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

Program is still running, progress is shown below

Show unfinished results

  • host ip address=27.3.74.251 (Thu Sep 22 08:02:33 2022)
  • waiting for system load (3.90) to calm down, total wait time: 24.49 sec (Thu Sep 22 08:02:33 2022)
  • waiting for system load (3.93) to calm down, total wait time: 49.74 sec (Thu Sep 22 08:02:57 2022)
  • waiting for system load (3.93) to calm down, total wait time: 1 min 15 sec (Thu Sep 22 08:03:23 2022)
  • running now (Thu Sep 22 08:03:48 2022)
  • converting pdb into xyzr (Thu Sep 22 08:03:48 2022)
  • waiting for system load (3.31) to calm down, total wait time: 1 min 27 sec (Thu Sep 22 08:03:48 2022)
  • waiting for system load (2.94) to calm down, total wait time: 1 min 35 sec (Thu Sep 22 08:04:00 2022)
  • running now (Thu Sep 22 08:04:08 2022)
  • completed conversion of PDB file: 2022.sep22.bfa.pdb (size: 187k) (Thu Sep 22 08:04:10 2022)
  • converted 5969 atoms of 5969 atoms (Thu Sep 22 08:04:10 2022)
  • found 5969 atoms in pdb (Thu Sep 22 08:04:10 2022)
  • waiting for system load (2.88) to calm down, total wait time: 1 min 42 sec (Thu Sep 22 08:04:10 2022)
  • waiting for system load (2.81) to calm down, total wait time: 1 min 48 sec (Thu Sep 22 08:04:17 2022)
  • running now (Thu Sep 22 08:04:23 2022)
  • running 3v all channel program (Thu Sep 22 08:04:23 2022)
  • waiting for system load (2.74) to calm down, total wait time: 1 min 53 sec (Thu Sep 22 08:04:23 2022)
  • waiting for system load (2.92) to calm down, total wait time: 2 min 0 sec (Thu Sep 22 08:04:28 2022)
  • running now (Thu Sep 22 08:04:35 2022)
  • created 3 channel files (Thu Sep 22 08:06:00 2022)
  • Download MRC files: 1 2 3 (Thu Sep 22 08:06:00 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 08:06:00 2022)
  • UCSF Chimera created Jmol compatible file (Thu Sep 22 08:06:05 2022)
  • compressing channel-001.obj (Thu Sep 22 08:06:05 2022)
  • waiting for system load (5.25) to calm down, total wait time: 3 min 17 sec (Thu Sep 22 08:06:05 2022)
  • waiting for system load (2.82) to calm down, total wait time: 3 min 23 sec (Thu Sep 22 08:07:22 2022)
  • running now (Thu Sep 22 08:07:28 2022)
  • waiting for system load (2.75) to calm down, total wait time: 3 min 29 sec (Thu Sep 22 08:07:28 2022)
  • waiting for system load (2.69) to calm down, total wait time: 3 min 34 sec (Thu Sep 22 08:07:33 2022)
  • running now (Thu Sep 22 08:07:38 2022)
  • UCSF Chimera completed in 1 min 39 sec (Thu Sep 22 08:07:38 2022)
  • analyzing volume (Thu Sep 22 08:07:38 2022)
  • normal CoM (-42.0, -31.6, -41.0) Å (Thu Sep 22 08:07:39 2022)
  • reduced center failed (Thu Sep 22 08:07:39 2022)
  • volume analysis completed in 317.09 msec (Thu Sep 22 08:07:39 2022)
  • compressing channel-001.mrc (Thu Sep 22 08:07:39 2022)
  • waiting for system load (2.59) to calm down, total wait time: 3 min 38 sec (Thu Sep 22 08:07:39 2022)
  • waiting for system load (2.59) to calm down, total wait time: 3 min 42 sec (Thu Sep 22 08:07:43 2022)
  • running now (Thu Sep 22 08:07:47 2022)
  • waiting for system load (2.54) to calm down, total wait time: 3 min 46 sec (Thu Sep 22 08:07:47 2022)
  • running now (Thu Sep 22 08:07:51 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 08:07:51 2022)
  • UCSF Chimera created Jmol compatible file (Thu Sep 22 08:08:01 2022)
  • compressing channel-002.obj (Thu Sep 22 08:08:01 2022)
  • waiting for system load (2.50) to calm down, total wait time: 3 min 49 sec (Thu Sep 22 08:08:01 2022)
  • running now (Thu Sep 22 08:08:04 2022)
  • waiting for system load (2.46) to calm down, total wait time: 3 min 52 sec (Thu Sep 22 08:08:04 2022)
  • running now (Thu Sep 22 08:08:08 2022)
  • UCSF Chimera completed in 17.19 sec (Thu Sep 22 08:08:08 2022)
  • analyzing volume (Thu Sep 22 08:08:08 2022)
