
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0347AL333_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL333_4-D2.T0347_D2.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 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
 ERROR! 0 0 32 71
#      Molecule1      Molecule2       DISTANCE
LGA    D     134      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    L     139      D     172          5.018
LGA    A     140      L     173           #
LGA    G     141      -       -           -
LGA    A     142      -       -           -
LGA    L     143      -       -           -
LGA    R     144      -       -           -
LGA    M     145      -       -           -
LGA    A     146      L     174          4.535
LGA    G     147      S     175          3.304
LGA    -       -      D     176           -
LGA    G     148      S     177          1.882
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    Y     149      D     180          0.885
LGA    A     150      A     181          2.972
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    K     151      E     184          1.899
LGA    V     152      A     185          2.282
LGA    -       -      M     186           -
LGA    -       -      K     187           -
LGA    I     153      L     188          1.764
LGA    I     154      A     189          2.731
LGA    -       -      K     190           -
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    P     155      A     194          1.512
LGA    F     156      R     195          2.198
LGA    S     157      H     196          2.475
LGA    E     158      L     197          3.676
LGA    -       -      P     198           -
LGA    F     159      G     199           #
LGA    G     160      W     200          1.125
LGA    W     161      C     201          5.306
LGA    A     162      G     202           -
LGA    D     163      V     203           -
LGA    F     164      E     204           -
LGA    L     165      -       -           -
LGA    R     166      -       -           -
LGA    R     167      -       -           -
LGA    R     168      -       -           -
LGA    I     169      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   71    5.0     16    3.01     6.25     16.051     0.514

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.730902 * X  +   0.129617 * Y  +   0.670061 * Z  +  -8.260801
  Y_new =   0.625635 * X  +  -0.265042 * Y  +   0.733712 * Z  +  59.408894
  Z_new =   0.272696 * X  +   0.955485 * Y  +   0.112627 * Z  + -83.332878 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.453464   -1.688129  [ DEG:    83.2773    -96.7227 ]
  Theta =  -0.276194   -2.865399  [ DEG:   -15.8247   -164.1753 ]
  Phi   =   2.433639   -0.707954  [ DEG:   139.4372    -40.5628 ]
 
# 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: T0347AL333_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_4-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   71   5.0   16   3.01    6.25  16.051
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_4-D2
REMARK Aligment from pdb entry: 1ltl_A
ATOM    529  N   ASP   134       4.398  74.560   4.371  1.00  0.00              
ATOM    530  CA  ASP   134       3.041  74.404   3.858  1.00  0.00              
ATOM    531  C   ASP   134       2.761  73.137   3.088  1.00  0.00              
ATOM    532  O   ASP   134       1.601  72.843   2.790  1.00  0.00              
ATOM    533  N   LEU   139       3.807  72.387   2.764  1.00  0.00              
ATOM    534  CA  LEU   139       3.633  71.135   2.053  1.00  0.00              
ATOM    535  C   LEU   139       3.282  70.053   3.030  1.00  0.00              
ATOM    536  O   LEU   139       3.019  68.917   2.653  1.00  0.00              
ATOM    537  N   ALA   140       3.287  70.392   4.301  1.00  0.00              
ATOM    538  CA  ALA   140       2.974  69.406   5.308  1.00  0.00              
ATOM    539  C   ALA   140       1.524  68.988   5.178  1.00  0.00              
ATOM    540  O   ALA   140       0.683  69.786   4.784  1.00  0.00              
ATOM    541  N   GLY   141       1.241  67.730   5.495  1.00  0.00              
ATOM    542  CA  GLY   141      -0.124  67.198   5.462  1.00  0.00              
ATOM    543  C   GLY   141      -0.810  67.559   4.158  1.00  0.00              
ATOM    544  O   GLY   141      -1.908  68.109   4.159  1.00  0.00              
ATOM    545  N   ALA   142      -0.148  67.237   3.051  1.00  0.00              
