[phenixbb] AssertionError in refinement

[Raja Dey]

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