
#######################################################
#                                                     #
#                        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 T0316TS168_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS168_4-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      -       -           -
LGA    R     221      -       -           -
LGA    M     222      -       -           -
LGA    M     223      G     220          1.345
LGA    T     224      R     221          0.873
LGA    V     225      M     222           #
LGA    D     226      -       -           -
LGA    G     227      -       -           -
LGA    R     228      -       -           -
LGA    D     229      -       -           -
LGA    M     230      M     223          2.264
LGA    G     231      T     224          2.569
LGA    E     232      V     225          4.859
LGA    H     233      D     226          3.351
LGA    A     234      -       -           -
LGA    G     235      G     227          4.003
LGA    L     236      R     228          2.302
LGA    M     237      D     229          2.996
LGA    Y     238      M     230          0.396
LGA    Y     239      G     231          3.444
LGA    -       -      E     232           -
LGA    T     240      H     233          4.244
LGA    I     241      A     234           -
LGA    G     242      G     235           -
LGA    Q     243      L     236           #
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    R     244      I     241          1.316
LGA    G     245      G     242           #
LGA    G     246      Q     243           -
LGA    L     247      R     244           -
LGA    G     248      G     245           -
LGA    I     249      G     246           -
LGA    G     250      L     247           -
LGA    G     251      G     248           -
LGA    Q     252      I     249           -
LGA    H     253      G     250           -
LGA    G     254      G     251           -
LGA    G     255      D     256           -
LGA    D     256      N     257           -
LGA    N     257      A     258           -
LGA    A     258      P     259           -
LGA    P     259      W     260           -
LGA    W     260      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    F     261      G     264          2.583
LGA    V     262      K     265          2.164
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    V     263      L     272          1.311
LGA    G     264      Y     273           #
LGA    K     265      -       -           -
LGA    D     266      -       -           -
LGA    L     267      -       -           -
LGA    S     268      -       -           -
LGA    K     269      -       -           -
LGA    N     270      -       -           -
LGA    I     271      -       -           -
LGA    L     272      -       -           -
LGA    Y     273      V     274          4.873
LGA    V     274      -       -           -
LGA    G     275      -       -           -
LGA    Q     276      G     275          2.802
LGA    G     277      Q     276          2.005
LGA    F     278      G     277          3.090
LGA    Y     279      F     278          2.614
LGA    H     280      Y     279           -
LGA    D     281      H     280           -
LGA    S     282      D     281           -
LGA    L     283      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   60    5.0     21    2.90     9.52     21.908     0.701

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.179032 * X  +  -0.442089 * Y  +  -0.878922 * Z  +  39.509392
  Y_new =  -0.906434 * X  +  -0.273225 * Y  +   0.322066 * Z  +  23.041430
  Z_new =  -0.382525 * X  +   0.854345 * Y  +  -0.351809 * Z  + -17.470278 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.961423   -1.180170  [ DEG:   112.3813    -67.6187 ]
  Theta =   0.392528    2.749065  [ DEG:    22.4902    157.5098 ]
  Phi   =  -1.765799    1.375793  [ DEG:  -101.1729     78.8271 ]
 
# 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: T0316TS168_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_4-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   21   2.90    9.52  21.908
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_4-D2
PFRMAT TS
TARGET T0316
MODEL 4
PARENT N/A
ATOM    220  CA  GLY   220      44.925  28.585 -22.783  1.00 25.00           C
ATOM    221  CA  ARG   221      47.726  26.660 -21.083  1.00 25.00           C
ATOM    222  CA  MET   222      47.145  23.299 -19.455  1.00 25.00           C
ATOM    223  CA  MET   223      44.478  22.540 -21.956  1.00 25.00           C
ATOM    224  CA  THR   224      41.997  20.815 -24.218  1.00 25.00           C