ATOM    546  CA  ALA   142      -0.637  67.529   1.715  1.00  0.00              
ATOM    547  C   ALA   142      -0.945  66.244   0.954  1.00  0.00              
ATOM    548  O   ALA   142      -1.844  66.213   0.124  1.00  0.00              
ATOM    549  N   LEU   143      -0.205  65.183   1.243  1.00  0.00              
ATOM    550  CA  LEU   143      -0.416  63.925   0.558  1.00  0.00              
ATOM    551  C   LEU   143      -0.886  62.842   1.496  1.00  0.00              
ATOM    552  O   LEU   143      -0.770  62.967   2.713  1.00  0.00              
ATOM    553  N   ARG   144      -1.423  61.772   0.920  1.00  0.00              
ATOM    554  CA  ARG   144      -1.909  60.630   1.698  1.00  0.00              
ATOM    555  C   ARG   144      -1.782  59.319   0.943  1.00  0.00              
ATOM    556  O   ARG   144      -1.751  59.297  -0.279  1.00  0.00              
ATOM    557  N   MET   145       4.007  63.074  -8.411  1.00  0.00              
ATOM    558  CA  MET   145       5.249  63.376  -9.073  1.00  0.00              
ATOM    559  C   MET   145       5.993  64.380  -8.211  1.00  0.00              
ATOM    560  O   MET   145       5.953  65.607  -8.462  1.00  0.00              
ATOM    561  N   ALA   146       6.657  63.836  -7.187  1.00  0.00              
ATOM    562  CA  ALA   146       7.452  64.592  -6.224  1.00  0.00              
ATOM    563  C   ALA   146       8.646  65.273  -6.864  1.00  0.00              
ATOM    564  O   ALA   146       9.457  64.627  -7.491  1.00  0.00              
ATOM    565  N   GLY   147       8.750  66.579  -6.712  1.00  0.00              
ATOM    566  CA  GLY   147       9.891  67.299  -7.259  1.00  0.00              
ATOM    567  C   GLY   147      10.691  67.855  -6.071  1.00  0.00              
ATOM    568  O   GLY   147      10.129  68.511  -5.185  1.00  0.00              
ATOM    569  N   GLY   148      11.997  67.614  -6.050  1.00  0.00              
ATOM    570  CA  GLY   148      12.779  68.123  -4.948  1.00  0.00              
ATOM    571  C   GLY   148      14.258  67.842  -5.041  1.00  0.00              
ATOM    572  O   GLY   148      14.736  67.267  -6.018  1.00  0.00              
ATOM    573  N   TYR   149      14.995  68.244  -4.017  1.00  0.00              
ATOM    574  CA  TYR   149      16.431  68.022  -4.016  1.00  0.00              
ATOM    575  C   TYR   149      16.771  66.649  -3.458  1.00  0.00              
ATOM    576  O   TYR   149      16.203  66.217  -2.453  1.00  0.00              
ATOM    577  N   ALA   150      17.675  65.933  -4.110  1.00  0.00              
ATOM    578  CA  ALA   150      18.019  64.626  -3.570  1.00  0.00              
ATOM    579  C   ALA   150      19.115  64.832  -2.538  1.00  0.00              
ATOM    580  O   ALA   150      20.174  65.391  -2.819  1.00  0.00              
ATOM    581  N   LYS   151      18.840  64.397  -1.325  1.00  0.00              
ATOM    582  CA  LYS   151      19.793  64.574  -0.262  1.00  0.00              
ATOM    583  C   LYS   151      20.201  63.210   0.268  1.00  0.00              
ATOM    584  O   LYS   151      19.546  62.182   0.020  1.00  0.00              
ATOM    585  N   VAL   152      21.311  63.183   0.977  1.00  0.00              
ATOM    586  CA  VAL   152      21.704  61.922   1.541  1.00  0.00              
ATOM    587  C   VAL   152      22.057  62.116   3.006  1.00  0.00              
ATOM    588  O   VAL   152      22.429  63.211   3.440  1.00  0.00              
ATOM    589  N   ILE   153      21.922  61.037   3.761  1.00  0.00              
ATOM    590  CA  ILE   153      22.219  61.077   5.167  1.00  0.00              
ATOM    591  C   ILE   153      22.687  59.743   5.696  1.00  0.00              
ATOM    592  O   ILE   153      22.123  58.702   5.362  1.00  0.00              
ATOM    593  N   ILE   154      23.724  59.786   6.534  1.00  0.00              
ATOM    594  CA  ILE   154      24.280  58.585   7.140  1.00  0.00              
ATOM    595  C   ILE   154      23.449  58.151   8.329  1.00  0.00              
ATOM    596  O   ILE   154      23.183  58.927   9.247  1.00  0.00              
ATOM    597  N   PRO   155      23.033  56.896   8.287  1.00  0.00              
ATOM    598  CA  PRO   155      22.237  56.298   9.343  1.00  0.00              
ATOM    599  C   PRO   155      23.117  55.950  10.530  1.00  0.00              
ATOM    600  O   PRO   155      24.010  55.114  10.418  1.00  0.00              
ATOM    601  N   PHE   156      22.849  56.582  11.669  1.00  0.00              
