
#######################################################
#                                                     #
#                        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    6 (   30),  selected    6 , name T0372TS103_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS103_1_2-D1.T0372_D1.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.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    K     290      C      97          2.017
LGA    Y     291      S      98          1.257
LGA    M     292      N      99          0.880
LGA    A     293      M     100          0.604
LGA    C     294      R     101          0.492
LGA    L     295      A     102          0.485
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  126    5.0      6    1.10     0.00      4.640     0.500

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.211878 * X  +   0.632452 * Y  +  -0.745059 * Z  + -42.574242
  Y_new =   0.877169 * X  +  -0.213075 * Y  +  -0.430318 * Z  +  58.861950
  Z_new =  -0.430909 * X  +  -0.744717 * Y  +  -0.509621 * Z  +  94.389717 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.170918    0.970675  [ DEG:  -124.3844     55.6156 ]
  Theta =   0.445500    2.696093  [ DEG:    25.5253    154.4747 ]
  Phi   =   1.807804   -1.333789  [ DEG:   103.5795    -76.4205 ]
 
# 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: T0372TS103_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS103_1_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  126   5.0    6   1.10    0.00   4.640
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS103_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1z5x_U
ATOM    825  N   LYS   290      26.353  48.983   5.795  1.00  1.00
ATOM    826  CA  LYS   290      26.599  50.277   6.417  1.00  1.00
ATOM    827  C   LYS   290      25.484  50.574   7.414  1.00  1.00
ATOM    828  O   LYS   290      24.864  49.649   7.940  1.00  1.00
ATOM    829  CB  LYS   290      26.609  51.385   5.360  1.00  1.00
ATOM    830  N   TYR   291      21.810  52.682   8.191  1.00  1.00
ATOM    831  CA  TYR   291      20.676  53.133   7.392  1.00  1.00
ATOM    832  C   TYR   291      21.018  54.485   6.786  1.00  1.00
ATOM    833  O   TYR   291      20.886  54.672   5.573  1.00  1.00
ATOM    834  CB  TYR   291      19.366  53.307   8.227  1.00  1.00
ATOM    835  N   MET   292      21.485  55.414   7.625  1.00  1.00
ATOM    836  CA  MET   292      21.810  56.776   7.179  1.00  1.00
ATOM    837  C   MET   292      22.898  56.842   6.133  1.00  1.00
ATOM    838  O   MET   292      22.790  57.592   5.173  1.00  1.00
ATOM    839  CB  MET   292      22.190  57.654   8.368  1.00  1.00
ATOM    840  N   ALA   293      23.954  56.068   6.306  1.00  1.00
ATOM    841  CA  ALA   293      25.006  56.094   5.317  1.00  1.00
ATOM    842  C   ALA   293      24.502  55.563   3.969  1.00  1.00
ATOM    843  O   ALA   293      24.879  56.071   2.903  1.00  1.00
ATOM    844  CB  ALA   293      26.175  55.263   5.785  1.00  1.00
ATOM    845  N   CYS   294      23.654  54.536   4.032  1.00  1.00
ATOM    846  CA  CYS   294      23.068  53.913   2.844  1.00  1.00
ATOM    847  C   CYS   294      22.157  54.900   2.122  1.00  1.00
ATOM    848  O   CYS   294      22.231  55.061   0.903  1.00  1.00
ATOM    849  CB  CYS   294      22.253  52.674   3.228  1.00  1.00
ATOM    850  N   LEU   295      21.279  55.540   2.888  1.00  1.00
ATOM    851  CA  LEU   295      20.350  56.521   2.351  1.00  1.00
ATOM    852  C   LEU   295      21.092  57.684   1.721  1.00  1.00
ATOM    853  O   LEU   295      20.886  58.037   0.566  1.00  1.00
ATOM    854  CB  LEU   295      19.459  57.057   3.469  1.00  1.00
TER
END
