
#######################################################
#                                                     #
#                        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   46 (  232),  selected   46 , name T0363TS437_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS437_3-D1.T0363_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    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    N      11      I      13          2.997
LGA    Q      12      N      14          2.134
LGA    I      13      I      15          2.105
LGA    N      14      E      16          0.611
LGA    I      15      I      17          1.575
LGA    E      16      A      18          1.392
LGA    I      17      Y      19          3.169
LGA    A      18      A      20          1.586
LGA    Y      19      F      21          1.258
LGA    A      20      -       -           -
LGA    F      21      P      22          3.023
LGA    P      22      E      23          2.629
LGA    E      23      R      24          1.905
LGA    R      24      Y      25          1.234
LGA    Y      25      Y      26          2.551
LGA    Y      26      L      27          1.565
LGA    L      27      K      28          0.970
LGA    K      28      S      29          2.092
LGA    S      29      F      30          3.852
LGA    F      30      -       -           -
LGA    Q      31      -       -           -
LGA    V      32      -       -           -
LGA    D      33      Q      31          3.105
LGA    E      34      V      32           -
LGA    G      35      D      33           -
LGA    I      36      -       -           -
LGA    T      37      -       -           -
LGA    V      38      -       -           -
LGA    Q      39      -       -           -
LGA    T      40      -       -           -
LGA    A      41      -       -           -
LGA    I      42      -       -           -
LGA    T      43      -       -           -
LGA    Q      44      -       -           -
LGA    S      45      E      34          1.808
LGA    G      46      G      35          3.132
LGA    I      47      I      36          2.932
LGA    L      48      -       -           -
LGA    S      49      -       -           -
LGA    Q      50      T      37          4.702
LGA    F      51      V      38          5.031
LGA    P      52      Q      39          3.130
LGA    E      53      T      40          3.010
LGA    I      54      A      41          2.466
LGA    -       -      I      42           -
LGA    D      55      T      43          2.598
LGA    -       -      Q      44           -
LGA    L      56      S      45          1.493
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     29    2.63    20.69     45.226     1.064

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.407305 * X  +  -0.090019 * Y  +  -0.908845 * Z  +  92.198273
  Y_new =   0.685017 * X  +   0.628046 * Y  +  -0.369202 * Z  + -67.255165
  Z_new =   0.604032 * X  +  -0.772952 * Y  +  -0.194142 * Z  + -135.563690 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.816875    1.324717  [ DEG:  -104.0993     75.9007 ]
  Theta =  -0.648551   -2.493042  [ DEG:   -37.1592   -142.8408 ]
  Phi   =   2.107230   -1.034363  [ DEG:   120.7354    -59.2646 ]
 
# 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: T0363TS437_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS437_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   29   2.63   20.69  45.226
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS437_3-D1
PFRMAT TS
TARGET T0363
MODEL     3 REFINED
PARENT N/A
ATOM     88  N   ASN    11      20.633   4.243   7.130  1.00   .00
ATOM     89  CA  ASN    11      19.085   4.418   7.017  1.00   .00
ATOM     90  C   ASN    11      18.527   5.975   6.913  1.00   .00
ATOM     91  O   ASN    11      17.661   6.268   6.091  1.00   .00
ATOM     92  CB  ASN    11      18.477   3.636   8.237  1.00   .00
ATOM     96  N   GLN    12      19.059   6.934   7.767  1.00   .00
ATOM     97  CA  GLN    12      18.593   8.414   7.705  1.00   .00
ATOM     98  C   GLN    12      19.843   9.492   7.928  1.00   .00
ATOM     99  O   GLN    12      20.006  10.097   9.004  1.00   .00
ATOM    100  CB  GLN    12      17.431   8.576   8.751  1.00   .00
ATOM    105  N   ILE    13      20.687   9.692   6.849  1.00   .00
ATOM    106  CA  ILE    13      21.885  10.680   6.905  1.00   .00
ATOM    107  C   ILE    13      21.965  11.553   5.529  1.00   .00
ATOM    108  O   ILE    13      22.550  11.131   4.524  1.00   .00
ATOM    109  CB  ILE    13      23.186   9.848   7.160  1.00   .00
ATOM    113  N   ASN    14      21.367  12.783   5.519  1.00   .00
ATOM    114  CA  ASN    14      21.403  13.691   4.248  1.00   .00
ATOM    115  C   ASN    14      22.807  14.540   4.120  1.00   .00
ATOM    116  O   ASN    14      23.010  15.544   4.822  1.00   .00
ATOM    117  CB  ASN    14      20.136  14.589   4.308  1.00   .00
ATOM    121  N   ILE    15      23.751  14.089   3.227  1.00   .00
ATOM    122  CA  ILE    15      25.114  14.825   3.051  1.00   .00
ATOM    123  C   ILE    15      25.025  16.099   2.020  1.00   .00
ATOM    124  O   ILE    15      24.740  15.950   0.819  1.00   .00
ATOM    125  CB  ILE    15      26.183  13.765   2.622  1.00   .00
ATOM    129  N   GLU    16      25.281  17.332   2.544  1.00   .00
ATOM    130  CA  GLU    16      25.243  18.618   1.668  1.00   .00
ATOM    131  C   GLU    16      26.773  19.127   1.366  1.00   .00
ATOM    132  O   GLU    16      27.410  19.768   2.213  1.00   .00
ATOM    133  CB  GLU    16      24.372  19.654   2.456  1.00   .00
ATOM    138  N   ILE    17      27.333  18.814   0.140  1.00   .00
ATOM    139  CA  ILE    17      28.772  19.233  -0.231  1.00   .00
ATOM    140  C   ILE    17      28.876  20.767  -0.789  1.00   .00
ATOM    141  O   ILE    17      28.539  21.038  -1.958  1.00   .00
ATOM    142  CB  ILE    17      29.303  18.179  -1.242  1.00   .00
ATOM    146  N   ALA    18      29.362  21.714   0.071  1.00   .00
ATOM    147  CA  ALA    18      29.532  23.198  -0.333  1.00   .00
ATOM    148  C   ALA    18      31.073  23.521  -0.784  1.00   .00
ATOM    149  O   ALA    18      32.011  23.559   0.040  1.00   .00
ATOM    150  CB  ALA    18      29.071  24.055   0.891  1.00   .00
ATOM    151  N   TYR    19      31.278  23.745  -2.105  1.00   .00
ATOM    152  CA  TYR    19      32.688  24.057  -2.666  1.00   .00
ATOM    153  C   TYR    19      33.253  25.561  -2.316  1.00   .00
ATOM    154  O   TYR    19      32.487  26.492  -2.034  1.00   .00
ATOM    155  CB  TYR    19      32.554  23.865  -4.214  1.00   .00
ATOM    163  N   ALA    20      34.628  25.796  -2.417  1.00   .00
ATOM    164  CA  ALA    20      35.225  27.273  -2.200  1.00   .00
ATOM    165  C   ALA    20      35.030  28.221  -3.592  1.00   .00
ATOM    166  O   ALA    20      35.912  28.926  -4.075  1.00   .00
ATOM    167  CB  ALA    20      36.694  27.080  -1.748  1.00   .00
ATOM    168  N   PHE    21      33.815  28.104  -4.121  1.00   .00
ATOM    169  CA  PHE    21      33.276  28.762  -5.358  1.00   .00
ATOM    170  C   PHE    21      31.619  28.440  -5.243  1.00   .00
ATOM    171  O   PHE    21      31.204  27.454  -4.560  1.00   .00
ATOM    172  CB  PHE    21      33.925  28.110  -6.647  1.00   .00
ATOM    179  N   PRO    22      30.643  29.236  -5.868  1.00   .00
ATOM    180  CA  PRO    22      29.115  28.932  -5.694  1.00   .00
ATOM    181  C   PRO    22      28.477  27.517  -6.315  1.00   .00
ATOM    182  O   PRO    22      27.580  27.521  -7.166  1.00   .00
ATOM    183  CB  PRO    22      28.538  30.240  -6.301  1.00   .00
ATOM    184  CG  PRO    22      29.591  30.731  -7.338  1.00   .00
ATOM    185  CD  PRO    22      30.955  30.417  -6.702  1.00   .00
ATOM    186  N   GLU    23      28.970  26.363  -5.788  1.00   .00
ATOM    187  CA  GLU    23      28.454  24.959  -6.205  1.00   .00
ATOM    188  C   GLU    23      28.105  24.091  -4.844  1.00   .00
ATOM    189  O   GLU    23      29.005  23.679  -4.066  1.00   .00
ATOM    190  CB  GLU    23      29.524  24.295  -7.129  1.00   .00
ATOM    195  N   ARG    24      26.771  23.840  -4.604  1.00   .00
ATOM    196  CA  ARG    24      26.280  23.038  -3.362  1.00   .00
ATOM    197  C   ARG    24      25.503  21.655  -3.799  1.00   .00
ATOM    198  O   ARG    24      24.384  21.687  -4.332  1.00   .00
ATOM    199  CB  ARG    24      25.368  24.010  -2.542  1.00   .00
ATOM    206  N   TYR    25      26.133  20.454  -3.564  1.00   .00
ATOM    207  CA  TYR    25      25.472  19.099  -3.955  1.00   .00
ATOM    208  C   TYR    25      24.697  18.371  -2.692  1.00   .00
ATOM    209  O   TYR    25      25.326  17.883  -1.722  1.00   .00
ATOM    210  CB  TYR    25      26.590  18.207  -4.565  1.00   .00
ATOM    218  N   TYR    26      23.317  18.341  -2.751  1.00   .00
ATOM    219  CA  TYR    26      22.453  17.702  -1.618  1.00   .00
ATOM    220  C   TYR    26      22.111  16.110  -1.837  1.00   .00
ATOM    221  O   TYR    26      21.214  15.736  -2.615  1.00   .00
ATOM    222  CB  TYR    26      21.161  18.584  -1.565  1.00   .00
ATOM    230  N   LEU    27      22.846  15.216  -1.110  1.00   .00
ATOM    231  CA  LEU    27      22.624  13.700  -1.204  1.00   .00
ATOM    232  C   LEU    27      21.534  13.165  -0.106  1.00   .00
ATOM    233  O   LEU    27      21.873  12.775   1.018  1.00   .00
ATOM    234  CB  LEU    27      24.028  13.055  -1.001  1.00   .00
ATOM    238  N   LYS    28      20.209  13.167  -0.486  1.00   .00
ATOM    239  CA  LYS    28      19.071  12.676   0.462  1.00   .00
ATOM    240  C   LYS    28      19.170  11.100   0.987  1.00   .00
ATOM    241  O   LYS    28      20.024  10.310   0.536  1.00   .00
ATOM    242  CB  LYS    28      17.764  12.946  -0.342  1.00   .00
ATOM    247  N   SER    29      18.247  10.680   1.944  1.00   .00
ATOM    248  CA  SER    29      18.217   9.191   2.510  1.00   .00
ATOM    249  C   SER    29      17.773   7.976   1.421  1.00   .00
ATOM    250  O   SER    29      16.899   7.129   1.656  1.00   .00
ATOM    251  CB  SER    29      17.293   9.241   3.754  1.00   .00
ATOM    253  N   PHE    30      18.470   8.001   0.291  1.00   .00
ATOM    254  CA  PHE    30      18.329   6.996  -0.892  1.00   .00
ATOM    255  C   PHE    30      19.788   7.022  -1.639  1.00   .00
ATOM    256  O   PHE    30      20.474   6.002  -1.719  1.00   .00
ATOM    257  CB  PHE    30      17.102   7.380  -1.793  1.00   .00
ATOM    264  N   GLN    31      20.257   8.272  -2.110  1.00   .00
ATOM    265  CA  GLN    31      21.666   8.442  -2.718  1.00   .00
ATOM    266  C   GLN    31      22.820   8.188  -1.561  1.00   .00
ATOM    267  O   GLN    31      23.736   7.387  -1.768  1.00   .00
ATOM    268  CB  GLN    31      21.720   9.872  -3.356  1.00   .00
ATOM    273  N   VAL    32      22.691   8.850  -0.327  1.00   .00
ATOM    274  CA  VAL    32      23.689   8.596   0.846  1.00   .00
ATOM    275  C   VAL    32      23.707   7.007   1.346  1.00   .00
ATOM    276  O   VAL    32      24.774   6.462   1.645  1.00   .00
ATOM    277  CB  VAL    32      23.296   9.587   1.974  1.00   .00
ATOM    280  N   ASP    33      22.494   6.293   1.355  1.00   .00
ATOM    281  CA  ASP    33      22.433   4.772   1.719  1.00   .00
ATOM    282  C   ASP    33      23.353   3.810   0.728  1.00   .00
ATOM    283  O   ASP    33      23.857   2.768   1.158  1.00   .00
ATOM    284  CB  ASP    33      20.922   4.373   1.690  1.00   .00
ATOM    288  N   GLU    34      23.568   4.236  -0.575  1.00   .00
ATOM    289  CA  GLU    34      24.485   3.476  -1.556  1.00   .00
ATOM    290  C   GLU    34      26.119   3.603  -1.216  1.00   .00
ATOM    291  O   GLU    34      26.916   2.811  -1.725  1.00   .00
ATOM    292  CB  GLU    34      24.139   4.046  -2.981  1.00   .00
ATOM    297  N   GLY    35      26.556   4.606  -0.345  1.00   .00
ATOM    298  CA  GLY    35      28.074   4.758   0.022  1.00   .00
ATOM    299  C   GLY    35      28.433   5.900   1.063  1.00   .00
ATOM    300  O   GLY    35      29.210   6.805   0.764  1.00   .00
ATOM    301  N   ILE    36      27.874   5.817   2.310  1.00   .00
ATOM    302  CA  ILE    36      28.190   6.865   3.441  1.00   .00
ATOM    303  C   ILE    36      28.321   6.077   4.864  1.00   .00
ATOM    304  O   ILE    36      27.316   5.829   5.563  1.00   .00
ATOM    305  CB  ILE    36      27.089   7.972   3.445  1.00   .00
ATOM    309  N   THR    37      29.581   5.678   5.259  1.00   .00
ATOM    310  CA  THR    37      29.799   4.884   6.585  1.00   .00
ATOM    311  C   THR    37      30.001   5.847   7.914  1.00   .00
ATOM    312  O   THR    37      31.051   6.491   8.085  1.00   .00
ATOM    313  CB  THR    37      31.022   3.927   6.334  1.00   .00
ATOM    316  N   VAL    38      28.968   5.888   8.831  1.00   .00
ATOM    317  CA  VAL    38      29.051   6.763  10.144  1.00   .00
ATOM    318  C   VAL    38      29.664   5.934  11.423  1.00   .00
ATOM    319  O   VAL    38      28.923   5.310  12.184  1.00   .00
ATOM    320  CB  VAL    38      27.608   7.310  10.390  1.00   .00
ATOM    323  N   GLN    39      31.055   5.960  11.583  1.00   .00
ATOM    324  CA  GLN    39      31.848   5.172  12.743  1.00   .00
ATOM    325  C   GLN    39      31.041   4.581  14.063  1.00   .00
ATOM    326  O   GLN    39      30.651   3.421  14.051  1.00   .00
ATOM    327  CB  GLN    39      33.087   6.052  13.088  1.00   .00
ATOM    332  N   THR    40      30.814   5.376  15.171  1.00   .00
ATOM    333  CA  THR    40      30.023   4.802  16.438  1.00   .00
ATOM    334  C   THR    40      28.384   4.583  16.217  1.00   .00
ATOM    335  O   THR    40      27.759   3.790  16.926  1.00   .00
ATOM    336  CB  THR    40      30.319   5.782  17.623  1.00   .00
ATOM    339  N   ALA    41      27.764   5.316  15.224  1.00   .00
ATOM    340  CA  ALA    41      26.274   5.158  14.913  1.00   .00
ATOM    341  C   ALA    41      25.941   3.870  13.929  1.00   .00
ATOM    342  O   ALA    41      24.893   3.259  14.079  1.00   .00
ATOM    343  CB  ALA    41      25.813   6.515  14.345  1.00   .00
ATOM    344  N   ILE    42      26.871   3.459  12.964  1.00   .00
ATOM    345  CA  ILE    42      26.622   2.190  12.051  1.00   .00
ATOM    346  C   ILE    42      26.708   0.707  12.872  1.00   .00
ATOM    347  O   ILE    42      27.366  -0.261  12.482  1.00   .00
ATOM    348  CB  ILE    42      27.641   2.329  10.856  1.00   .00
ATOM    352  N   THR    43      25.966   0.677  13.979  1.00   .00
ATOM    353  CA  THR    43      25.811  -0.527  14.946  1.00   .00
ATOM    354  C   THR    43      24.243  -0.497  15.501  1.00   .00
ATOM    355  O   THR    43      23.490  -1.462  15.332  1.00   .00
ATOM    356  CB  THR    43      26.925  -0.386  16.050  1.00   .00
ATOM    359  N   GLN    44      23.804   0.684  16.102  1.00   .00
ATOM    360  CA  GLN    44      22.367   0.899  16.560  1.00   .00
ATOM    361  C   GLN    44      21.623   1.877  15.450  1.00   .00
ATOM    362  O   GLN    44      22.222   2.833  14.937  1.00   .00
ATOM    363  CB  GLN    44      22.434   1.541  17.971  1.00   .00
ATOM    368  N   SER    45      20.346   1.597  15.073  1.00   .00
ATOM    369  CA  SER    45      19.607   2.462  13.947  1.00   .00
ATOM    370  C   SER    45      19.312   4.097  14.191  1.00   .00
ATOM    371  O   SER    45      18.172   4.572  14.040  1.00   .00
ATOM    372  CB  SER    45      18.338   1.648  13.597  1.00   .00
ATOM    374  N   GLY    46      20.376   4.876  14.489  1.00   .00
ATOM    375  CA  GLY    46      20.270   6.461  14.664  1.00   .00
ATOM    376  C   GLY    46      21.597   7.156  14.079  1.00   .00
ATOM    377  O   GLY    46      22.412   7.708  14.828  1.00   .00
ATOM    378  N   ILE    47      21.769   7.061  12.723  1.00   .00
ATOM    379  CA  ILE    47      23.027   7.600  11.954  1.00   .00
ATOM    380  C   ILE    47      23.815   8.986  12.406  1.00   .00
ATOM    381  O   ILE    47      25.050   8.998  12.465  1.00   .00
ATOM    382  CB  ILE    47      22.606   7.645  10.448  1.00   .00
ATOM    386  N   LEU    48      23.092  10.117  12.703  1.00   .00
ATOM    387  CA  LEU    48      23.795  11.461  13.144  1.00   .00
ATOM    388  C   LEU    48      23.239  12.102  14.567  1.00   .00
ATOM    389  O   LEU    48      23.423  13.286  14.843  1.00   .00
ATOM    390  CB  LEU    48      23.684  12.427  11.924  1.00   .00
ATOM    394  N   SER    49      22.581  11.273  15.474  1.00   .00
ATOM    395  CA  SER    49      22.091  11.811  16.878  1.00   .00
ATOM    396  C   SER    49      23.327  11.876  17.960  1.00   .00
ATOM    397  O   SER    49      23.466  12.857  18.701  1.00   .00
ATOM    398  CB  SER    49      20.895  10.920  17.323  1.00   .00
ATOM    400  N   GLN    50      24.223  10.819  17.963  1.00   .00
ATOM    401  CA  GLN    50      25.480  10.832  18.841  1.00   .00
ATOM    402  C   GLN    50      26.648  11.766  18.047  1.00   .00
ATOM    403  O   GLN    50      26.329  12.549  17.136  1.00   .00
ATOM    404  CB  GLN    50      25.858   9.300  19.026  1.00   .00
ATOM    409  N   PHE    51      27.972  11.623  18.372  1.00   .00
ATOM    410  CA  PHE    51      29.080  12.434  17.582  1.00   .00
ATOM    411  C   PHE    51      30.074  11.434  16.720  1.00   .00
ATOM    412  O   PHE    51      31.300  11.359  17.009  1.00   .00
ATOM    413  CB  PHE    51      29.793  13.325  18.633  1.00   .00
ATOM    420  N   PRO    52      29.563  10.633  15.630  1.00   .00
ATOM    421  CA  PRO    52      30.456   9.707  14.812  1.00   .00
ATOM    422  C   PRO    52      31.210  10.465  13.568  1.00   .00
ATOM    423  O   PRO    52      31.037  11.672  13.314  1.00   .00
ATOM    424  CB  PRO    52      29.339   8.682  14.347  1.00   .00
ATOM    425  CG  PRO    52      28.104   9.593  14.044  1.00   .00
ATOM    426  CD  PRO    52      28.107  10.621  15.195  1.00   .00
ATOM    427  N   GLU    53      32.015   9.693  12.796  1.00   .00
ATOM    428  CA  GLU    53      32.747  10.259  11.555  1.00   .00
ATOM    429  C   GLU    53      32.043   9.628  10.214  1.00   .00
ATOM    430  O   GLU    53      32.183   8.426   9.937  1.00   .00
ATOM    431  CB  GLU    53      34.249   9.896  11.715  1.00   .00
ATOM    436  N   ILE    54      31.265  10.472   9.425  1.00   .00
ATOM    437  CA  ILE    54      30.531   9.947   8.160  1.00   .00
ATOM    438  C   ILE    54      31.457   9.948   6.810  1.00   .00
ATOM    439  O   ILE    54      31.655  10.986   6.144  1.00   .00
ATOM    440  CB  ILE    54      29.211  10.768   8.028  1.00   .00
ATOM    444  N   ASP    55      32.000   8.739   6.430  1.00   .00
ATOM    445  CA  ASP    55      32.898   8.598   5.167  1.00   .00
ATOM    446  C   ASP    55      32.057   8.426   3.770  1.00   .00
ATOM    447  O   ASP    55      31.578   7.322   3.426  1.00   .00
ATOM    448  CB  ASP    55      33.827   7.376   5.459  1.00   .00
ATOM    452  N   LEU    56      31.920   9.563   2.997  1.00   .00
ATOM    453  CA  LEU    56      31.151   9.557   1.644  1.00   .00
ATOM    454  C   LEU    56      32.051   8.956   0.398  1.00   .00
ATOM    455  O   LEU    56      33.060   9.539  -0.007  1.00   .00
ATOM    456  CB  LEU    56      30.701  11.025   1.414  1.00   .00
TER   
END
