Roger, Given that PAK value is the number of clashing residues I doubt that in this case it is a loop clash etc.
As a general comment though you are absolutely correct. Cheers, Ed Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Roger Rowlett <rrowl...@colgate.edu> </div><div>Date:06/17/2014 10:52 AM (GMT-05:00) </div><div>To: CCP4BB@JISCMAIL.AC.UK </div><div>Subject: Re: [ccp4bb] packing test PHASER </div><div> </div>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: rrowl...@colgate.edu 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
