Regarding the warning message "The top solution from a TF rescoring did not
pack”, I get this on all the PHASER jobs that I have run recently, but looking
through the PHASER log file I cannot see any evidence for packing failure.
It may be that the failure is buried in an obscure place in the very long log
file, but if I search for “pack” then I get the output summarised below, all of
which, apart from the ADVISORY, suggests to me that there is no problem at all
with the packing.
Perhaps someone on the PHASER team can cast light on this.
Andrew
Extracts from PHASER log file:
TRANSLATION FUNCTIONS
---------------------
Target Function: FAST LETF1
Translation Packing Function applied: top peak will pack
Translation Packing Cutoff: 50%
Sampling: 1.82 Angstroms
===============================================
----------------
PACKING FUNCTION
----------------
There are 4 solutions to pack
Packing analysis
0% 100%
|=====| DONE
<!--SUMMARY_BEGIN-->
Packing Table
-------------
Solutions accepted if pairwise clashes less than 10 % of trace atoms
#in #out Clash-% Symm TF-SET ROT TFpk# TF TFZ SpaceGroup
1 Top1 0.741 -- 1 1 1 325.94 26.03 P 1
2 2 1.058 -- 1 2 1 293.29 24.34 P 1
3 3 0.952 -- 1 3 1 245.70 21.88 P 1
4 4 0.847 -- 1 4 1 211.49 20.11 P 1
4 accepted of 4 solutions
4 pack of 4 accepted solutions
==================================================
-------------------
TRANSLATION PACKING
-------------------
Translation Packing Cutoff: 50%
All solutions have been packed
==================================================
Packing Fast Search Translations...
9871 peaks
500 peaks over 1049.74 checked for packing
Translation peak 1 first to be kept
Done
<!--SUMMARY_BEGIN-->
New Top Packing Fast Translation Function FSS = 2181.37 (TFZ=46.3) at Trial
#1
<!--SUMMARY_END-->
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There was 1 site over 67.5% of top
1 peak selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.719 0.122 0.890 2181.4 46.35
Top 1 translations before clustering will be rescored
Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 1
0% 100%
|==| DONE
Packing LLG Translations: pass 1 of 11...
1 peaks
No peaks over 1878.46 - no packing check
Packing LLG Translations: pass 2 of 11...
1 peaks
1 peaks over 1878.46 checked for packing
Translation peak 1 first to be kept
Done
Exit: found a peak that packs
-==================================================
*** AND THEN ***
------------------------------------------------------------------------------------------
Advisory: The top solution from a TF rescoring did not pack
------------------------------------------------------------------------------------------
-==================================================
-
> On 18 Sep 2017, at 15:06, Eleanor Dodson <[email protected]> wrote:
>
> You need to provide a bit more information.
>
> First of all about the data processing..
>
> Is the space group correct?
> ways of being misled are:
> Non-crystallographic translations with a shift of ~0.5 along an axis - say a.
> This will generate absences in the odd h 0 0 reflections and can make the
> space group appear to be P 21 21 21 whilst it is really P 2 21 21..
>
> Perfect twinning can have the same effect. In an orthorhombix space group
> this can usually only occur if two axes have approximately the same length,
> but the data processing stats can indicate if that is the case.
>
> Then - re PHASER. The packing rejection criteria may be set too severely -
> that seems the case for your solution.
>
> Best check on any MR solution is: does it refine - give it 20 cycles of
> mindless refinement and see if the R and FreeR go down.
>
> Then look at the maps and see if there are obvious corrections to be made..
>
> Eleanor
>
> On 18 September 2017 at 14:59, Satvik Kumar <[email protected]
> <mailto:[email protected]>> wrote:
> Dear Crystallographers,
>
> I am trying to solve a structure in the space group P212121. Based on
> Matthews coefficient, there are 4 molecules in the asymmetric unit.
>
> Based on my limited reading about using of Phaser, I understand that a single
> chain should be used as search model even though many copies are present in
> asymmetric unit. Am I correct?
>
> So when I use a single chain as search model and ask Phaser to search for 4
> molecules, Phaser identifies a single solution with a warning "The top
> solution from a TF rescoring did not pack" and a warning "Search request
> requires more scattering than defined in composition. Composition increased
> to accommodate search components". But the final values reported "PAK=2
> LLG=1065 TFZ==22.6" indicate that phaser has solved the problem.
>
> Can anyone please explain the meaning of the warning.
>
> When I inspect the arrangement of the chains (attachment), I observe minimal
> contact between the chains and a large cavity in the center. Can a crystal
> form this way?
>
> I have also tried using the dimer as search model and asking phaser to search
> for 2 molecules. Even in this case, Phaser finds a single solution but the
> warning and the advisory still appear as before. The numbers reported reduce
> a bit to "PAK=1 LLG=722 TFZ==29.2".
>
> Please help me in understanding these results.
>
> Thanks,
> Satvik
>
>
>
