3v Running Log for JobId '2023.jan23.063'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=132.183.4.6 (Mon Jan 23 17:55:48 2023)
  • converting pdb into xyzr (Mon Jan 23 17:55:48 2023)
  • completed conversion of PDB file: 2023.jan23.063.pdb (size: 110k) (Mon Jan 23 17:55:51 2023)
  • converted 3518 atoms of 3518 atoms (Mon Jan 23 17:55:51 2023)
  • found 3518 atoms in pdb (Mon Jan 23 17:55:51 2023)
  • starting probe size 0.000 (Mon Jan 23 17:55:51 2023)
  • running 3v volume program (Mon Jan 23 17:55:51 2023)
  • smoothing out volume (Mon Jan 23 17:55:51 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 17:55:51 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 17:55:59 2023)
  • compressing 2023.jan23.063-0.0.obj (Mon Jan 23 17:55:59 2023)
  • UCSF Chimera completed in 8.92 sec (Mon Jan 23 17:56:00 2023)
  • analyzing volume (Mon Jan 23 17:56:00 2023)
  • normal CoM (0.8, -1.8, -5.6) Å (Mon Jan 23 17:56:06 2023)
  • reduced center failed (Mon Jan 23 17:56:07 2023)
  • volume analysis completed in 7.14 sec (Mon Jan 23 17:56:07 2023)
  • compressing 2023.jan23.063-0.0.mrc (Mon Jan 23 17:56:07 2023)
  • starting probe size 3.000 (Mon Jan 23 17:56:07 2023)
  • running 3v volume program (Mon Jan 23 17:56:07 2023)
  • smoothing out volume (Mon Jan 23 17:56:08 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 17:56:08 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 17:56:16 2023)
  • compressing 2023.jan23.063-3.0.obj (Mon Jan 23 17:56:16 2023)
  • UCSF Chimera completed in 9.05 sec (Mon Jan 23 17:56:17 2023)
  • analyzing volume (Mon Jan 23 17:56:17 2023)
  • normal CoM (0.6, -1.8, -5.4) Å (Mon Jan 23 17:56:25 2023)
  • reduced center failed (Mon Jan 23 17:56:26 2023)
  • volume analysis completed in 9.15 sec (Mon Jan 23 17:56:26 2023)
  • compressing 2023.jan23.063-3.0.mrc (Mon Jan 23 17:56:26 2023)
  • starting probe size 6.000 (Mon Jan 23 17:56:26 2023)
  • running 3v volume program (Mon Jan 23 17:56:26 2023)
  • smoothing out volume (Mon Jan 23 17:56:27 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 17:56:27 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 17:56:36 2023)
  • compressing 2023.jan23.063-6.0.obj (Mon Jan 23 17:56:36 2023)
  • UCSF Chimera completed in 9.46 sec (Mon Jan 23 17:56:37 2023)
  • analyzing volume (Mon Jan 23 17:56:37 2023)
  • normal CoM (0.7, -1.4, -3.3) Å (Mon Jan 23 17:56:46 2023)
  • reduced center failed (Mon Jan 23 17:56:47 2023)
  • volume analysis completed in 10.64 sec (Mon Jan 23 17:56:47 2023)
  • compressing 2023.jan23.063-6.0.mrc (Mon Jan 23 17:56:47 2023)
  • starting probe size 9.000 (Mon Jan 23 17:56:48 2023)
  • running 3v volume program (Mon Jan 23 17:56:48 2023)
  • smoothing out volume (Mon Jan 23 17:56:50 2023)
  • imaging volume (download mrc) with UCSF Chimera (Mon Jan 23 17:56:50 2023)
  • UCSF Chimera created Jmol compatible file (Mon Jan 23 17:56:59 2023)
  • compressing 2023.jan23.063-9.0.obj (Mon Jan 23 17:56:59 2023)
  • UCSF Chimera completed in 10.01 sec (Mon Jan 23 17:57:00 2023)
  • analyzing volume (Mon Jan 23 17:57:00 2023)
  • normal CoM (6.0, -0.3, -6.3) Å (Mon Jan 23 17:57:10 2023)
  • reduced center failed (Mon Jan 23 17:57:11 2023)
  • volume analysis completed in 11.73 sec (Mon Jan 23 17:57:11 2023)
  • compressing 2023.jan23.063-9.0.mrc (Mon Jan 23 17:57:11 2023)
  • tarring file list (Mon Jan 23 17:57:12 2023)
  • compressing 2023.jan23.063-0.0.mrc (Mon Jan 23 17:57:12 2023)
  • compressing 2023.jan23.063-3.0.mrc (Mon Jan 23 17:57:12 2023)
  • compressing 2023.jan23.063-6.0.mrc (Mon Jan 23 17:57:12 2023)
  • compressing 2023.jan23.063-9.0.mrc (Mon Jan 23 17:57:12 2023)
  • FINISHED (Mon Jan 23 17:57:12 2023)

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Log file display

Show last lines of log file  
Terminal display
		
wrote to mrc file: /var/www/html/3vee/output/2023/jan23/063/2023.jan23.063-9.0.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 2023.jan23.063-9.0.obj 
Message: UCSF Chimera completed in 10.01 sec 
OBJFILE /var/www/html/3vee/output/2023/jan23/063/2023.jan23.063-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (6.0, -0.3, -6.3) Å 
Message: reduced center failed 
Message: volume analysis completed in 11.73 sec 
Message: compressing 2023.jan23.063-9.0.mrc 
Message: tarring file list 
Message: compressing 2023.jan23.063-0.0.mrc 
Message: compressing 2023.jan23.063-3.0.mrc 
Message: compressing 2023.jan23.063-6.0.mrc 
Message: compressing 2023.jan23.063-9.0.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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