
#######################################################
#                                                     #
#                        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   90 (   90),  selected   90 , name T0316TS393_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS393_4-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284           -
LGA    S     285      S     285           -
LGA    T     286      T     286           -
LGA    S     287      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    L     288      T     304           #
LGA    E     289      -       -           -
LGA    A     290      -       -           -
LGA    S     291      -       -           -
LGA    Q     292      -       -           -
LGA    V     293      -       -           -
LGA    H     294      -       -           -
LGA    F     295      -       -           -
LGA    T     296      -       -           -
LGA    R     297      -       -           -
LGA    E     298      -       -           -
LGA    M     299      -       -           -
LGA    P     300      -       -           -
LGA    E     301      -       -           -
LGA    E     302      -       -           -
LGA    F     303      -       -           -
LGA    T     304      -       -           -
LGA    L     305      -       -           -
LGA    E     306      -       -           -
LGA    C     307      -       -           -
LGA    T     308      -       -           -
LGA    A     309      -       -           -
LGA    K     310      -       -           -
LGA    F     311      L     305          3.340
LGA    R     312      E     306          2.236
LGA    Y     313      C     307           -
LGA    R     314      T     308           -
LGA    Q     315      A     309           -
LGA    P     316      K     310           -
LGA    D     317      F     311           -
LGA    S     318      R     312           -
LGA    K     319      Y     313           -
LGA    V     320      R     314           -
LGA    T     321      Q     315           -
LGA    V     322      P     316           -
LGA    H     323      D     317           -
LGA    V     324      S     318           -
LGA    K     325      K     319           -
LGA    G     326      V     320           -
LGA    E     327      T     321           -
LGA    K     328      -       -           -
LGA    T     329      -       -           -
LGA    E     330      -       -           -
LGA    V     331      V     322          3.089
LGA    I     332      H     323          3.360
LGA    F     333      V     324          2.356
LGA    A     334      K     325          1.397
LGA    E     335      G     326          2.343
LGA    P     336      E     327          2.251
LGA    Q     337      K     328          1.220
LGA    R     338      T     329          1.948
LGA    A     339      E     330          1.606
LGA    I     340      V     331          3.872
LGA    T     341      I     332           -
LGA    P     342      F     333           -
LGA    G     343      A     334           -
LGA    Q     344      E     335           -
LGA    A     345      -       -           -
LGA    V     346      -       -           -
LGA    V     347      P     336           #
LGA    F     348      Q     337          2.838
LGA    Y     349      -       -           -
LGA    D     350      R     338          2.951
LGA    G     351      A     339          1.033
LGA    E     352      I     340          5.548
LGA    E     353      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    C     354      A     363          4.583
LGA    L     355      Y     364          2.376
LGA    G     356      R     365          2.646
LGA    G     357      D     366          2.027
LGA    G     358      G     367          2.360
LGA    L     359      Q     368           -
LGA    I     360      V     369           -
LGA    D     361      C     370           -
LGA    N     362      Q     371           -
LGA    A     363      Y     372           -
LGA    Y     364      I     373           -
LGA    R     365      -       -           -
LGA    D     366      -       -           -
LGA    G     367      -       -           -
