[phenixbb] Error in the end of phenix-refine with NCS

José Trincão trincao at dq.fct.unl.pt
Thu Apr 22 03:47:51 PDT 2010

I ran 2 jobs of phenix.refine with ncs (disabled automatic definition) and real-space refinement, weight optimization, 3 macrocycles. In the end of the third macrocycle I got these error messages for both:
===================== NCS restraints at end of refinement =====================

NCS restraint group 1:
  NCS operator 1:
    Reference selection: "chain A"
        Other selection: "chain B"
    Number of atom pairs: 9281
Traceback (most recent call last):
  File "/usr/local/phenix-1.6.1-357/phenix/phenix/command_line/refine.py", line 11, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/command_line.py", line 89, in run
  File "/usr/local/phenix-1.6.1-357/phenix/phenix/refinement/driver.py", line 1187, in run
    out        = log)
  File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 713, in show_operators
    ncs_operators.show(sites_cart=sites_cart, out=out, prefix=prefix+"  ")
  File "/usr/local/phenix-1.6.1-357/cctbx_project/mmtbx/ncs/restraints.py", line 470, in show
    prefix=prefix+"  ")
  File "/usr/local/phenix-1.6.1-357/cctbx_project/libtbx/utils.py", line 690, in write
IOError: [Errno 5] Input/output error

What could be the problem?



José Trincão, PhD	CQFB at FCT-UNL
2829-516 Caparica, Portugal

"It's very hard to make predictions... especially about the future" - Niels Bohr

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