Hi Everyone!
Has anyone else encountered a refinement/regularisation issue in coot where
refinement produces a phi NaN? It seems to be fairly new and specific to
0.9.5 and will completely freeze the coot process. Unfortunately the only
info I can give is that it seems to be stochastic but rather uncommon and
model/map independent. While frozen coot uses very little resources and
responds to a SIGTERM command.
Best,
Victor
Coot version:
0.9.5 (revision-count 10365)
[with guile 1.8.8 embedded]
[with python 2.7.18 embedded]
Builder_info: build-host: ubuntu1604 on: Tue 16 Mar 0116.02 EDT 2021 by
paule
Binary type: Linux-x86_64-ubuntu-16.04.6-python-gtk2
Final terminal output before freezing:
(0) " CD2"/1/chainid="Ao"/8/PHE, occ: 1.000 with B-factor: 30.000 element:
" C" at (307.355,222.991,262.787) : 0.402
addition of target position restraints: pre and post sizes: 5750 5751
WARNING: observed torsion phi is a NAN!
debug-info: nan/nan
debug-info: atom indices: 3
debug-info: atom indices: 8
debug-info: atom indices: 9
debug-info: atom indices: 10
debug-info: atom indices: 19
debug-info: P1: xyz = ( nan, nan, nan)
debug-info: P2: xyz = ( nan, nan, nan)
debug-info: P3: xyz = ( nan, nan, nan)
debug-info: P4: xyz = ( nan, nan, nan)
debug-info: P5: xyz = ( nan, nan, nan)
debug-info: a: xyz = ( nan, nan, nan)
debug-info: b: xyz = ( nan, nan, nan)
debug-info: c: xyz = ( nan, nan, nan)
debug-info: d: xyz = ( nan, nan, nan)
in distortion_score_rama() 0 nan nan nan
in distortion_score_rama() 1 nan nan nan
in distortion_score_rama() 2 nan nan nan
in distortion_score_rama() 3 nan nan nan
in distortion_score_rama() 4 nan nan nan
in distortion_score_rama() 5 nan nan nan
in distortion_score_rama() 6 nan nan nan
in distortion_score_rama() 7 nan nan nan
in distortion_score_rama() 8 nan nan nan
in distortion_score_rama() 9 nan nan nan
in distortion_score_rama() 10 nan nan nan
in distortion_score_rama() 11 nan nan nan
in distortion_score_rama() 12 nan nan nan
in distortion_score_rama() 13 nan nan nan
in distortion_score_rama() 14 nan nan nan
WARNING: observed torsion psi is a NAN!
debug-info: nan/nan
debug-info: atom indices: 3
debug-info: atom indices: 8
debug-info: atom indices: 9
debug-info: atom indices: 10
debug-info: atom indices: 19
debug-info: P1: xyz = ( nan, nan, nan)
debug-info: P2: xyz = ( nan, nan, nan)
debug-info: P3: xyz = ( nan, nan, nan)
debug-info: P4: xyz = ( nan, nan, nan)
debug-info: P5: xyz = ( nan, nan, nan)
debug-info: a: xyz = ( nan, nan, nan)
debug-info: b: xyz = ( nan, nan, nan)
debug-info: c: xyz = ( nan, nan, nan)
debug-info: d: xyz = ( nan, nan, nan)
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