  • normal CoM (-44.9, -24.1, -43.7) Å (Thu Sep 22 08:08:08 2022)
  • reduced center failed (Thu Sep 22 08:08:08 2022)
  • volume analysis completed in 305.42 msec (Thu Sep 22 08:08:08 2022)
  • compressing channel-002.mrc (Thu Sep 22 08:08:08 2022)
  • waiting for system load (2.46) to calm down, total wait time: 3 min 55 sec (Thu Sep 22 08:08:08 2022)
  • running now (Thu Sep 22 08:08:11 2022)
  • waiting for system load (2.42) to calm down, total wait time: 3 min 58 sec (Thu Sep 22 08:08:11 2022)
  • running now (Thu Sep 22 08:08:14 2022)
  • imaging volume (download mrc) with UCSF Chimera (Thu Sep 22 08:08:14 2022)
  • UCSF Chimera created Jmol compatible file (Thu Sep 22 08:08:22 2022)
  • compressing channel-003.obj (Thu Sep 22 08:08:22 2022)
  • waiting for system load (2.44) to calm down, total wait time: 4 min 1 sec (Thu Sep 22 08:08:22 2022)
  • running now (Thu Sep 22 08:08:25 2022)
  • waiting for system load (2.32) to calm down, total wait time: 4 min 4 sec (Thu Sep 22 08:08:25 2022)
  • running now (Thu Sep 22 08:08:28 2022)
  • UCSF Chimera completed in 13.47 sec (Thu Sep 22 08:08:28 2022)
  • analyzing volume (Thu Sep 22 08:08:28 2022)
  • normal CoM (-39.7, -25.2, -42.8) Å (Thu Sep 22 08:08:28 2022)
  • reduced center failed (Thu Sep 22 08:08:29 2022)
  • volume analysis completed in 0.58 sec (Thu Sep 22 08:08:29 2022)
  • compressing channel-003.mrc (Thu Sep 22 08:08:29 2022)
  • waiting for system load (2.30) to calm down, total wait time: 4 min 6 sec (Thu Sep 22 08:08:29 2022)
  • running now (Thu Sep 22 08:08:31 2022)
  • waiting for system load (2.30) to calm down, total wait time: 4 min 8 sec (Thu Sep 22 08:08:31 2022)
  • running now (Thu Sep 22 08:08:33 2022)
  • tarring file list (Thu Sep 22 08:08:33 2022)
  • waiting for system load (2.30) to calm down, total wait time: 4 min 11 sec (Thu Sep 22 08:08:33 2022)
  • running now (Thu Sep 22 08:08:36 2022)
  • waiting for system load (2.27) to calm down, total wait time: 4 min 13 sec (Thu Sep 22 08:08:36 2022)
  • running now (Thu Sep 22 08:08:38 2022)
  • compressing channel-001.mrc (Thu Sep 22 08:08:38 2022)
  • waiting for system load (2.27) to calm down, total wait time: 4 min 15 sec (Thu Sep 22 08:08:38 2022)
  • running now (Thu Sep 22 08:08:40 2022)
  • compressing channel-002.mrc (Thu Sep 22 08:08:40 2022)
  • waiting for system load (2.17) to calm down, total wait time: 4 min 17 sec (Thu Sep 22 08:08:40 2022)
  • running now (Thu Sep 22 08:08:42 2022)
  • compressing channel-003.mrc (Thu Sep 22 08:08:42 2022)
  • waiting for system load (2.17) to calm down, total wait time: 4 min 18 sec (Thu Sep 22 08:08:42 2022)
  • running now (Thu Sep 22 08:08:43 2022)
  • FINISHED (Thu Sep 22 08:08:43 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 (2.30) to calm down, total wait time: 4 min 6 sec 
Message: running now 
Message: waiting for system load (2.30) to calm down, total wait time: 4 min 8 sec 
Message: running now 
Message: tarring file list 
Message: waiting for system load (2.30) to calm down, total wait time: 4 min 11 sec 
Message: running now 
Message: waiting for system load (2.27) to calm down, total wait time: 4 min 13 sec 
Message: running now 
Message: compressing channel-001.mrc 
Message: waiting for system load (2.27) to calm down, total wait time: 4 min 15 sec 
Message: running now 
Message: compressing channel-002.mrc 
Message: waiting for system load (2.17) to calm down, total wait time: 4 min 17 sec 
Message: running now 
Message: compressing channel-003.mrc 
Message: waiting for system load (2.17) to calm down, total wait time: 4 min 18 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
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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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