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

zach powers zachary.charlop-powers at mssm.edu
Fri Apr 17 15:06:54 PDT 2009


Thanks for the suggestions, everyone.

I am pretty sure I have the spacegroup and the protein-per-unit-cell 
correct. The mathews coefficient is at the maximum for P3 with 3 
molecules but near the minimum for the other spacegroups.

It was also suggested to me that i may have one of two problems:

1)that my protein may sit on the axis of symmetry.
2)that I many have a high degree of NCS which would falsely generate a 
high z-score.

i will follow up on these suggestions.

thanks again for your time
zach cp



On 04/17/2009 10:32 AM, sbiswas2 at ncsu.edu wrote:
> Hi,
> It could be a problem of space group as rightly pointed out by one of us.
> Try re running and ask phaser to find the space group for you this helps
> sometimes.  I dont think its a good idea to increase the clashes, at least
> thats what the phaser manual says. Also I noticed that your RFZ is higher
> than TFZ does anyone else think this is a problem?
> Shya
>
>
> Department of Structural Biochemistry,
> NCstate University,
> Raleigh,
> NC27695
>
>
>    
>> 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
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>>      
>
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