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
Hi Raja, if this problem still exist in the latest version of PHENIX, then I can only fix it having your data and model and the exact command you use (since it's almost impossible to find why it crashes this way without reproducing the crash locally). So if it still crashing and you are interested in fixing it, please send me the data, model and the command. As always, I will keep your data confidential. Cheers, Pavel. On 9/16/2008 3:34 PM, Raja Dey wrote:
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Pavel Afonine -
Raja Dey -
Ralf W. Grosse-Kunstleve