
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0316TS393_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS393_2-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220          1.790
LGA    R     221      R     221          1.721
LGA    M     222      M     222          3.111
LGA    M     223      M     223          2.246
LGA    T     224      T     224          1.644
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    V     225      D     229          3.389
LGA    D     226      M     230          4.714
LGA    G     227      G     231           -
LGA    R     228      -       -           -
LGA    D     229      -       -           -
LGA    M     230      -       -           -
LGA    G     231      -       -           -
LGA    E     232      E     232           #
LGA    H     233      H     233          2.137
LGA    A     234      A     234          2.635
LGA    G     235      G     235          3.582
LGA    L     236      L     236          3.618
LGA    M     237      M     237          3.143
LGA    Y     238      Y     238          1.165
LGA    Y     239      Y     239          1.392
LGA    T     240      T     240          2.626
LGA    I     241      I     241          5.189
LGA    G     242      G     242          2.488
LGA    Q     243      Q     243          3.802
LGA    R     244      R     244          4.649
LGA    G     245      G     245          4.511
LGA    G     246      G     246          3.361
LGA    L     247      L     247          3.535
LGA    -       -      G     248           -
LGA    G     248      I     249          1.901
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    I     249      P     259          3.895
LGA    G     250      W     260          1.724
LGA    G     251      F     261           #
LGA    Q     252      V     262           -
LGA    H     253      V     263           -
LGA    G     254      G     264           -
LGA    G     255      -       -           -
LGA    D     256      -       -           -
LGA    N     257      -       -           -
LGA    A     258      -       -           -
LGA    P     259      -       -           -
LGA    W     260      K     265           #
LGA    F     261      D     266          3.027
LGA    V     262      L     267          3.441
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    V     263      Y     273           #
LGA    G     264      V     274           -
LGA    K     265      G     275           -
LGA    D     266      Q     276           -
LGA    L     267      G     277           -
LGA    -       -      F     278           -
LGA    S     268      Y     279           #
LGA    K     269      H     280          3.046
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    N     270      L     283          2.678
LGA    I     271      -       -           -
LGA    L     272      -       -           -
LGA    Y     273      -       -           -
LGA    V     274      -       -           -
LGA    G     275      -       -           -
LGA    Q     276      -       -           -
LGA    G     277      -       -           -
LGA    F     278      -       -           -
LGA    Y     279      -       -           -
LGA    H     280      -       -           -
LGA    D     281      -       -           -
LGA    S     282      -       -           -
LGA    L     283      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   60    5.0     29    3.15    68.97     27.821     0.893

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.540155 * X  +  -0.740898 * Y  +   0.399128 * Z  +  31.186724
  Y_new =   0.691738 * X  +  -0.660992 * Y  +  -0.290839 * Z  +  18.660213
  Z_new =   0.479302 * X  +   0.118993 * Y  +   0.869546 * Z  + -15.527203 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.136001   -3.005592  [ DEG:     7.7923   -172.2077 ]
  Theta =  -0.499860   -2.641733  [ DEG:   -28.6399   -151.3602 ]
  Phi   =   2.233761   -0.907832  [ DEG:   127.9851    -52.0149 ]
 
# 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: T0316TS393_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_2-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64   60   5.0   29   3.15   68.97  27.821
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_2-D2
PFRMAT TS
TARGET T0316
MODEL 2
PARENT N/A
ATOM    220  CA  GLY   220      45.325  23.382 -21.297  1.00 25.00           C
ATOM    221  CA  ARG   221      42.265  21.982 -23.036  1.00 25.00           C
ATOM    222  CA  MET   222      39.817  20.021 -20.874  1.00 25.00           C
ATOM    223  CA  MET   223      37.512  18.942 -23.644  1.00 25.00           C
ATOM    224  CA  THR   224      34.848  17.472 -25.833  1.00 25.00           C
