Increase the number of allowed clashes in Phaser, re-run it then look at
the packing of the solution found and identify the source of the
clashes. Possibilities for the clash issue include:
1. Wrong space group
2. Flexible loops or termini in search model not present or
differently arranged in your crystal target
Once you look at the packing in Coot or Pymol, you will have a good idea
of what to do next. If the problem is flexible loops or misplaced N- or
C-termini, you can delete these regions from your search model (they are
not helping you phase anyway) and re-run Phaser with an appropriately
truncated search model.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [log in to unmask]
On 6/17/2014 10:44 AM, Almudena Ponce Salvatierra wrote:
> Dear ccp4 users,
>
> I get the following message from Phaser when I do a molecular
> replacement with two ensembles. One of the ensembles is placed but the
> second one is not placed, and then it says this:
>
> Solutions with Z-scores greater than 13.0 (the threshold indicating a
> definite
>
> solution) were rejected for failing packing test
>
> #1 TFZ=16.8 PAK=487
>
> #2 TFZ=17.4 PAK=440
>
> #3 TFZ=17.0 PAK=312
>
> #4 TFZ=16.7 PAK=294
>
> #5 TFZ=16.8 PAK=227
>
> #6 TFZ=16.6 PAK=284
>
> #7 TFZ=16.2 PAK=219
>
> #8 TFZ=16.3 PAK=287
>
> #9 TFZ=16.1 PAK=186
>
> #10 TFZ=16.6 PAK=277
>
> #11 TFZ=16.7 PAK=204
>
> #12 TFZ=16.8 PAK=404
>
> #13 TFZ=15.9 PAK=271
>
> #14 TFZ=15.8 PAK=194
>
> #15 TFZ=14.9 PAK=229
>
> #16 TFZ=16.4 PAK=368
>
> #17 TFZ=17.3 PAK=194
>
> #18 TFZ=15.2 PAK=240
>
> #19 TFZ=16.1 PAK=325
>
> #20 TFZ=15.3 PAK=455
>
> #21 TFZ=16.5 PAK=298
>
> #22 TFZ=16.6 PAK=290
>
> #23 TFZ=15.2 PAK=259
>
> #24 TFZ=16.2 PAK=194
>
> #25 TFZ=16.1 PAK=314
>
> #26 TFZ=16.3 PAK=194
>
> #27 TFZ=16.3 PAK=387
>
> #28 TFZ=15.6 PAK=193
>
> #29 TFZ=15.7 PAK=219
>
> #30 TFZ=15.6 PAK=474
>
> #31 TFZ=15.1 PAK=194
>
> #32 TFZ=15.4 PAK=339
>
> #33 TFZ=15.5 PAK=210
>
> #34 TFZ=15.2 PAK=300
>
> #35 TFZ=15.6 PAK=186
>
> #36 TFZ=16.2 PAK=216
>
> #37 TFZ=14.9 PAK=182
>
> #38 TFZ=15.7 PAK=279
>
> #39 TFZ=15.5 PAK=285
>
> #40 TFZ=15.0 PAK=374
>
> #41 TFZ=15.4 PAK=404
>
> #42 TFZ=15.3 PAK=185
>
> #43 TFZ=15.6 PAK=227
>
> #44 TFZ=14.8 PAK=364
>
> #45 TFZ=15.7 PAK=193
>
> #46 TFZ=14.5 PAK=448
>
> #47 TFZ=14.6 PAK=219
>
> #48 TFZ=15.5 PAK=210
>
> #49 TFZ=15.7 PAK=189
>
> #50 TFZ=15.0 PAK=193
>
> #51 TFZ=15.0 PAK=281
>
> #52 TFZ=15.2 PAK=202
>
>
> And the list still continues for a bit. How should I think about this?
> I would assume that the clashes are too many only by seeing those
> numbers, but maybe there is something else to take into account?
>
> Thanks a lot in advance.
>
> Best wishes,
>
> Almudena
>
>
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
