3v Running Log for JobId '2019.sep10.fe5'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=195.209.233.168 (Tue Sep 10 05:44:08 2019)
  • waiting for system load (5.05) to calm down, total wait time: 66.53 sec (Tue Sep 10 05:44:08 2019)
  • waiting for system load (5.02) to calm down, total wait time: 2 min 12 sec (Tue Sep 10 05:45:14 2019)
  • running now (Tue Sep 10 05:46:19 2019)
  • downloading pdb file (Tue Sep 10 05:46:19 2019)
  • waiting for system load (2.32) to calm down, total wait time: 2 min 14 sec (Tue Sep 10 05:46:19 2019)
  • running now (Tue Sep 10 05:46:22 2019)
  • failed to download pdb id: 4pqe (Tue Sep 10 05:46:22 2019)
  • waiting for system load (2.32) to calm down, total wait time: 2 min 16 sec (Tue Sep 10 05:46:22 2019)
  • running now (Tue Sep 10 05:46:24 2019)
  • trying download pdb id again without bio unit (Tue Sep 10 05:46:27 2019)
  • waiting for system load (2.13) to calm down, total wait time: 2 min 18 sec (Tue Sep 10 05:46:27 2019)
  • running now (Tue Sep 10 05:46:28 2019)
  • waiting for system load (2.04) to calm down, total wait time: 2 min 19 sec (Tue Sep 10 05:46:28 2019)
  • running now (Tue Sep 10 05:46:30 2019)
  • completed download of PDB id 4pqe (size: 365 k, 4611 lines) (Tue Sep 10 05:46:30 2019)
  • waiting for system load (2.04) to calm down, total wait time: 2 min 20 sec (Tue Sep 10 05:46:30 2019)
  • running now (Tue Sep 10 05:46:31 2019)
  • converting pdb into xyzr (Tue Sep 10 05:46:31 2019)
  • waiting for system load (2.04) to calm down, total wait time: 2 min 22 sec (Tue Sep 10 05:46:31 2019)
  • running now (Tue Sep 10 05:46:32 2019)
  • completed conversion of PDB file: 4pqe-2019.sep10.fe5.pdb (size: 128k) (Tue Sep 10 05:46:38 2019)
  • converted 4087 atoms of 4087 atoms (Tue Sep 10 05:46:38 2019)
  • found 4087 atoms in pdb (Tue Sep 10 05:46:38 2019)
  • waiting for system load (3.55) to calm down, total wait time: 2 min 38 sec (Tue Sep 10 05:46:38 2019)
  • waiting for system load (2.76) to calm down, total wait time: 2 min 44 sec (Tue Sep 10 05:46:55 2019)
  • running now (Tue Sep 10 05:47:00 2019)
  • running 3v volume program (Tue Sep 10 05:47:00 2019)
  • waiting for system load (2.54) to calm down, total wait time: 2 min 48 sec (Tue Sep 10 05:47:00 2019)
  • running now (Tue Sep 10 05:47:04 2019)
  • waiting for system load (7.93) to calm down, total wait time: 8 min 21 sec (Tue Sep 10 05:47:54 2019)
  • running now (Tue Sep 10 05:53:27 2019)
  • smoothing out volume (Tue Sep 10 05:53:27 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 10 05:53:27 2019)
  • UCSF Chimera created Jmol compatible file (Tue Sep 10 05:53:36 2019)
  • compressing 4pqe-2019.sep10.fe5.obj (Tue Sep 10 05:53:36 2019)
  • UCSF Chimera completed in 5 min 43 sec (Tue Sep 10 05:53:37 2019)
  • analyzing volume (Tue Sep 10 05:53:37 2019)
  • normal CoM (-5.4, -3.6, 0.7) Å (Tue Sep 10 05:53:39 2019)
  • reduced center failed (Tue Sep 10 05:53:39 2019)
  • volume analysis completed in 2.25 sec (Tue Sep 10 05:53:39 2019)
  • compressing 4pqe-2019.sep10.fe5.mrc (Tue Sep 10 05:53:39 2019)
  • FINISHED (Tue Sep 10 05:53:39 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: running 3v volume program 
Message: waiting for system load (2.54) to calm down, total wait time: 2 min 48 sec 
Message: running now 
wrote to mrc file: /var/www/html/3vee/output/2019/sep10/fe5/4pqe-2019.sep10.fe5.mrc 
Message: waiting for system load (7.93) to calm down, total wait time: 8 min 21 sec 
Message: running now 
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 4pqe-2019.sep10.fe5.obj 
Message: UCSF Chimera completed in 5 min 43 sec 
OBJFILE /var/www/html/3vee/output/2019/sep10/fe5/4pqe-2019.sep10.fe5.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.4, -3.6, 0.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.25 sec 
Message: compressing 4pqe-2019.sep10.fe5.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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