3v Running Log for JobId '2022.sep22.131'

Program is still running, progress is shown below

Show unfinished results

  • host ip address=27.3.74.251 (Thu Sep 22 09:46:49 2022)
  • waiting for system load (2.91) to calm down, total wait time: 7.07 sec (Thu Sep 22 09:46:49 2022)
  • waiting for system load (3.08) to calm down, total wait time: 16.17 sec (Thu Sep 22 09:46:56 2022)
  • waiting for system load (3.45) to calm down, total wait time: 30.97 sec (Thu Sep 22 09:47:05 2022)
  • waiting for system load (3.64) to calm down, total wait time: 49.47 sec (Thu Sep 22 09:47:20 2022)
  • running now (Thu Sep 22 09:47:39 2022)
  • converting pdb into xyzr (Thu Sep 22 09:47:39 2022)
  • waiting for system load (3.79) to calm down, total wait time: 1 min 11 sec (Thu Sep 22 09:47:39 2022)
  • waiting for system load (3.94) to calm down, total wait time: 1 min 37 sec (Thu Sep 22 09:48:01 2022)
  • waiting for system load (4.02) to calm down, total wait time: 2 min 4 sec (Thu Sep 22 09:48:26 2022)
  • waiting for system load (4.01) to calm down, total wait time: 2 min 32 sec (Thu Sep 22 09:48:54 2022)
  • running now (Thu Sep 22 09:49:21 2022)
  • completed conversion of PDB file: 2022.sep22.131.pdb (size: 65k) (Thu Sep 22 09:49:23 2022)
  • converted 2095 atoms of 2095 atoms (Thu Sep 22 09:49:23 2022)
  • found 2095 atoms in pdb (Thu Sep 22 09:49:23 2022)
  • waiting for system load (3.93) to calm down, total wait time: 2 min 57 sec (Thu Sep 22 09:49:23 2022)
  • waiting for system load (3.25) to calm down, total wait time: 3 min 9 sec (Thu Sep 22 09:49:48 2022)
  • running now (Thu Sep 22 09:49:59 2022)
  • running 3v all channel program (Thu Sep 22 09:49:59 2022)
  • waiting for system load (2.98) to calm down, total wait time: 3 min 16 sec (Thu Sep 22 09:49:59 2022)
  • waiting for system load (2.83) to calm down, total wait time: 3 min 23 sec (Thu Sep 22 09:50:07 2022)
  • running now (Thu Sep 22 09:50:14 2022)
  • created 3 channel files (Thu Sep 22 09:50:45 2022)
  • Download MRC files: 1 2 3 (Thu Sep 22 09:50:45 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 09:50:45 2022)
  • UCSF Chimera created Jmol compatible file (Thu Sep 22 09:50:48 2022)
  • compressing channel-001.obj (Thu Sep 22 09:50:48 2022)
  • waiting for system load (4.18) to calm down, total wait time: 3 min 55 sec (Thu Sep 22 09:50:48 2022)
  • waiting for system load (3.16) to calm down, total wait time: 4 min 5 sec (Thu Sep 22 09:51:20 2022)
  • running now (Thu Sep 22 09:51:31 2022)
  • waiting for system load (2.98) to calm down, total wait time: 4 min 13 sec (Thu Sep 22 09:51:31 2022)
  • waiting for system load (2.90) to calm down, total wait time: 4 min 20 sec (Thu Sep 22 09:51:39 2022)
  • running now (Thu Sep 22 09:51:46 2022)
  • UCSF Chimera completed in 60.66 sec (Thu Sep 22 09:51:46 2022)
  • analyzing volume (Thu Sep 22 09:51:46 2022)
  • normal CoM (-32.3, -29.4, -33.0) Å (Thu Sep 22 09:51:46 2022)
  • reduced center failed (Thu Sep 22 09:51:46 2022)
  • volume analysis completed in 21.25 msec (Thu Sep 22 09:51:46 2022)
  • compressing channel-001.mrc (Thu Sep 22 09:51:46 2022)
  • waiting for system load (2.76) to calm down, total wait time: 4 min 25 sec (Thu Sep 22 09:51:46 2022)
  • waiting for system load (2.70) to calm down, total wait time: 4 min 30 sec (Thu Sep 22 09:51:51 2022)
  • running now (Thu Sep 22 09:51:56 2022)
  • waiting for system load (2.57) to calm down, total wait time: 4 min 34 sec (Thu Sep 22 09:51:56 2022)
  • waiting for system load (2.52) to calm down, total wait time: 4 min 38 sec (Thu Sep 22 09:52:00 2022)
  • running now (Thu Sep 22 09:52:04 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 09:52:04 2022)
  • UCSF Chimera created Jmol compatible file (Thu Sep 22 09:52:07 2022)
  • compressing channel-002.obj (Thu Sep 22 09:52:07 2022)
  • waiting for system load (2.56) to calm down, total wait time: 4 min 42 sec (Thu Sep 22 09:52:07 2022)
  • waiting for system load (2.51) to calm down, total wait time: 4 min 45 sec (Thu Sep 22 09:52:11 2022)
  • running now (Thu Sep 22 09:52:15 2022)
  • waiting for system load (2.51) to calm down, total wait time: 4 min 49 sec (Thu Sep 22 09:52:15 2022)
  • running now (Thu Sep 22 09:52:18 2022)
