[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?

   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):
"/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:])
line 89, in run
   File "/usr/local/phenix-1.5-2/phenix/phenix/refinement/driver.py",  
line 1121, in run
     call_back_handler       = call_back_handler)
"/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line  
552, in refinement_machine
     target_weights_params, main, h_params, log, params)
"/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line  
839, in __init__
     minimized = self.minimize()
"/usr/local/phenix-1.5-2/phenix/phenix/refinement/strategies.py", line  
918, in minimize
     h_params                 = self.h_params)
"/usr/local/phenix-1.5-2/cctbx_project/mmtbx/refinement/minimization.py", line  
39, in __init__
"/usr/local/phenix-1.5-2/cctbx_project/mmtbx/refinement/minimization.py", line  
222, in regularize_h_and_update_xray_structure
   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__
AttributeError: 'NoneType' object has no attribute 'simple'

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