
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    5 (   25),  selected    5 , name T0354TS102_1
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS102_1.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

# WARNING! The change of the distance cutoff DIST may give you better result.

 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
 ERROR! 0 0 5 122
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      E       2           -
LGA    H     126      I       3          2.032
LGA    H     127      Q       4          2.960
LGA    H     128      E       5          2.172
LGA    -       -      I       6           -
LGA    H     129      S       7          0.972
LGA    -       -      K       8           -
LGA    -       -      L       9           -
LGA    H     130      A      10          0.872
LGA    -       -      I      11           -
LGA    -       -      E      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      D      16           -
LGA    -       -      I      17           -
LGA    -       -      K      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      I      22           -
LGA    -       -      I      23           -
LGA    -       -      E      24           -
LGA    -       -      L      25           -
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    -       -      M      37           -
LGA    -       -      I      38           -
LGA    -       -      V      39           -
LGA    -       -      A      40           -
LGA    -       -      T      41           -
LGA    -       -      G      42           -
LGA    -       -      D      43           -
LGA    -       -      S      44           -
LGA    -       -      N      45           -
LGA    -       -      R      46           -
LGA    -       -      Q      47           -
LGA    -       -      V      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      L      51           -
LGA    -       -      A      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      K      58           -
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    -       -      E      61           -
LGA    -       -      A      62           -
LGA    -       -      G      63           -
LGA    -       -      V      64           -
LGA    -       -      D      65           -
LGA    -       -      I      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    -       -      V      78           -
LGA    -       -      L      79           -
LGA    -       -      V      80           -
LGA    -       -      D      81           -
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    -       -      H      88           -
LGA    -       -      V      89           -
LGA    -       -      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    -       -      Y      98           -
LGA    -       -      D      99           -
LGA    -       -      I     100           -
LGA    -       -      E     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    -       -      K     108           -
LGA    -       -      P     109           -
LGA    -       -      S     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    -       -      A     115           -
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    -       -      P     118           -
LGA    -       -      W     119           -
LGA    -       -      S     120           -
LGA    -       -      A     121           -
LGA    -       -      V     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  122    5.0      5    1.97     0.00      3.735     0.242

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.472240 * X  +  -0.766528 * Y  +   0.435229 * Z  +  37.760384
  Y_new =  -0.586616 * X  +  -0.095244 * Y  +  -0.804245 * Z  +  61.828766
  Z_new =   0.657929 * X  +  -0.635109 * Y  +  -0.404680 * Z  +  50.721783 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.138108    1.003484  [ DEG:  -122.5046     57.4954 ]
  Theta =  -0.718066   -2.423527  [ DEG:   -41.1421   -138.8578 ]
  Phi   =  -2.248593    0.893000  [ DEG:  -128.8349     51.1651 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0354TS102_1                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS102_1.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  122   5.0    5   1.97    0.00   3.735
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS102_1
PFRMAT TS
TARGET T0354
MODEL 1
PARENT 1zko_A
ATOM      1  N   HIS   126      51.588  18.444  15.319  1.00  1.00
ATOM      2  CA  HIS   126      50.710  19.034  16.367  1.00  1.00
ATOM      3  C   HIS   126      51.510  19.365  17.609  1.00  1.00
ATOM      4  O   HIS   126      52.405  18.617  18.003  1.00  1.00
ATOM      5  CB  HIS   126      49.565  18.083  16.707  1.00  1.00
ATOM      6  N   HIS   127      51.168  20.491  18.219  1.00  1.00
ATOM      7  CA  HIS   127      51.919  21.030  19.340  1.00  1.00
ATOM      8  C   HIS   127      51.093  20.984  20.612  1.00  1.00
ATOM      9  O   HIS   127      49.862  21.035  20.555  1.00  1.00
ATOM     10  CB  HIS   127      52.382  22.445  19.010  1.00  1.00
ATOM     11  N   HIS   128      51.775  20.850  21.748  1.00  1.00
ATOM     12  CA  HIS   128      51.119  20.737  23.048  1.00  1.00
ATOM     13  C   HIS   128      50.185  21.918  23.302  1.00  1.00
ATOM     14  O   HIS   128      50.597  23.077  23.245  1.00  1.00
ATOM     15  CB  HIS   128      52.180  20.630  24.148  1.00  1.00
ATOM     16  N   HIS   129      48.920  21.613  23.570  1.00  1.00
ATOM     17  CA  HIS   129      47.926  22.644  23.825  1.00  1.00
ATOM     18  C   HIS   129      48.192  23.321  25.160  1.00  1.00
ATOM     19  O   HIS   129      48.429  22.649  26.158  1.00  1.00
ATOM     20  CB  HIS   129      46.535  22.017  23.835  1.00  1.00
ATOM     21  N   HIS   130      48.163  24.650  25.158  1.00  1.00
ATOM     22  CA  HIS   130      48.198  25.420  26.392  1.00  1.00
ATOM     23  C   HIS   130      46.853  25.306  27.091  1.00  1.00
ATOM     24  O   HIS   130      45.832  25.052  26.453  1.00  1.00
ATOM     25  CB  HIS   130      48.447  26.895  26.119  1.00  1.00
TER
END