ATOM    225  CA  VAL   225      35.689  19.710 -28.782  1.00 25.00           C
ATOM    226  CA  ASP   226      32.379  21.633 -28.410  1.00 25.00           C
ATOM    227  CA  GLY   227      30.873  19.587 -25.601  1.00 25.00           C
ATOM    228  CA  ARG   228      29.875  18.143 -22.216  1.00 25.00           C
ATOM    229  CA  ASP   229      33.311  17.828 -20.620  1.00 25.00           C
ATOM    230  CA  MET   230      34.997  21.213 -20.192  1.00 25.00           C
ATOM    231  CA  GLY   231      36.938  22.727 -17.364  1.00 25.00           C
ATOM    232  CA  GLU   232      37.337  25.352 -20.096  1.00 25.00           C
ATOM    233  CA  HIS   233      40.853  24.814 -18.625  1.00 25.00           C
ATOM    234  CA  ALA   234      43.935  25.824 -16.722  1.00 25.00           C
ATOM    235  CA  GLY   235      45.973  22.675 -16.221  1.00 25.00           C
ATOM    236  CA  LEU   236      44.045  22.157 -12.988  1.00 25.00           C
ATOM    237  CA  MET   237      40.515  23.177 -13.876  1.00 25.00           C
ATOM    238  CA  TYR   238      38.631  26.388 -13.580  1.00 25.00           C
ATOM    239  CA  TYR   239      34.947  25.569 -13.599  1.00 25.00           C
ATOM    240  CA  THR   240      32.355  22.829 -14.093  1.00 25.00           C
ATOM    241  CA  ILE   241      28.621  23.657 -13.997  1.00 25.00           C
ATOM    242  CA  GLY   242      26.593  21.456 -16.412  1.00 25.00           C
ATOM    243  CA  GLN   243      26.946  24.868 -18.056  1.00 25.00           C
ATOM    244  CA  ARG   244      29.385  22.557 -19.844  1.00 25.00           C
ATOM    245  CA  GLY   245      32.310  24.439 -18.317  1.00 25.00           C
ATOM    246  CA  GLY   246      30.949  27.250 -16.111  1.00 25.00           C
ATOM    247  CA  LEU   247      33.493  28.611 -18.544  1.00 25.00           C
ATOM    248  CA  GLY   248      32.123  28.209 -22.059  1.00 25.00           C
ATOM    249  CA  ILE   249      28.528  26.975 -22.285  1.00 25.00           C
ATOM    250  CA  GLY   250      29.276  23.716 -24.174  1.00 25.00           C
ATOM    251  CA  GLY   251      33.030  23.456 -24.042  1.00 25.00           C
ATOM    252  CA  GLN   252      36.618  24.217 -25.029  1.00 25.00           C
ATOM    253  CA  HIS   253      39.347  23.487 -27.632  1.00 25.00           C
ATOM    254  CA  GLY   254      42.522  24.044 -29.650  1.00 25.00           C
ATOM    255  CA  GLY   255      43.727  25.590 -26.362  1.00 25.00           C
ATOM    256  CA  ASP   256      47.071  23.919 -27.069  1.00 25.00           C
ATOM    257  CA  ASN   257      48.639  20.713 -25.718  1.00 25.00           C
ATOM    258  CA  ALA   258      46.666  18.161 -23.785  1.00 25.00           C
ATOM    259  CA  PRO   259      43.001  17.252 -24.005  1.00 25.00           C
ATOM    260  CA  TRP   260      43.053  17.107 -20.175  1.00 25.00           C
ATOM    261  CA  PHE   261      42.669  15.362 -16.889  1.00 25.00           C
ATOM    262  CA  VAL   262      39.783  13.748 -15.023  1.00 25.00           C
ATOM    263  CA  VAL   263      36.374  15.224 -14.263  1.00 25.00           C
ATOM    264  CA  GLY   264      33.826  13.339 -12.140  1.00 25.00           C
ATOM    265  CA  LYS   265      30.158  12.785 -12.923  1.00 25.00           C
ATOM    266  CA  ASP   266      26.971  12.222 -14.912  1.00 25.00           C
ATOM    267  CA  LEU   267      24.986   9.034 -15.316  1.00 25.00           C
ATOM    268  CA  SER   268      23.258  10.662 -18.256  1.00 25.00           C
ATOM    269  CA  LYS   269      23.663  14.412 -18.154  1.00 25.00           C
ATOM    270  CA  ASN   270      26.895  16.378 -17.628  1.00 25.00           C
ATOM    271  CA  ILE   271      29.799  18.705 -16.783  1.00 25.00           C
ATOM    272  CA  LEU   272      32.202  15.748 -16.524  1.00 25.00           C
ATOM    273  CA  TYR   273      34.699  13.404 -18.231  1.00 25.00           C
ATOM    274  CA  VAL   274      37.140  10.622 -17.303  1.00 25.00           C
ATOM    275  CA  GLY   275      39.096   7.454 -16.414  1.00 25.00           C
ATOM    276  CA  GLN   276      36.268   4.947 -17.105  1.00 25.00           C
ATOM    277  CA  GLY   277      34.669   2.958 -14.278  1.00 25.00           C
ATOM    278  CA  PHE   278      32.673   1.215 -16.998  1.00 25.00           C
ATOM    279  CA  TYR   279      30.762   0.057 -20.102  1.00 25.00           C
ATOM    280  CA  HIS   280      30.899   3.319 -22.003  1.00 25.00           C
ATOM    281  CA  ASP   281      27.369   4.265 -23.044  1.00 25.00           C
ATOM    282  CA  SER   282      25.324   7.177 -21.627  1.00 25.00           C
ATOM    283  CA  LEU   283      28.370   8.381 -19.641  1.00 25.00           C
TER
END
