[phenixbb] Crash after Torsion Angle Refinement
Ulrich Baumann
ulrich.baumann at ibc.unibe.ch
Wed Oct 7 05:26:23 PDT 2009
Dear Phenix-Gurus,
running Phenix-1.5-2 under RHEL 5, 64 bit I get the following error
message -- this appears to occur after the actual torsion angle
refinement. Hydrogens were added, custom-defined bonds excluded. Could
anybody help me out, please?
Thanks,
Ulrich
merge clusters with multiple connections: 1 pass
suppressing allowed origin shifts: True
new target temperature: 2500.00 K
step= 1 temperature= 2500.0 rmsd=0.0459 r_work=0.2537 r_free=0.3224
step= 25 temperature= 2394.4 rmsd=0.3481 r_work=0.2575 r_free=0.3316
step= 50 temperature= 2284.4 rmsd=0.3254 r_work=0.2505 r_free=0.3287
step= 75 temperature= 2174.4 rmsd=0.3205 r_work=0.2476 r_free=0.3271
step= 100 temperature= 2064.4 rmsd=0.3189 r_work=0.2461 r_free=0.3261
step= 125 temperature= 1954.4 rmsd=0.3205 r_work=0.2451 r_free=0.3255
step= 150 temperature= 1844.4 rmsd=0.3254 r_work=0.2443 r_free=0.3252
step= 175 temperature= 1734.4 rmsd=0.3287 r_work=0.2437 r_free=0.3250
step= 200 temperature= 1624.4 rmsd=0.3329 r_work=0.2432 r_free=0.3250
step= 225 temperature= 1514.4 rmsd=0.3393 r_work=0.2427 r_free=0.3250
step= 250 temperature= 1404.4 rmsd=0.3433 r_work=0.2424 r_free=0.3249
step= 275 temperature= 1294.4 rmsd=0.3479 r_work=0.2421 r_free=0.3250
step= 300 temperature= 1184.4 rmsd=0.3543 r_work=0.2419 r_free=0.3251
step= 325 temperature= 1074.4 rmsd=0.3581 r_work=0.2416 r_free=0.3250
step= 350 temperature= 964.4 rmsd=0.3629 r_work=0.2414 r_free=0.3251
step= 375 temperature= 854.4 rmsd=0.3687 r_work=0.2413 r_free=0.3251
step= 400 temperature= 744.4 rmsd=0.3722 r_work=0.2411 r_free=0.3252
step= 425 temperature= 634.4 rmsd=0.3771 r_work=0.2409 r_free=0.3252
step= 450 temperature= 524.4 rmsd=0.3819 r_work=0.2408 r_free=0.3252
step= 475 temperature= 414.4 rmsd=0.3854 r_work=0.2407 r_free=0.3253
step= 500 temperature= 304.4 rmsd=0.3906 r_work=0.2406 r_free=0.3254
allowed origin shift velocity corrections applied (magnitudes):
n: 501
min: 0
max: 1.30923e-16
mean: 1.24537e-17
sum of allowed origin shift velocity corrections (vectors):
(0.00000, 0.00000, -0.00000)
================================ xyz refinement
===============================
Traceback (most recent call last):
File
"/usr/local/phenix-1.5-2/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-1.5-2/phenix/phenix/refinement/command_line.py",
line 89, in run
call_back_handler=call_back_handler)
File "/usr/local/phenix-1.5-2/phenix/phenix/refinement/driver.py",
line 1121, in run
call_back_handler = call_back_handler)
File
"/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line
552, in refinement_machine
target_weights_params, main, h_params, log, params)
File
"/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line
839, in __init__
minimized = self.minimize()
File
"/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line
918, in minimize
h_params = self.h_params)
File
"/usr/local/phenix-1.5-2/cctbx_project/mmtbx/refinement/minimization.py", line
39, in __init__
self.regularize_h_and_update_xray_structure()
File
"/usr/local/phenix-1.5-2/cctbx_project/mmtbx/refinement/minimization.py", line
222, in regularize_h_and_update_xray_structure
self.h_params.xh_bond_distance_deviation_limit)
File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/model.py", line
167, in idealize_h
for t in self.xh_connectivity_table():
File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/model.py", line
118, in xh_connectivity_table
xray_structure = xray_structure).table
File "/usr/local/phenix-1.5-2/cctbx_project/mmtbx/model.py", line
47, in __init__
xray_structure.sites_cart()).bond_proxies.simple
AttributeError: 'NoneType' object has no attribute 'simple'
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