[phenixbb] AssertionError in refinement
Raja Dey
rdey at usc.edu
Tue Sep 16 15:34:22 PDT 2008
Dear PhenixBB Members,
I am getting the following error while I am running the refinement given below: It stopped after a while. I enclosed the last part of the log file.
phenix.refine gat.mtz gat-tlsmd.pdb simulated_annealing=true strategy=rigid_body+individual_sites+group_adp+individual_adp+tls tls.params output.prefix=final_1 --overwrite
================================ ADP refinement ===============================
----------TLS refinement----------
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2491 r_free = 0.3251 target = 3.621992 convergence test = off |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 15)----------------|
| r_work = 0.2437 r_free = 0.3120 target = 3.588460 convergence test = off |
|-----------------------------------------------------------------------------|
|-Information about rigid groups----------------------------------------------|
| Total number of atoms = 1591 Number of rigid groups = 3 |
| group: start point: end point: |
| x B atom residue <> x B atom residue |
| 1: -3.758 92.66 N MET 259 <> 10.389 94.12 CD2 LEU 300 |
| 2: 14.264 58.92 N ILE 301 <> 1.800 100.80 O THR 315 |
| 3: 1.098 66.36 N SER 316 <> -10.129 70.49 CE MET 368 |
|-----------------------------------------------------------------------------|
Traceback (most recent call last):
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run
call_back_after_monitor_collect=call_back_after_monitor_collect)
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run
call_back_after_monitor_collect = call_back_after_monitor_collect)
File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 549, in refinement_machine
h_params = h_params)
File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/refinement/adp_refinement.py", line 153, in __init__
tools.split_u(fmodels.fmodel_xray().xray_structure, tls_selections, offset)
File "/usr/local/phenix-1.3b-rc6/mmtbx/mmtbx/tls/tools.py", line 498, in split_u
assert (u_iso < 0.0).count(True) == 0
AssertionError
While I can successfully run similar refinement on another project.
I have another question. Inclusion of individual_adp in strategy increases R and R(free) in one case(2.8 A data), while decreases in another case (3.6 A data). Both are at the final stage of refinement. Is there any explanation?
Looking forward to hearing from you...
Thanking you in advance...
Raja
More information about the phenixbb
mailing list