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]
[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 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-SalvatierraMacromolecular crystallography and Nucleic acid chemistryMax Planck Institute for Biophysical ChemistryAm Fassberg 11 37077 GöttingenGermany