3v Running Log for JobId '2019.dec02.066'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=130.179.244.50 (Mon Dec 2 17:52:05 2019)
  • converting pdb into xyzr (Mon Dec 2 17:52:05 2019)
  • completed conversion of PDB file: 2019.dec02.066.pdb (size: 549k) (Mon Dec 2 17:52:21 2019)
  • converted 17576 atoms of 19144 atoms (Mon Dec 2 17:52:21 2019)
  • found 17576 atoms in pdb (Mon Dec 2 17:52:21 2019)
  • starting probe size 1.000 (Mon Dec 2 17:52:21 2019)
  • running 3v volume program (Mon Dec 2 17:52:21 2019)
  • smoothing out volume (Mon Dec 2 17:52:21 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:52:22 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:52:39 2019)
  • compressing 2019.dec02.066-1.0.obj (Mon Dec 2 17:52:39 2019)
  • UCSF Chimera completed in 19.06 sec (Mon Dec 2 17:52:40 2019)
  • analyzing volume (Mon Dec 2 17:52:40 2019)
  • normal CoM (-44.0, -1.8, 36.0) Å (Mon Dec 2 17:52:54 2019)
  • reduced center failed (Mon Dec 2 17:52:56 2019)
  • volume analysis completed in 15.86 sec (Mon Dec 2 17:52:56 2019)
  • compressing 2019.dec02.066-1.0.mrc (Mon Dec 2 17:52:56 2019)
  • starting probe size 4.000 (Mon Dec 2 17:52:58 2019)
  • running 3v volume program (Mon Dec 2 17:52:58 2019)
  • smoothing out volume (Mon Dec 2 17:52:59 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:53:00 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:53:15 2019)
  • compressing 2019.dec02.066-4.0.obj (Mon Dec 2 17:53:15 2019)
  • UCSF Chimera completed in 16.48 sec (Mon Dec 2 17:53:16 2019)
  • analyzing volume (Mon Dec 2 17:53:16 2019)
  • normal CoM (-43.4, -2.1, 35.9) Å (Mon Dec 2 17:53:32 2019)
  • reduced center failed (Mon Dec 2 17:53:36 2019)
  • volume analysis completed in 19.63 sec (Mon Dec 2 17:53:36 2019)
  • compressing 2019.dec02.066-4.0.mrc (Mon Dec 2 17:53:36 2019)
  • starting probe size 7.000 (Mon Dec 2 17:53:36 2019)
  • running 3v volume program (Mon Dec 2 17:53:36 2019)
  • smoothing out volume (Mon Dec 2 17:53:41 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:53:42 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:53:56 2019)
  • compressing 2019.dec02.066-7.0.obj (Mon Dec 2 17:53:56 2019)
  • UCSF Chimera completed in 16.19 sec (Mon Dec 2 17:53:57 2019)
  • analyzing volume (Mon Dec 2 17:53:57 2019)
  • normal CoM (-43.2, -1.5, 36.0) Å (Mon Dec 2 17:54:15 2019)
  • reduced center failed (Mon Dec 2 17:54:20 2019)
  • volume analysis completed in 22.47 sec (Mon Dec 2 17:54:20 2019)
  • compressing 2019.dec02.066-7.0.mrc (Mon Dec 2 17:54:20 2019)
  • starting probe size 10.000 (Mon Dec 2 17:54:21 2019)
  • running 3v volume program (Mon Dec 2 17:54:21 2019)
  • smoothing out volume (Mon Dec 2 17:54:30 2019)
  • imaging volume (download mrc) with UCSF Chimera (Mon Dec 2 17:54:31 2019)
  • UCSF Chimera created Jmol compatible file (Mon Dec 2 17:54:46 2019)
  • compressing 2019.dec02.066-10.0.obj (Mon Dec 2 17:54:46 2019)
  • UCSF Chimera completed in 16.42 sec (Mon Dec 2 17:54:47 2019)
  • analyzing volume (Mon Dec 2 17:54:47 2019)
  • normal CoM (-43.2, -1.5, 36.0) Å (Mon Dec 2 17:55:06 2019)
  • reduced center failed (Mon Dec 2 17:55:12 2019)
  • volume analysis completed in 24.83 sec (Mon Dec 2 17:55:12 2019)
  • compressing 2019.dec02.066-10.0.mrc (Mon Dec 2 17:55:12 2019)
  • tarring file list (Mon Dec 2 17:55:12 2019)
  • compressing 2019.dec02.066-1.0.mrc (Mon Dec 2 17:55:12 2019)
  • compressing 2019.dec02.066-4.0.mrc (Mon Dec 2 17:55:12 2019)
  • compressing 2019.dec02.066-7.0.mrc (Mon Dec 2 17:55:12 2019)
  • compressing 2019.dec02.066-10.0.mrc (Mon Dec 2 17:55:12 2019)
  • FINISHED (Mon Dec 2 17:55:12 2019)

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Log file display

Show last lines of log file 
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2019/dec02/066/2019.dec02.066-10.0.mrc 
Message: smoothing out volume 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.dec02.066-10.0.obj 
Message: UCSF Chimera completed in 16.42 sec 
OBJFILE /var/www/html/3vee/output/2019/dec02/066/2019.dec02.066-10.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (-43.2, -1.5, 36.0) Å 
Message: reduced center failed 
Message: volume analysis completed in 24.83 sec 
Message: compressing 2019.dec02.066-10.0.mrc 
Message: tarring file list 
Message: compressing 2019.dec02.066-1.0.mrc 
Message: compressing 2019.dec02.066-4.0.mrc 
Message: compressing 2019.dec02.066-7.0.mrc 
Message: compressing 2019.dec02.066-10.0.mrc 
Message: FINISHED 
		


Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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