LGA    Q     368      -       -           -
LGA    V     369      -       -           -
LGA    C     370      -       -           -
LGA    Q     371      -       -           -
LGA    Y     372      -       -           -
LGA    I     373      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     21    2.84     9.52     15.303     0.713

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.877724 * X  +   0.446196 * Y  +  -0.174672 * Z  +  15.514887
  Y_new =  -0.203967 * X  +   0.018055 * Y  +  -0.978811 * Z  +   9.103285
  Z_new =  -0.433588 * X  +   0.894753 * Y  +   0.106857 * Z  +  -7.523405 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.451933   -1.689659  [ DEG:    83.1897    -96.8103 ]
  Theta =   0.448470    2.693122  [ DEG:    25.6955    154.3045 ]
  Phi   =  -0.228329    2.913263  [ DEG:   -13.0823    166.9177 ]
 
# 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_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_4-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   90   90   5.0   21   2.84    9.52  15.303
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_4-D3
PFRMAT TS
TARGET T0316
MODEL 4
PARENT N/A
ATOM    284  CA  MET   284      18.008  -1.781   1.425  1.00 25.00           C
ATOM    285  CA  SER   285      18.422  -1.778  -2.382  1.00 25.00           C
ATOM    286  CA  THR   286      21.356  -4.059  -1.725  1.00 25.00           C
ATOM    287  CA  SER   287      24.278  -1.834  -0.678  1.00 25.00           C
ATOM    288  CA  LEU   288      21.477   0.615  -0.202  1.00 25.00           C
ATOM    289  CA  GLU   289      18.360   2.808  -0.236  1.00 25.00           C
ATOM    290  CA  ALA   290      15.419   4.962   0.724  1.00 25.00           C
ATOM    291  CA  SER   291      15.141   8.652   1.384  1.00 25.00           C
ATOM    292  CA  GLN   292      14.897  10.677   4.577  1.00 25.00           C
ATOM    293  CA  VAL   293      17.330  13.107   2.909  1.00 25.00           C
ATOM    294  CA  HIS   294      18.024  16.746   1.871  1.00 25.00           C
ATOM    295  CA  PHE   295      20.785  18.971   0.576  1.00 25.00           C
ATOM    296  CA  THR   296      22.381  21.094   3.260  1.00 25.00           C
ATOM    297  CA  ARG   297      23.893  23.952   5.279  1.00 25.00           C
ATOM    298  CA  GLU   298      25.412  27.108   6.720  1.00 25.00           C
ATOM    299  CA  MET   299      24.758  29.844   9.243  1.00 25.00           C
ATOM    300  CA  PRO   300      21.248  30.872  10.389  1.00 25.00           C
ATOM    301  CA  GLU   301      18.329  32.414   8.544  1.00 25.00           C
ATOM    302  CA  GLU   302      14.890  31.865   7.054  1.00 25.00           C
ATOM    303  CA  PHE   303      12.706  29.970   4.634  1.00 25.00           C
ATOM    304  CA  THR   304      12.510  26.460   3.193  1.00 25.00           C
ATOM    305  CA  LEU   305      13.139  23.294   1.240  1.00 25.00           C
ATOM    306  CA  GLU   306      13.767  19.962  -0.401  1.00 25.00           C
ATOM    307  CA  CYS   307      15.110  16.796  -2.105  1.00 25.00           C
ATOM    308  CA  THR   308      17.512  13.807  -2.240  1.00 25.00           C
ATOM    309  CA  ALA   309      19.028  10.464  -1.338  1.00 25.00           C
ATOM    310  CA  LYS   310      19.280   8.121   1.587  1.00 25.00           C
ATOM    311  CA  PHE   311      18.177   6.313   4.732  1.00 25.00           C
ATOM    312  CA  ARG   312      17.415   2.613   4.670  1.00 25.00           C
ATOM    313  CA  TYR   313      17.629  -0.662   6.579  1.00 25.00           C
ATOM    314  CA  ARG   314      17.526  -3.228   9.409  1.00 25.00           C
ATOM    315  CA  GLN   315      17.115  -4.813  12.870  1.00 25.00           C
ATOM    316  CA  PRO   316      16.230  -7.832  15.101  1.00 25.00           C
ATOM    317  CA  ASP   317      14.610  -8.123  18.532  1.00 25.00           C
ATOM    318  CA  SER   318      13.547  -5.817  21.402  1.00 25.00           C
ATOM    319  CA  LYS   319      15.605  -3.321  23.399  1.00 25.00           C
ATOM    320  CA  VAL   320      19.386  -2.975  23.417  1.00 25.00           C
ATOM    321  CA  THR   321      20.769   0.267  24.927  1.00 25.00           C
