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NORMA GroEl output : 




 ------ NORMA INSTALLATION TEST STARTED ------ 

This test will perform a number of computations using the different parts of NORMA.
Testing component: groel
It will abort if an unexpected error occurs.
Should you be unable to solve the problem, please contact
Karsten Suhre 

testing groel case ..
setting up URO in groel directory
aide-memoire
go.MASK
go.O
go_instance.O
go.PDBSYM
ncs_rms
splits
d/d7.scr
d/data.d
d/fmt
d/o2u.scr
e/c2pv
e/ctl
e/emft
e/fiting
e/job
e/oic
e/oic_fiting
e/pv2c
e/scat
i/dato.i3
running one step of NMA and URO on groel
func.sh computing NMA and URO for input parameters 7 0
pert_multi_mode.sh ./d/1aonA.pdb 7 0
computing normal modes for 1aonA using DIAGRTB
running pdbmat
automatic determination of NRBL (NRBL = nresidues/200 + 1)
525 non-zero elements, NRBL set to 3
running diagrtb
applying MODE=7 with DQ=0 to 1aonA
====================================================
echo "starting URO job using the following parameters"
EM-map     = GroEl.ezd
PDB-file   = ./d/1aonA.NMApert.pdb
NMAX       = 25
RESOLUTION = 15.0 .. 400.0
====================================================
get the map
get the symmetry files
generate data.d file
generating xyz.d file
Fourier transform of the EM box
Molecular scattering factors of each of the search models
copying initial positions to local dir
generating modlist
Initial positional variables of the independent molecules
fiting
FUNC*1000 = 32727
FUNC*1000 = 32660
FUNC*1000 = 32691
Generation of optimized coordinates
mol1_1
mol1_1 >>> Aa.pdb
generate a file for ono
NEED modlist AND box.sym FILES
copy initial O view
URO finished, here is the convergence ...
 # 1  293.3   94.9    9.4 -0.2238  0.0373  0.1798   61.3  80.0  76.5  32.7
 # 1  293.3   92.7    8.8 -0.2246  0.0387  0.1820   61.5  79.4  76.4  32.7
func.sh terminated for input parameters 7 0
Full fitting with NORMA (based on NORMA.inp)
 opening NORMA.inp for NAMELIST input
 reading NAMELIST param
 dumping NAMELIST param:
&PARAM 
 NDIM = 1, 
 DY =  200., 
 NITER = 50, 
 TEMPTR =  50., 
 NANNEAL = 0, 
 NROUND = 1, 
 LRAND = F, 
 TOL =  0.00100000005, 
 MODE = 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0, 
 PB =  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.
  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.
  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.
  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.
  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.
  0.  0.  0.  0.  0.  0., 
 SEED =  42.4710999, 
 NVERB = 1/
 SEED =   42.4710999
 initial values will NOT be randomized
 Round  1 out of  1
 computing initial values
monitor=  32749.000000, p=  7    100.000000
monitor=  31953.000000, p=  7   -100.000000
 amebsa minimization/annealing step  1 out of  1
 temp =         0.
monitor=  24867.000000, p=  7   -300.000000
monitor=  21875.000000, p=  7   -500.000000
monitor=  25231.000000, p=  7   -900.000000
monitor=  21675.000000, p=  7   -700.000000
monitor=  25231.000000, p=  7   -900.000000
monitor=  21549.000000, p=  7   -600.000000
monitor=  21875.000000, p=  7   -500.000000
monitor=  21669.000000, p=  7   -650.000000
monitor=  21600.000000, p=  7   -550.000000
monitor=  21512.000000, p=  7   -575.000000
monitor=  21600.000000, p=  7   -550.000000
monitor=  21531.000000, p=  7   -587.500000
 minimum =      21512.
 iter =        38
 *** result for this round ***
 1 -575.
 minimum =   21512.
 computing final solution
monitor=  21512.000000, p=  7   -575.000000
 *** Final result ***
 1 -575.
 Final minimum =   21512.
computing an animation for the final NORMA fitting
7 -0 
 # 1  292.7   90.9    9.0 -0.2254  0.0393  0.1837   61.5  78.5  76.4  32.7
7 -57.5 
 # 1  292.5   94.8    8.7 -0.2236  0.0394  0.1770   61.8  78.7  76.5  32.4
7 -115 
 # 1  292.0   96.9    7.8 -0.2216  0.0396  0.1725   62.4  77.6  76.8  31.8
7 -172.5 
 # 1  291.6  126.8    7.8 -0.2122 -0.0077  0.1490   69.3  77.4  84.0  27.0
7 -230 
 # 1  285.0  125.3    3.0 -0.2120 -0.0005  0.1501   70.3  76.7  83.2  26.1
7 -287.5 
 # 1  281.0  124.4   -0.2 -0.2106  0.0052  0.1500   71.5  77.1  83.1  25.2
7 -345 
 # 1  276.6  122.5   -7.4 -0.2066  0.0112  0.1529   72.8  77.5  82.6  24.1
7 -402.5 
 # 1  274.7  121.7   -9.6 -0.2052  0.0138  0.1525   74.1  76.8  82.6  23.1
7 -460 
 # 1  271.7  121.0  -12.0 -0.2043  0.0155  0.1524   75.0  76.1  82.3  22.3
7 -517.5 
 # 1  267.8  120.3  -15.4 -0.2031  0.0161  0.1532   75.7  76.1  81.8  21.7
7 -575 
 # 1  265.3  119.8  342.5 -0.2020  0.0167  0.1532   76.0  76.1  81.2  21.5
Your animated PDB file is anim.pdb
testing groel case .. done

 ------ NORMA INSTALLATION TEST TERMINATED ------ 
add the following line to your .bashrc or run the following command prior to using NORMA

source /tmp/eraseme.25880.NORMA.tmpdir/NORMA-1.0/software/setup.sh



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This page is maintained by Karsten Suhre, last modification: 13 June 2006