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:
[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-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany