[phenixbb] Autobuild
Heather L Condurso
condurso at bc.edu
Fri Sep 6 14:54:33 PDT 2013
I'm a bit confused about what is going on with my autobuild run. I solved
a structure from anomalous data to 2.7A but many loops are missing. I ran
phaser with the current model and native data that extends to 2.4A and got
a solution and started autobuild from there. I used mostly the default
settings and rebuild_in_place=False. After a pretty short time I realized
the run was over and at the bottom of the log I see this:
Cycle 3 R/Rfree=0.28/0.35 Built=488 Placed=467
AutoBuild_build_cycle AutoBuild Run 162 Fri Sep 6 14:33:39 2013
Deciding if we should continue...
Recent R change per cycle: 0.0
Ending these build cycles as the recent change in R per cycle has been
0.0 and the required value of change is -0.005
and the R is somewhat acceptable at 0.276670644792
All done with build cycles in this region
AutoBuild_set_up_build AutoBuild Run 162 Fri Sep 6 14:33:40 2013
All omit/non-omit regions completed
finished AutoBuild Run 162 Fri Sep 6 14:33:40 2013
Finishing AutoBuild Run 162
Facts written to AutoBuild_run_162_/AutoBuild_Facts.dat
AutoBuild Run 162
Summary of model-building for run 162 Fri Sep 6 14:33:40 2013
Files are in the directory: /Users/heather/Desktop/M/AutoBuild_run_162_/
Starting mtz file:
/Users/heather/Desktop/M/ImportRawData_run_4_/A-3_xx_PHX.mtz
Sequence file: /Users/heather/Desktop/M/m.pir
Best solution on cycle: 2 R/Rfree=0.26/0.33
Summary of output files for Solution 1 from rebuild cycle 2
--- Model (PDB file) ---
pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb
--- Model (CIF file) ---
cif_pdb_file: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.cif
--- Refinement log file ---
log_refine:
/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_refine
--- Model-building log file ---
log: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log
--- Model-map correlation log file ---
log_eval: /Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.log_eval
--- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT
FOFCWT PHFOFCWT ---
refine_map_coeffs:
/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_map_coeffs.mtz
--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag
---
refine_data:
/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz
--- Density-modified map coefficients FWT PHWT ---
denmod_map_coeffs:
/Users/heather/Desktop//AutoBuild_run_162_/overall_best_denmod_map_coeffs.mtz
You might consider making one very good model now with:
phenix.autobuild \
data=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best_refine_data.mtz
\
model=/Users/heather/Desktop/M/AutoBuild_run_162_/overall_best.pdb \
rebuild_in_place=True \
seq_file=/Users/heather/Desktop/M/m.pir
My full sequence is 325 amino acids so only about 75% is build in. I am
hoping autobuild can help find at least some of these missing residues.
Why would the change in R be zero? What is meant by "You might consider
making one very good model now with:"? I tried running autobuild with
these new files and rebuild_in_place=true and get the same type of message.
Is this the best that autobuild can do? I also ran the phaser solution
through refinement and can significantly lower the Rs from 0.26/0.33 to
0.22/0.30. I appreciate any advice on how best to proceed.
I am using 1.8.2-1472 if that matters.
Thanks,
Heather
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