WEll - I think this explains your crazy B values - you have somehow
*normalised* the data at processing stagr.
>From the pointless log..
You usually dont need a reference data set and certainly not a set of
calculated structure factors.
Do you have CCP4I2 installed?
If so just feed the integrated data through the processing and send me the
log perhaps?
....
*Reference list generated by structure factor calculation*
from coordinate file
/home/janani-ganesh/Documents/JG/XData/K232Q_24042025_P72A5/CCP4I/K232Q_P72_phaser.1_refmac1.pdb
Spacegroup: P 32 2 1
Cell: 81.84 81.84 134.77 90.00 90.00 120.00
Maximum resolution used: 1.884
Number of reflections: 42901
I*ntensity normalisation: B-factor = -8.7*
*And taken from the phenix log:*
Note that the <Fobs> at low resolution is slightly LOWER than at the
highest resolution! This is unlikely. for a protein!
.....
F_model = k_total * (F_calc + k_mask * F_mask)
k_total = k_isotropic * k_anisotropic
Resolution Compl Nwork Nfree R_work <Fobs> <Fmodel> kiso kani
kmask
38.004-13.464 66.21 90 6 0.5449 232.778 190.690 0.824 0.739
0.353
13.427-11.087 93.58 99 3 0.1952 *459.972 428.082 *1.279 0.749
0.340
11.084-9.179 91.06 153 10 0.1983 502.739 469.985 1.271 0.749
0.330
9.142-7.564 88.75 271 13 0.2210 405.976 376.935 1.215 0.751
0.329
7.548-6.244 92.16 492 25 0.2733 342.193 302.079 1.212 0.751
0.328
6.239-5.156 97.23 895 51 0.2545 365.657 321.767 1.164 0.750
0.321
5.153-4.256 97.19 1575 83 0.1988 487.348 449.464 1.271 0.749
0.270
4.256-3.514 99.83 2815 149 0.2169 582.502 526.163 1.702 0.748
0.084
3.514-2.902 99.89 4989 263 0.2427 597.717 534.626 2.337 0.747
0.060
2.901-2.396 99.85 8718 460 0.2988 532.605 456.384 2.752 0.744
0.000
2.396-2.103 97.60 9284 494 0.3208 *546.159 458.454* 3.232 0.742
0.000
So fix your data processing first - then your B factors should become
sensible and the R factors also - you are overweighting the high resolution
data greatly
And if the crystal is twinned the space group is actually P 32..
Cheers Eleanor
On Wed, 28 May 2025 at 08:04, Janani Ganesh <[email protected]> wrote:
> Dear Professor,
>
> Thank you for your response. I had tried out TLS as well to understand the
> trend, but it did not work. I am attaching the detwin and pointless log
> files for your reference.
>
> I even set the B-factors to an arbitrary value of 30 and performed
> refinement with overall B-factors, but there was no change in the B-factors
> at all.
> Is it possible for you to look at my data and help me with this issue?
>
>
> With my best regards,
> Janani Ganesh
> PhD Scholar, Protein Crystallography Section,
> Homi Bhabha National Institute,
> Mumbai, India.
> Contact No: +91-22-25594062 / +91-7506237778
>
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