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Take a look at FINAL SELECTION section.
In a first case you have 2 CLASHES between trace atoms in solution while in
second there are none and hence you get a model from phaser.
If you want model with the template A just change the number of allowed clashes
before starting pahser.
Andrzej
劉家欣(OZ) wrote:
Dear ALL:
My data had a high Z-score(>10) with A template, but not output pdb. I
check it out twice, it still not output pdb file.
With the same conditions, another Z-score(<10) was obtained with B
template. And this time, we had a output pdb file.
However, the score from B template was small than the one from A template.
It confused me a lot. Any one had some appropriate explanation about that?
Thank you very much.
jaishin
The .sol are described as below:
A.template
---------------
FINAL SELECTION
---------------
Mean (Sigma) used for final selection = -156.312 (24.0562)
Number of solutions stored before final selection = 4
Number of solutions stored (deleted) after final selection = 4 (0)
Fast Translation Function Table: Space Group R 3
------------------------------------------------
#SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble
1 1 192.15 (14.77) - - - -
ensemble1
1 2 160.66 (13.95) - - - -
ensemble1
1 3 160.29 (11.75) - - - -
ensemble1
1 4 148.37 (13.35) - - - -
ensemble1
---- ------
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT
PACKING 1.3.2 ***
*************************************************************************************
Ensemble: ensemble1
-------------------
Structure with lowest rms = xxxx.pdb (1.5)
Trace length before selecting conserved = 763
Trace length after selecting conserved = 763
Solutions rejected if number of clashes > 0
# #CLASHES # ACCEPTED
1 2 NO
2 2 NO
3 2 NO
4 2 NO
0 accepted of 4 solutions
##################################################################################################
B.template:
---------------
FINAL SELECTION
---------------
Mean (Sigma) used for final selection = -11.0591 (8.95763)
Number of solutions stored before final selection = 3
Number of solutions stored (deleted) after final selection = 1 (2)
Fast Translation Function Table: Space Group R 3
------------------------------------------------
#SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble
1 1 77.48 ( 9.52) - - - -
ensemble1
1 2 49.54 ( 6.77) - - - -
ensemble1
1 3 45.14 ( 6.69) - - - -
ensemble1
---- ------
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT
PACKING 1.3.2 ***
*************************************************************************************
Ensemble: ensemble1
-------------------
Structure with lowest rms = .xxxxpdb (1.5)
Trace length before selecting conserved = 338
Trace length after selecting conserved = 338
Solutions rejected if number of clashes > 0
# #CLASHES # ACCEPTED
1 0 1 YES
1 accepted of 1 solutions
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND
PHASING 1.3.2 ***
*************************************************************************************
Space-Group Name (Number): R 3 (146)
Resolution of All Data (Number): 2.40 29.91 (35489)
Resolution of Selected Data (Number): 2.50 29.91 (31379)
Refinement Table: Space Group R 3
---------------------------------
#+ = input number #* = output number
Unsorted (refinement order) Sorted in LL-gain order
Initial Refined Initial Refined
#+ LL-gain LL-gain Unique #* #+ LL-gain LL-gain Unique
=#* =#+
1 77.48 88.24 YES 1 1 77.48 88.24
YES
Mean used for final selection = -11.0591
Sigma used for final selection = 8.95763
Number of solutions stored before final selection = 1
Number of solutions stored (deleted) after final selection = 1 (0)
*************************************************************************************
*** Phaser Module: PERMUTATIONS AND
SPACEGROUPS 1.3.2 ***
*************************************************************************************
NEW BEST SOLUTION: TOP LL-GAIN 88.236222
PERMUTATION #1
SEARCH ENSEMBLE ensemble1
SPACE GROUP: R 3
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND
PHASING 1.3.2 ***
*************************************************************************************
Space-Group Name (Number): R 3 (146)
Resolution of All Data (Number): 2.40 29.91 (35489)
Resolution of Selected Data (Number): 2.40 29.91 (35489)
Refinement Table: Space Group R 3
---------------------------------
#+ = input number #* = output number
Unsorted (refinement order) Sorted in LL-gain order
Initial Refined Initial Refined
#+ LL-gain LL-gain Unique #* #+ LL-gain LL-gain Unique
=#* =#+
1 88.58 88.58 YES 1 1 88.58 88.58
YES
Mean and Standard deviation for final selection not set
No final selection
------------
OUTPUT FILES
------------
0803_3.sol
0803_3.1.pdb
0803_3.1.mtz
--
< Andrzej Lyskowski (andrzej[dot]lyskowski[at]uni-graz[dot]at)
< Chemistry Institute - Phys. Chem./Structural Biology
< Heinrichstrasse 28
< A-8010 Graz, Austria
< Tel.: 43 316 380 54 69
< Fax.: 34 316 380 98 50
> A designer knows he has achieved perfection
> not when there is nothing left to add,
> but when there is nothing left to take away.
> Antoine de Saint-Exupery