ATOM    602  CA  PHE   156      23.614  56.353  12.895  1.00  0.00              
ATOM    603  C   PHE   156      23.631  54.880  13.301  1.00  0.00              
ATOM    604  O   PHE   156      22.618  54.176  13.198  1.00  0.00              
ATOM    605  N   SER   157      24.790  54.431  13.772  1.00  0.00              
ATOM    606  CA  SER   157      24.982  53.049  14.207  1.00  0.00              
ATOM    607  C   SER   157      25.242  52.091  13.033  1.00  0.00              
ATOM    608  O   SER   157      25.908  51.065  13.201  1.00  0.00              
ATOM    609  N   GLU   158      24.719  52.417  11.852  1.00  0.00              
ATOM    610  CA  GLU   158      24.939  51.584  10.662  1.00  0.00              
ATOM    611  C   GLU   158      26.127  52.143   9.897  1.00  0.00              
ATOM    612  O   GLU   158      26.890  51.400   9.283  1.00  0.00              
ATOM    613  N   PHE   159      26.280  53.462   9.961  1.00  0.00              
ATOM    614  CA  PHE   159      27.371  54.158   9.290  1.00  0.00              
ATOM    615  C   PHE   159      27.181  54.211   7.761  1.00  0.00              
ATOM    616  O   PHE   159      28.043  54.714   7.037  1.00  0.00              
ATOM    617  N   GLY   160      26.033  53.719   7.290  1.00  0.00              
ATOM    618  CA  GLY   160      25.722  53.706   5.865  1.00  0.00              
ATOM    619  C   GLY   160      24.824  54.865   5.416  1.00  0.00              
ATOM    620  O   GLY   160      23.829  55.170   6.059  1.00  0.00              
ATOM    621  N   TRP   161      25.193  55.521   4.320  1.00  0.00              
ATOM    622  CA  TRP   161      24.383  56.599   3.805  1.00  0.00              
ATOM    623  C   TRP   161      23.148  56.021   3.148  1.00  0.00              
ATOM    624  O   TRP   161      23.119  54.855   2.800  1.00  0.00              
ATOM    625  N   ALA   162      22.126  56.853   2.981  1.00  0.00              
ATOM    626  CA  ALA   162      20.847  56.460   2.385  1.00  0.00              
ATOM    627  C   ALA   162      20.321  57.701   1.702  1.00  0.00              
ATOM    628  O   ALA   162      20.502  58.795   2.223  1.00  0.00              
ATOM    629  N   ASP   163      19.668  57.573   0.554  1.00  0.00              
ATOM    630  CA  ASP   163      19.177  58.792  -0.092  1.00  0.00              
ATOM    631  C   ASP   163      17.716  59.060   0.177  1.00  0.00              
ATOM    632  O   ASP   163      16.933  58.137   0.374  1.00  0.00              
ATOM    633  N   PHE   164      17.346  60.333   0.203  1.00  0.00              
ATOM    634  CA  PHE   164      15.947  60.693   0.415  1.00  0.00              
ATOM    635  C   PHE   164      15.654  61.946  -0.390  1.00  0.00              
ATOM    636  O   PHE   164      16.574  62.659  -0.792  1.00  0.00              
ATOM    637  N   LEU   165      14.384  62.211  -0.654  1.00  0.00              
ATOM    638  CA  LEU   165      14.072  63.423  -1.396  1.00  0.00              
ATOM    639  C   LEU   165      13.500  64.497  -0.502  1.00  0.00              
ATOM    640  O   LEU   165      12.585  64.253   0.294  1.00  0.00              
ATOM    641  N   ARG   166      14.057  65.691  -0.645  1.00  0.00              
ATOM    642  CA  ARG   166      13.605  66.858   0.095  1.00  0.00              
ATOM    643  C   ARG   166      12.635  67.524  -0.876  1.00  0.00              
ATOM    644  O   ARG   166      13.038  68.195  -1.837  1.00  0.00              
ATOM    645  N   ARG   167       2.728  67.358  -7.239  1.00  0.00              
ATOM    646  CA  ARG   167       1.707  67.386  -8.272  1.00  0.00              
ATOM    647  C   ARG   167       1.110  65.995  -8.440  1.00  0.00              
ATOM    648  O   ARG   167       1.796  64.985  -8.288  1.00  0.00              
ATOM    649  N   ARG   168      -0.173  65.933  -8.754  1.00  0.00              
ATOM    650  CA  ARG   168      -0.785  64.638  -8.946  1.00  0.00              
ATOM    651  C   ARG   168      -0.754  64.244 -10.417  1.00  0.00              
ATOM    652  O   ARG   168      -0.664  65.096 -11.305  1.00  0.00              
ATOM    653  N   ILE   169      -0.812  62.943 -10.667  1.00  0.00              
ATOM    654  CA  ILE   169      -0.781  62.434 -12.025  1.00  0.00              
ATOM    655  C   ILE   169      -2.135  61.858 -12.400  1.00  0.00              
ATOM    656  O   ILE   169      -2.543  62.017 -13.578  1.00  0.00              
END
