Greetings fellow crystallographers,<br><br>This past weekend, I collected some new data on my new project, indexed, scaled it, and found a phaser solution. The resolution is 3.6 A and I need to find one of the protein components, so I&#39;m slowly refining piece-by-piece so I don&#39;t overdo it and flatten out the missing protein. To do this, I simply do rigid body and tls refinements for decreasingly smaller pieces of the protein I&#39;ve already found. This method worked for me in the past for a similar structure. However, this time, as the refinement is finishing up, I get an input/output error and the program shuts down. Sometimes I get similar errors, and I can fix them by simply running the job again, overwriting the failed job, but this time that doesn&#39;t seem to be working. Here&#39;s the output from my .log file:<br>

<br>Traceback (most recent call last):<br>  File &quot;/programs/phenix-1.5-2/phenix/phenix/command_line/refine.py&quot;, line 11, in &lt;module&gt;<br>    command_line.run(command_name=&quot;phenix.refine&quot;, args=sys.argv[1:])<br>

  File &quot;/programs/phenix-1.5-2/phenix/phenix/refinement/command_line.py&quot;, line 89, in run<br>    call_back_handler=call_back_handler)<br>  File &quot;/programs/phenix-1.5-2/phenix/phenix/refinement/driver.py&quot;, line 1121, in run<br>

    call_back_handler       = call_back_handler)<br>  File &quot;/programs/phenix-1.5-2/phenix/phenix/refinement/strategies.py&quot;, line 428, in refinement_machine<br>    monitors   = monitors)<br>  File &quot;/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py&quot;, line 559, in __init__<br>

    out    = log)<br>  File &quot;/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/rigid_body.py&quot;, line 619, in show<br>    translations=t_vec)<br>  File &quot;/programs/phenix-1.5-2/cctbx_project/mmtbx/refinement/print_statistics.py&quot;, line 161, in show_rigid_body_rotations_and_translations<br>

    % euler_angle_convention, suffix=frame)<br>  File &quot;/programs/phenix-1.5-2/cctbx_project/libtbx/utils.py&quot;, line 652, in write<br>    file_object.write(str)<br>IOError: [Errno 5] Input/output error<br><br>Again, the only thing I&#39;ve done is made a few rigid body and tls groups. Please advise!<br>

<br>Thanks,<br>Geoff<br clear="all"><br>-- <br>Geoffrey K. Feld<br><br>Department of Chemistry<br>492 Stanley Hall<br>University of California, Berkeley<br><br>&quot;Vigilia pretium libertatis&quot;<br>