3v Running Log for JobId '2019.sep10.2c2'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=195.209.233.168 (Tue Sep 10 05:45:59 2019)
  • waiting for system load (2.81) to calm down, total wait time: 6.03 sec (Tue Sep 10 05:45:59 2019)
  • waiting for system load (2.58) to calm down, total wait time: 10.07 sec (Tue Sep 10 05:46:05 2019)
  • running now (Tue Sep 10 05:46:09 2019)
  • downloading pdb file (Tue Sep 10 05:46:09 2019)
  • waiting for system load (2.38) to calm down, total wait time: 12.8 sec (Tue Sep 10 05:46:09 2019)
  • running now (Tue Sep 10 05:46:12 2019)
  • failed to download pdb id: 4PQE (Tue Sep 10 05:46:12 2019)
  • waiting for system load (2.38) to calm down, total wait time: 15.53 sec (Tue Sep 10 05:46:12 2019)
  • running now (Tue Sep 10 05:46:14 2019)
  • trying download pdb id again without bio unit (Tue Sep 10 05:46:17 2019)
  • waiting for system load (2.35) to calm down, total wait time: 18.09 sec (Tue Sep 10 05:46:17 2019)
  • running now (Tue Sep 10 05:46:19 2019)
  • waiting for system load (2.32) to calm down, total wait time: 20.49 sec (Tue Sep 10 05:46:19 2019)
  • running now (Tue Sep 10 05:46:22 2019)
  • completed download of PDB id 4PQE (size: 365 k, 4611 lines) (Tue Sep 10 05:46:22 2019)
  • waiting for system load (2.32) to calm down, total wait time: 22.89 sec (Tue Sep 10 05:46:22 2019)
  • running now (Tue Sep 10 05:46:24 2019)
  • converting pdb into xyzr (Tue Sep 10 05:46:24 2019)
  • waiting for system load (2.13) to calm down, total wait time: 24.43 sec (Tue Sep 10 05:46:24 2019)
  • running now (Tue Sep 10 05:46:26 2019)
  • completed conversion of PDB file: 4PQE-2019.sep10.2c2.pdb (size: 128k) (Tue Sep 10 05:46:29 2019)
  • converted 4087 atoms of 4087 atoms (Tue Sep 10 05:46:29 2019)
  • found 4087 atoms in pdb (Tue Sep 10 05:46:29 2019)
  • waiting for system load (2.04) to calm down, total wait time: 25.66 sec (Tue Sep 10 05:46:29 2019)
  • running now (Tue Sep 10 05:46:30 2019)
  • running 3v volume program (Tue Sep 10 05:46:30 2019)
  • waiting for system load (2.04) to calm down, total wait time: 26.88 sec (Tue Sep 10 05:46:30 2019)
  • running now (Tue Sep 10 05:46:31 2019)
  • waiting for system load (3.55) to calm down, total wait time: 43.56 sec (Tue Sep 10 05:46:39 2019)
  • waiting for system load (2.76) to calm down, total wait time: 49.12 sec (Tue Sep 10 05:46:55 2019)
  • running now (Tue Sep 10 05:47:01 2019)
  • smoothing out volume (Tue Sep 10 05:47:01 2019)
  • waiting for system load (2.54) to calm down, total wait time: 52.87 sec (Tue Sep 10 05:47:01 2019)
  • running now (Tue Sep 10 05:47:05 2019)
  • imaging volume (download mrc) with UCSF Chimera (Tue Sep 10 05:47:05 2019)
  • UCSF Chimera created Jmol compatible file (Tue Sep 10 05:47:40 2019)
  • compressing 4PQE-2019.sep10.2c2.obj (Tue Sep 10 05:47:40 2019)
  • waiting for system load (7.82) to calm down, total wait time: 6 min 10 sec (Tue Sep 10 05:47:40 2019)
  • running now (Tue Sep 10 05:52:57 2019)
  • UCSF Chimera completed in 6 min 19 sec (Tue Sep 10 05:52:58 2019)
  • analyzing volume (Tue Sep 10 05:52:58 2019)
  • normal CoM (-5.4, -3.6, 0.7) Å (Tue Sep 10 05:53:00 2019)
  • reduced center failed (Tue Sep 10 05:53:00 2019)
  • volume analysis completed in 2.26 sec (Tue Sep 10 05:53:00 2019)
  • compressing 4PQE-2019.sep10.2c2.mrc (Tue Sep 10 05:53:00 2019)
  • FINISHED (Tue Sep 10 05:53:00 2019)

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Log file display

Show last lines of log file 
Terminal display
		
Message: waiting for system load (2.76) to calm down, total wait time: 49.12 sec 
Message: running now 
Message: smoothing out volume 
Message: waiting for system load (2.54) to calm down, total wait time: 52.87 sec 
Message: running now 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 4PQE-2019.sep10.2c2.obj 
Message: waiting for system load (7.82) to calm down, total wait time: 6 min 10 sec 
Message: running now 
Message: UCSF Chimera completed in 6 min 19 sec 
OBJFILE /var/www/html/3vee/output/2019/sep10/2c2/4PQE-2019.sep10.2c2.obj.gz 
Message: analyzing volume 
Message: normal CoM (-5.4, -3.6, 0.7) Å 
Message: reduced center failed 
Message: volume analysis completed in 2.26 sec 
Message: compressing 4PQE-2019.sep10.2c2.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
Download source code
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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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