ATOM    322  CA  VAL   322      21.827   3.323  26.832  1.00 25.00           C
ATOM    323  CA  HIS   323      21.229   6.935  25.903  1.00 25.00           C
ATOM    324  CA  VAL   324      22.224   9.702  23.451  1.00 25.00           C
ATOM    325  CA  LYS   325      23.000  12.469  20.926  1.00 25.00           C
ATOM    326  CA  GLY   326      19.818  14.038  19.587  1.00 25.00           C
ATOM    327  CA  GLU   327      20.266  13.382  15.913  1.00 25.00           C
ATOM    328  CA  LYS   328      19.586  12.721  12.190  1.00 25.00           C
ATOM    329  CA  THR   329      20.192  11.424   8.637  1.00 25.00           C
ATOM    330  CA  GLU   330      22.136   9.180   6.279  1.00 25.00           C
ATOM    331  CA  VAL   331      23.460   6.127   4.432  1.00 25.00           C
ATOM    332  CA  ILE   332      25.859   3.339   5.436  1.00 25.00           C
ATOM    333  CA  PHE   333      28.036   0.529   4.043  1.00 25.00           C
ATOM    334  CA  ALA   334      29.894  -1.046   6.986  1.00 25.00           C
ATOM    335  CA  GLU   335      33.119  -0.240   8.704  1.00 25.00           C
ATOM    336  CA  PRO   336      33.706   2.131   5.751  1.00 25.00           C
ATOM    337  CA  GLN   337      32.116   3.386   2.562  1.00 25.00           C
ATOM    338  CA  ARG   338      29.687   6.347   2.142  1.00 25.00           C
ATOM    339  CA  ALA   339      26.852   4.420   0.483  1.00 25.00           C
ATOM    340  CA  ILE   340      25.614   2.148  -2.269  1.00 25.00           C
ATOM    341  CA  THR   341      27.622  -0.680  -3.840  1.00 25.00           C
ATOM    342  CA  PRO   342      25.927  -3.797  -5.042  1.00 25.00           C
ATOM    343  CA  GLY   343      26.171  -1.780  -8.278  1.00 25.00           C
ATOM    344  CA  GLN   344      29.354   0.230  -8.110  1.00 25.00           C
ATOM    345  CA  ALA   345      27.360   3.420  -8.564  1.00 25.00           C
ATOM    346  CA  VAL   346      26.420   7.151  -8.665  1.00 25.00           C
ATOM    347  CA  VAL   347      24.184  10.223  -8.169  1.00 25.00           C
ATOM    348  CA  PHE   348      20.535  11.259  -7.773  1.00 25.00           C
ATOM    349  CA  TYR   349      20.640  15.044  -8.382  1.00 25.00           C
ATOM    350  CA  ASP   350      22.294  17.737 -10.493  1.00 25.00           C
ATOM    351  CA  GLY   351      26.047  17.403 -11.301  1.00 25.00           C
ATOM    352  CA  GLU   352      26.536  14.836 -14.100  1.00 25.00           C
ATOM    353  CA  GLU   353      24.211  12.382 -12.500  1.00 25.00           C
ATOM    354  CA  CYS   354      27.088   9.856 -12.438  1.00 25.00           C
ATOM    355  CA  LEU   355      29.890   7.604 -11.309  1.00 25.00           C
ATOM    356  CA  GLY   356      28.954   4.244 -12.835  1.00 25.00           C
ATOM    357  CA  GLY   357      27.265   0.878 -12.923  1.00 25.00           C
ATOM    358  CA  GLY   358      29.292  -2.327 -12.945  1.00 25.00           C
ATOM    359  CA  LEU   359      25.729  -3.528 -13.037  1.00 25.00           C
ATOM    360  CA  ILE   360      23.265  -5.243 -10.747  1.00 25.00           C
ATOM    361  CA  ASP   361      24.947  -8.644 -10.547  1.00 25.00           C
ATOM    362  CA  ASN   362      26.008 -12.221  -9.831  1.00 25.00           C
ATOM    363  CA  ALA   363      26.140 -15.901  -8.730  1.00 25.00           C
ATOM    364  CA  TYR   364      27.385 -19.461  -8.323  1.00 25.00           C
ATOM    365  CA  ARG   365      28.406 -23.081  -7.841  1.00 25.00           C
ATOM    366  CA  ASP   366      27.753 -24.643  -4.424  1.00 25.00           C
ATOM    367  CA  GLY   367      26.411 -27.448  -2.189  1.00 25.00           C
ATOM    368  CA  GLN   368      25.556 -25.905   1.219  1.00 25.00           C
ATOM    369  CA  VAL   369      25.521 -22.617   3.034  1.00 25.00           C
ATOM    370  CA  CYS   370      27.351 -19.884   4.865  1.00 25.00           C
ATOM    371  CA  GLN   371      28.332 -18.187   8.104  1.00 25.00           C
ATOM    372  CA  TYR   372      28.725 -18.098  11.896  1.00 25.00           C
ATOM    373  CA  ILE   373      30.860 -20.188  14.311  1.00 25.00           C
TER
END