  • UCSF Chimera completed in 14.32 sec (Thu Sep 22 09:52:18 2022)
  • analyzing volume (Thu Sep 22 09:52:18 2022)
  • normal CoM (-34.1, -29.1, -31.7) Å (Thu Sep 22 09:52:18 2022)
  • reduced center failed (Thu Sep 22 09:52:18 2022)
  • volume analysis completed in 17.72 msec (Thu Sep 22 09:52:18 2022)
  • compressing channel-002.mrc (Thu Sep 22 09:52:18 2022)
  • waiting for system load (2.47) to calm down, total wait time: 4 min 52 sec (Thu Sep 22 09:52:18 2022)
  • waiting for system load (2.51) to calm down, total wait time: 4 min 56 sec (Thu Sep 22 09:52:21 2022)
  • running now (Thu Sep 22 09:52:25 2022)
  • waiting for system load (2.47) to calm down, total wait time: 4 min 59 sec (Thu Sep 22 09:52:25 2022)
  • running now (Thu Sep 22 09:52:28 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 09:52:28 2022)
  • UCSF Chimera created Jmol compatible file (Thu Sep 22 09:52:32 2022)
  • compressing channel-003.obj (Thu Sep 22 09:52:32 2022)
  • waiting for system load (2.52) to calm down, total wait time: 5 min 3 sec (Thu Sep 22 09:52:32 2022)
  • running now (Thu Sep 22 09:52:35 2022)
  • waiting for system load (2.47) to calm down, total wait time: 5 min 6 sec (Thu Sep 22 09:52:35 2022)
  • running now (Thu Sep 22 09:52:38 2022)
  • UCSF Chimera completed in 10.16 sec (Thu Sep 22 09:52:38 2022)
  • analyzing volume (Thu Sep 22 09:52:38 2022)
  • normal CoM (-34.4, -28.8, -33.3) Å (Thu Sep 22 09:52:38 2022)
  • reduced center failed (Thu Sep 22 09:52:38 2022)
  • volume analysis completed in 17.06 msec (Thu Sep 22 09:52:38 2022)
  • compressing channel-003.mrc (Thu Sep 22 09:52:38 2022)
  • waiting for system load (2.47) to calm down, total wait time: 5 min 9 sec (Thu Sep 22 09:52:38 2022)
  • running now (Thu Sep 22 09:52:42 2022)
  • waiting for system load (2.44) to calm down, total wait time: 5 min 12 sec (Thu Sep 22 09:52:42 2022)
  • running now (Thu Sep 22 09:52:45 2022)
  • tarring file list (Thu Sep 22 09:52:45 2022)
  • waiting for system load (2.40) to calm down, total wait time: 5 min 15 sec (Thu Sep 22 09:52:45 2022)
  • running now (Thu Sep 22 09:52:48 2022)
  • waiting for system load (2.40) to calm down, total wait time: 5 min 18 sec (Thu Sep 22 09:52:48 2022)
  • running now (Thu Sep 22 09:52:51 2022)
  • compressing channel-001.mrc (Thu Sep 22 09:52:51 2022)
  • waiting for system load (2.37) to calm down, total wait time: 5 min 21 sec (Thu Sep 22 09:52:51 2022)
  • running now (Thu Sep 22 09:52:53 2022)
  • compressing channel-002.mrc (Thu Sep 22 09:52:53 2022)
  • waiting for system load (2.37) to calm down, total wait time: 5 min 23 sec (Thu Sep 22 09:52:53 2022)
  • running now (Thu Sep 22 09:52:56 2022)
  • compressing channel-003.mrc (Thu Sep 22 09:52:56 2022)
  • waiting for system load (2.34) to calm down, total wait time: 5 min 26 sec (Thu Sep 22 09:52:56 2022)
  • running now (Thu Sep 22 09:52:59 2022)
  • FINISHED (Thu Sep 22 09:52:59 2022)

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Log file display

Show last lines of log file 
Terminal display
		
Message: compressing channel-003.mrc 
Message: waiting for system load (2.47) to calm down, total wait time: 5 min 9 sec 
Message: running now 
Message: waiting for system load (2.44) to calm down, total wait time: 5 min 12 sec 
Message: running now 
Message: tarring file list 
Message: waiting for system load (2.40) to calm down, total wait time: 5 min 15 sec 
Message: running now 
Message: waiting for system load (2.40) to calm down, total wait time: 5 min 18 sec 
Message: running now 
Message: compressing channel-001.mrc 
Message: waiting for system load (2.37) to calm down, total wait time: 5 min 21 sec 
Message: running now 
Message: compressing channel-002.mrc 
Message: waiting for system load (2.37) to calm down, total wait time: 5 min 23 sec 
Message: running now 
Message: compressing channel-003.mrc 
Message: waiting for system load (2.34) to calm down, total wait time: 5 min 26 sec 
Message: running now 
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
Help
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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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