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