ATOM    225  CA  VAL   225      42.771  24.138 -25.899  1.00 25.00           C
ATOM    226  CA  ASP   226      40.614  27.122 -24.858  1.00 25.00           C
ATOM    227  CA  GLY   227      37.542  27.090 -22.545  1.00 25.00           C
ATOM    228  CA  ARG   228      35.073  25.855 -25.161  1.00 25.00           C
ATOM    229  CA  ASP   229      33.990  22.225 -24.810  1.00 25.00           C
ATOM    230  CA  MET   230      35.909  19.056 -23.966  1.00 25.00           C
ATOM    231  CA  GLY   231      35.978  15.889 -26.108  1.00 25.00           C
ATOM    232  CA  GLU   232      37.289  12.522 -25.014  1.00 25.00           C
ATOM    233  CA  HIS   233      36.385  11.102 -28.414  1.00 25.00           C
ATOM    234  CA  ALA   234      33.011  11.080 -30.181  1.00 25.00           C
ATOM    235  CA  GLY   235      33.685  14.843 -30.534  1.00 25.00           C
ATOM    236  CA  LEU   236      36.550  15.823 -32.774  1.00 25.00           C
ATOM    237  CA  MET   237      36.155  18.686 -30.308  1.00 25.00           C
ATOM    238  CA  TYR   238      37.289  21.912 -28.559  1.00 25.00           C
ATOM    239  CA  TYR   239      38.193  22.687 -24.947  1.00 25.00           C
ATOM    240  CA  THR   240      36.981  23.189 -21.351  1.00 25.00           C
ATOM    241  CA  ILE   241      34.282  22.509 -18.757  1.00 25.00           C
ATOM    242  CA  GLY   242      34.323  24.786 -15.695  1.00 25.00           C
ATOM    243  CA  GLN   243      34.398  21.254 -14.401  1.00 25.00           C
ATOM    244  CA  ARG   244      31.979  18.524 -13.402  1.00 25.00           C
ATOM    245  CA  GLY   245      34.445  16.619 -11.167  1.00 25.00           C
ATOM    246  CA  GLY   246      38.117  16.243 -11.764  1.00 25.00           C
ATOM    247  CA  LEU   247      40.877  17.156  -9.322  1.00 25.00           C
ATOM    248  CA  GLY   248      38.088  16.524  -6.832  1.00 25.00           C
ATOM    249  CA  ILE   249      35.894  13.471  -7.484  1.00 25.00           C
ATOM    250  CA  GLY   250      38.979  12.019  -9.140  1.00 25.00           C
ATOM    251  CA  GLY   251      39.611  10.820 -12.689  1.00 25.00           C
ATOM    252  CA  GLN   252      36.000   9.882 -12.099  1.00 25.00           C
ATOM    253  CA  HIS   253      36.152   6.108 -12.045  1.00 25.00           C
ATOM    254  CA  GLY   254      32.567   5.503 -11.039  1.00 25.00           C
ATOM    255  CA  GLY   255      29.135   6.147 -12.590  1.00 25.00           C
ATOM    256  CA  ASP   256      27.518   4.441 -15.596  1.00 25.00           C
ATOM    257  CA  ASN   257      30.835   3.773 -17.368  1.00 25.00           C
ATOM    258  CA  ALA   258      32.151   6.742 -19.391  1.00 25.00           C
ATOM    259  CA  PRO   259      33.487   8.494 -16.274  1.00 25.00           C
ATOM    260  CA  TRP   260      31.380  11.222 -14.611  1.00 25.00           C
ATOM    261  CA  PHE   261      33.937  14.085 -14.767  1.00 25.00           C
ATOM    262  CA  VAL   262      35.531  17.303 -16.041  1.00 25.00           C
ATOM    263  CA  VAL   263      36.618  18.998 -19.260  1.00 25.00           C
ATOM    264  CA  GLY   264      40.036  20.354 -20.309  1.00 25.00           C
ATOM    265  CA  LYS   265      43.298  18.447 -20.261  1.00 25.00           C
ATOM    266  CA  ASP   266      46.299  16.319 -21.216  1.00 25.00           C
ATOM    267  CA  LEU   267      49.069  15.155 -23.556  1.00 25.00           C
ATOM    268  CA  SER   268      46.724  14.903 -26.558  1.00 25.00           C
ATOM    269  CA  LYS   269      44.620  12.559 -24.473  1.00 25.00           C
ATOM    270  CA  ASN   270      41.959  14.234 -26.531  1.00 25.00           C
ATOM    271  CA  ILE   271      41.583  16.448 -23.505  1.00 25.00           C
ATOM    272  CA  LEU   272      38.461  15.449 -21.620  1.00 25.00           C
ATOM    273  CA  TYR   273      34.700  15.515 -21.223  1.00 25.00           C
ATOM    274  CA  VAL   274      32.073  16.553 -18.633  1.00 25.00           C
ATOM    275  CA  GLY   275      28.764  18.345 -18.550  1.00 25.00           C
ATOM    276  CA  GLN   276      27.260  19.707 -21.719  1.00 25.00           C
ATOM    277  CA  GLY   277      27.041  21.801 -24.842  1.00 25.00           C
ATOM    278  CA  PHE   278      23.577  22.751 -23.577  1.00 25.00           C
ATOM    279  CA  TYR   279      21.186  22.767 -20.613  1.00 25.00           C
ATOM    280  CA  HIS   280      22.501  26.271 -20.167  1.00 25.00           C
ATOM    281  CA  ASP   281      22.961  27.143 -16.553  1.00 25.00           C
ATOM    282  CA  SER   282      26.604  27.640 -17.624  1.00 25.00           C
ATOM    283  CA  LEU   283      27.779  26.906 -14.054  1.00 25.00           C
TER
END
