CAD on 9/16/98
data from CAD on 9/16/98
* Space group = I4 (number 79)
OVERALL FILE STATISTICS for resolution range 0.000 - 0.189
=======================
Col Sort Min Max Num % Mean Mean Resolution
Type Column
num order Missing complete abs. Low High
label
1 ASC 0 62 0 100.00 23.0 23.0 100.00 2.30
H H
2 NONE 0 62 0 100.00 23.7 23.7 100.00 2.30
H K
3 NONE 0 25 0 100.00 9.3 9.3 100.00 2.30
H L
4 NONE 3.3 251.9 1506 94.30 37.78 37.78 12.94 2.30
F Fnat
5 NONE 0.7 13.2 1506 94.30 3.72 3.72 12.94 2.30
Q SIGFnat
6 NONE 0.0 19.0 0 100.00 9.47 9.47 100.00 2.30
I FreeR_flag
No. of reflections used in FILE STATISTICS 26424
LIST OF REFLECTIONS
===================
0 0 2 ? ? 2.00
0 0 4 ? ? 19.00
0 0 6 ? ? 17.00
0 0 8 ? ? 8.00
0 0 10 ? ? 9.00
0 0 12 ? ? 11.00
0 0 14 115.21 4.52 2.00
0 0 16 39.50 2.14 19.00
0 0 18 53.09 2.61 17.00
0 0 20 75.79 3.39 8.00
&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
second dataset:
* Number of Reflections = 30193
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
From MTZUTILS, 10/ 6/98 10:02:22 after history:
From FREERFLAG, 10/ 6/98 10:02:21 with fraction 0.050
From FREERFLAG, 10/ 6/98 9:53:19 with fraction 0.050
From TRUNCATE, 10/ 6/98 9:53:15
From f2mtz, 10/ 6/98 9:53:14
data from CAD on 10/ 6/98
data from CAD on 10/ 6/98
From FREERFLAG, 10/ 6/98 10:02:21 with fraction 0.050
From FREERFLAG, 10/ 6/98 9:53:19 with fraction 0.050
From TRUNCATE, 10/ 6/98 9:53:15
From f2mtz, 10/ 6/98 9:53:14
data from CAD on 10/ 6/98
data from CAD on 10/ 6/98
OVERALL FILE STATISTICS for resolution range 0.000 - 0.207
=======================
Col Sort Min Max Num % Mean Mean Resolution
Type Column
num order Missing complete abs. Low High
label
1 ASC 0 64 0 100.00 24.1 24.1 100.00 2.20
H H
2 NONE 0 64 0 100.00 24.7 24.7 100.00 2.20
H K
3 NONE 0 26 0 100.00 9.7 9.7 100.00 2.20
H L
4 NONE 3.3 286.2 2853 90.55 39.08 39.08 13.91 2.20
F Fnat
5 NONE 0.8 13.6 2853 90.55 4.45 4.45 13.91 2.20
Q SIGFnat
6 NONE 0.0 19.0 0 100.00 9.47 9.47 100.00 2.20
I FreeR_flag
No. of reflections used in FILE STATISTICS 30193
LIST OF REFLECTIONS
===================
0 0 2 ? ? 2.00
0 0 4 ? ? 19.00
0 0 6 ? ? 17.00
0 0 8 ? ? 8.00
0 0 10 ? ? 9.00
0 0 12 ? ? 11.00
0 0 14 124.36 4.86 2.00
0 0 16 42.57 2.48 19.00
0 0 18 57.29 2.91 17.00
0 0 20 82.20 3.69 8.00
--
Dr Paula Regina Kuser
pkuser@lnls.br
Laboratorio Nacional de Luz Sincrotron - LNLS
Rua Giuseppe Maximo Scolfaro,10.000 Cep 13093-360-Campinas-SP / Brasil
Phone (019) 287-4520 - Ramais 348/317 Fax (019) 287-4632