3v Running Log for JobId '2019.aug24.dab'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=200.44.65.90 (Sat Aug 24 23:12:50 2019)
  • converting pdb into xyzr (Sat Aug 24 23:12:50 2019)
  • completed conversion of PDB file: 2019.aug24.dab.pdb (size: 135k) (Sat Aug 24 23:12:53 2019)
  • converted 4304 atoms of 4304 atoms (Sat Aug 24 23:12:53 2019)
  • found 4304 atoms in pdb (Sat Aug 24 23:12:53 2019)
  • starting probe size 0.000 (Sat Aug 24 23:12:53 2019)
  • running 3v volume program (Sat Aug 24 23:12:53 2019)
  • smoothing out volume (Sat Aug 24 23:12:53 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:12:53 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:13:02 2019)
  • compressing 2019.aug24.dab-0.0.obj (Sat Aug 24 23:13:02 2019)
  • UCSF Chimera completed in 9.38 sec (Sat Aug 24 23:13:02 2019)
  • analyzing volume (Sat Aug 24 23:13:02 2019)
  • normal CoM (2.2, -1.8, -8.5) Å (Sat Aug 24 23:13:04 2019)
  • reduced center failed (Sat Aug 24 23:13:04 2019)
  • volume analysis completed in 1.81 sec (Sat Aug 24 23:13:04 2019)
  • compressing 2019.aug24.dab-0.0.mrc (Sat Aug 24 23:13:04 2019)
  • starting probe size 3.000 (Sat Aug 24 23:13:04 2019)
  • running 3v volume program (Sat Aug 24 23:13:04 2019)
  • smoothing out volume (Sat Aug 24 23:13:05 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:13:05 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:13:15 2019)
  • compressing 2019.aug24.dab-3.0.obj (Sat Aug 24 23:13:15 2019)
  • UCSF Chimera completed in 10.21 sec (Sat Aug 24 23:13:15 2019)
  • analyzing volume (Sat Aug 24 23:13:15 2019)
  • normal CoM (2.3, -1.9, -6.5) Å (Sat Aug 24 23:13:17 2019)
  • reduced center failed (Sat Aug 24 23:13:17 2019)
  • volume analysis completed in 2.48 sec (Sat Aug 24 23:13:17 2019)
  • compressing 2019.aug24.dab-3.0.mrc (Sat Aug 24 23:13:17 2019)
  • starting probe size 6.000 (Sat Aug 24 23:13:17 2019)
  • running 3v volume program (Sat Aug 24 23:13:17 2019)
  • smoothing out volume (Sat Aug 24 23:13:18 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:13:18 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:13:28 2019)
  • compressing 2019.aug24.dab-6.0.obj (Sat Aug 24 23:13:28 2019)
  • UCSF Chimera completed in 10.19 sec (Sat Aug 24 23:13:28 2019)
  • analyzing volume (Sat Aug 24 23:13:28 2019)
  • normal CoM (-1.7, 0.0, -4.4) Å (Sat Aug 24 23:13:31 2019)
  • reduced center failed (Sat Aug 24 23:13:31 2019)
  • volume analysis completed in 2.97 sec (Sat Aug 24 23:13:31 2019)
  • compressing 2019.aug24.dab-6.0.mrc (Sat Aug 24 23:13:31 2019)
  • starting probe size 9.000 (Sat Aug 24 23:13:31 2019)
  • running 3v volume program (Sat Aug 24 23:13:31 2019)
  • smoothing out volume (Sat Aug 24 23:13:32 2019)
  • imaging volume (download mrc) with UCSF Chimera (Sat Aug 24 23:13:32 2019)
  • UCSF Chimera created Jmol compatible file (Sat Aug 24 23:13:42 2019)
  • compressing 2019.aug24.dab-9.0.obj (Sat Aug 24 23:13:42 2019)
  • UCSF Chimera completed in 10.31 sec (Sat Aug 24 23:13:43 2019)
  • analyzing volume (Sat Aug 24 23:13:43 2019)
  • normal CoM (0.3, -0.3, -8.2) Å (Sat Aug 24 23:13:46 2019)
  • reduced center failed (Sat Aug 24 23:13:46 2019)
  • volume analysis completed in 3.71 sec (Sat Aug 24 23:13:46 2019)
  • compressing 2019.aug24.dab-9.0.mrc (Sat Aug 24 23:13:46 2019)
  • tarring file list (Sat Aug 24 23:13:47 2019)
  • compressing 2019.aug24.dab-0.0.mrc (Sat Aug 24 23:13:47 2019)
  • compressing 2019.aug24.dab-3.0.mrc (Sat Aug 24 23:13:47 2019)
  • compressing 2019.aug24.dab-6.0.mrc (Sat Aug 24 23:13:47 2019)
  • compressing 2019.aug24.dab-9.0.mrc (Sat Aug 24 23:13:47 2019)
  • FINISHED (Sat Aug 24 23:13:47 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/aug24/dab/2019.aug24.dab-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.aug24.dab-9.0.obj 
Message: UCSF Chimera completed in 10.31 sec 
OBJFILE /var/www/html/3vee/output/2019/aug24/dab/2019.aug24.dab-9.0.obj.gz 
Message: analyzing volume 
Message: normal CoM (0.3, -0.3, -8.2) Å 
Message: reduced center failed 
Message: volume analysis completed in 3.71 sec 
Message: compressing 2019.aug24.dab-9.0.mrc 
Message: tarring file list 
Message: compressing 2019.aug24.dab-0.0.mrc 
Message: compressing 2019.aug24.dab-3.0.mrc 
Message: compressing 2019.aug24.dab-6.0.mrc 
Message: compressing 2019.aug24.dab-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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