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

[sbiswas2 at ncsu.edu]

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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