3v Running Log for JobId '2019.jun25.14e'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=122.116.71.154 (Tue Jun 25 23:57:22 2019)
  • converting pdb into xyzr (Tue Jun 25 23:57:22 2019)
  • completed conversion of PDB file: 2019.jun25.14e.pdb (size: 385k) (Tue Jun 25 23:57:30 2019)
  • converted 12324 atoms of 12324 atoms (Tue Jun 25 23:57:30 2019)
  • found 12324 atoms in pdb (Tue Jun 25 23:57:30 2019)
  • starting probe size 0.000 (Tue Jun 25 23:57:30 2019)
  • running 3v volume program (Tue Jun 25 23:57:30 2019)
  • smoothing out volume (Tue Jun 25 23:57:30 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:57:30 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:57:38 2019)
  • compressing 2019.jun25.14e-0.0.obj (Tue Jun 25 23:57:38 2019)
  • UCSF Chimera completed in 8.73 sec (Tue Jun 25 23:57:39 2019)
  • analyzing volume (Tue Jun 25 23:57:39 2019)
  • normal CoM (31.7, -4.3, -49.3) Å (Tue Jun 25 23:57:45 2019)
  • reduced center failed (Tue Jun 25 23:57:45 2019)
  • volume analysis completed in 6.1 sec (Tue Jun 25 23:57:45 2019)
  • compressing 2019.jun25.14e-0.0.mrc (Tue Jun 25 23:57:45 2019)
  • starting probe size 3.000 (Tue Jun 25 23:57:46 2019)
  • running 3v volume program (Tue Jun 25 23:57:46 2019)
  • smoothing out volume (Tue Jun 25 23:57:47 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:57:47 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:57:55 2019)
  • compressing 2019.jun25.14e-3.0.obj (Tue Jun 25 23:57:55 2019)
  • UCSF Chimera completed in 8.4 sec (Tue Jun 25 23:57:56 2019)
  • analyzing volume (Tue Jun 25 23:57:56 2019)
  • normal CoM (33.7, -6.2, -49.4) Å (Tue Jun 25 23:58:02 2019)
  • reduced center failed (Tue Jun 25 23:58:03 2019)
  • volume analysis completed in 7.34 sec (Tue Jun 25 23:58:03 2019)
  • compressing 2019.jun25.14e-3.0.mrc (Tue Jun 25 23:58:03 2019)
  • starting probe size 6.000 (Tue Jun 25 23:58:03 2019)
  • running 3v volume program (Tue Jun 25 23:58:03 2019)
  • smoothing out volume (Tue Jun 25 23:58:04 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:58:05 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:58:13 2019)
  • compressing 2019.jun25.14e-6.0.obj (Tue Jun 25 23:58:13 2019)
  • UCSF Chimera completed in 8.71 sec (Tue Jun 25 23:58:13 2019)
  • analyzing volume (Tue Jun 25 23:58:13 2019)
  • normal CoM (33.6, -6.1, -47.5) Å (Tue Jun 25 23:58:21 2019)
  • reduced center failed (Tue Jun 25 23:58:22 2019)
  • volume analysis completed in 8.81 sec (Tue Jun 25 23:58:22 2019)
  • compressing 2019.jun25.14e-6.0.mrc (Tue Jun 25 23:58:22 2019)
  • starting probe size 9.000 (Tue Jun 25 23:58:22 2019)
  • running 3v volume program (Tue Jun 25 23:58:22 2019)
  • smoothing out volume (Tue Jun 25 23:58:25 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Jun 25 23:58:25 2019)
  • UCSF Chimera created Jmol compatible file (Tue Jun 25 23:58:33 2019)
  • compressing 2019.jun25.14e-9.0.obj (Tue Jun 25 23:58:33 2019)
  • UCSF Chimera completed in 8.67 sec (Tue Jun 25 23:58:34 2019)
  • analyzing volume (Tue Jun 25 23:58:34 2019)
  • normal CoM (32.0, -3.7, -49.5) Å (Tue Jun 25 23:58:42 2019)
  • reduced center failed (Tue Jun 25 23:58:43 2019)
  • volume analysis completed in 9.62 sec (Tue Jun 25 23:58:43 2019)
  • compressing 2019.jun25.14e-9.0.mrc (Tue Jun 25 23:58:43 2019)
  • tarring file list (Tue Jun 25 23:58:44 2019)
  • compressing 2019.jun25.14e-0.0.mrc (Tue Jun 25 23:58:44 2019)
  • compressing 2019.jun25.14e-3.0.mrc (Tue Jun 25 23:58:44 2019)
  • compressing 2019.jun25.14e-6.0.mrc (Tue Jun 25 23:58:44 2019)
  • compressing 2019.jun25.14e-9.0.mrc (Tue Jun 25 23:58:44 2019)
  • FINISHED (Tue Jun 25 23:58:44 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/jun25/14e/2019.jun25.14e-9.0.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.jun25.14e-9.0.obj 
Message: UCSF Chimera completed in 8.67 sec 
OBJFILE /var/www/html/3vee/output/2019/jun25/14e/2019.jun25.14e-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (32.0, -3.7, -49.5) Å 
Message: reduced center failed 
Message: volume analysis completed in 9.62 sec 
Message: compressing 2019.jun25.14e-9.0.mrc 
Message: tarring file list 
Message: compressing 2019.jun25.14e-0.0.mrc 
Message: compressing 2019.jun25.14e-3.0.mrc 
Message: compressing 2019.jun25.14e-6.0.mrc 
Message: compressing 2019.jun25.14e-9.0.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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