[phenixbb] Problem in real space

Firdous Tarique kahkashantarique at gmail.com
Mon Jul 26 00:53:08 PDT 2021


Hi

I am getting the following error during real space refinement of the model
and map. Can anybody suggest what it is actually about. It is something
about geometry_restraints but I am not able to figure it out
where.

Can we do something in refinement settings Or change any threshold value to
avoid these problems?

Input is 80S.pdb ribosome and its corresponding em map.

 File
"/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py",
line 1486, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)

  File
"/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py",
line 1388, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)

  File
"/apps/PHENIX/1.18.2/phenix-1.18.2-3874/modules/cctbx_project/cctbx/geometry_restraints/manager.py",
line 1269, in check_bonded_distance_cutoff
    raise RuntimeError(msg)

Best regards

Firdous
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