[phenixbb] phenix.automr high zscore but too many clashes

[zach powers]

Hi,


I have a problem and i wonder if someone has had a similar experience. I 
have been using phenix.automr program to find an MR solution for  a 
protein.  When I ask Phaser to use copies=2 I find a number of solutions 
with poor z-scores (3-4). When I ask it to use copies=3, I get great 
Z-scores (see below) but no solution due to the high number of clashes 
(>100!).

As an x-ray newbie I am a bit perplexed of what to make of this: the 
solution is not good because there is not enough space in the unit cell 
to comfortably accommodate all three molecules yet the Z-score indicates 
the structure is good.

My structure does have several loops and these may be contributing to 
the clashing residues. As a newbie I have a newbie question - what does 
this mean (great z-score but no solutions)? Is this non-solution a 
possible solution if I play with it, or is the packing simply too tight 
and the Z-scores are not valid?

In the meantime I am chopping my protein into sub-domains as recommended 
in the Phaser documentation, but if anyone has seen something like this 
before, any suggestions are welcome.

thanks
zach charlop-powers




Packing Table: Space Group P 3
   ------------------------------
   Solutions accepted if number of clashes = 135 (lowest number of 
clashes in list)
   provided this number of clashes <= 10 (maximum number of allowed clashes)
   #  #Clashes #   Accepted Annotation
   1   188         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=10.4
   2   156         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=10.2
   3   151         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=9.8
   4   146         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=9.7
   5   187         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 
TFZ=10.5
   6   202         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=9.2
   7   170         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=9.1
   8   144         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 
TFZ=10.2
   9   177         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=9.1
   10  153         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.9
   11  150         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.8
   12  217         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.6
   13  182         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.6
   14  135         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.5
   15  175         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.3
   16  159         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.3
   17  192         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.3
   18  165         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 
TFZ=9.2
   19  169         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 
TFZ=9.1
   20  158         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.0
   21  173         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=8.0
   22  154         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 
TFZ=8.9
   23  206         NO       RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 
TFZ=7.8

   0 accepted of 23 solutions