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:
- Wrong space group
- 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:
[log in to unmask]" type="cite">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 definitesolution) 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
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Almudena Ponce-SalvatierraMacromolecular crystallography and Nucleic acid chemistryMax Planck Institute for Biophysical ChemistryAm Fassberg 11 37077 GöttingenGermany