
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS168_5-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      -       -           -
LGA    T     224      -       -           -
LGA    V     225      -       -           -
LGA    D     226      -       -           -
LGA    G     227      -       -           -
LGA    R     228      -       -           -
LGA    D     229      -       -           -
LGA    M     230      G     220          1.774
LGA    G     231      R     221          2.334
LGA    E     232      -       -           -
LGA    H     233      -       -           -
LGA    A     234      -       -           -
LGA    G     235      -       -           -
LGA    L     236      -       -           -
LGA    M     237      M     222          4.158
LGA    Y     238      M     223          4.181
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    Y     239      H     233          5.101
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    T     240      Y     238           #
LGA    I     241      Y     239          2.045
LGA    G     242      T     240           #
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    Q     243      G     245          2.488
LGA    R     244      G     246          3.898
LGA    G     245      -       -           -
LGA    G     246      -       -           -
LGA    L     247      -       -           -
LGA    G     248      -       -           -
LGA    I     249      -       -           -
LGA    G     250      -       -           -
LGA    G     251      L     247          1.411
LGA    Q     252      G     248          3.196
LGA    H     253      -       -           -
LGA    G     254      -       -           -
LGA    G     255      -       -           -
LGA    D     256      -       -           -
LGA    N     257      I     249           #
LGA    A     258      G     250          0.814
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    P     259      P     259           #
LGA    W     260      W     260          3.364
LGA    F     261      F     261          2.568
LGA    V     262      V     262          3.579
LGA    V     263      V     263          2.493
LGA    G     264      G     264          2.348
LGA    K     265      K     265          2.300
LGA    D     266      D     266          1.675
LGA    L     267      L     267          3.213
LGA    S     268      S     268          4.515
LGA    K     269      K     269          4.639
LGA    N     270      N     270          4.635
LGA    I     271      -       -           -
LGA    L     272      I     271          0.627
LGA    Y     273      L     272          3.756
LGA    V     274      Y     273          3.794
LGA    G     275      V     274           #
LGA    Q     276      G     275          4.921
LGA    G     277      Q     276           #
LGA    F     278      -       -           -
LGA    Y     279      G     277           #
LGA    H     280      F     278           #
LGA    -       -      Y     279           -
LGA    D     281      H     280          5.133
LGA    S     282      D     281          0.968
LGA    L     283      S     282          4.029
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   60    5.0     29    3.37    41.38     28.578     0.837

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.445186 * X  +   0.120406 * Y  +  -0.887306 * Z  +  36.421204
  Y_new =   0.642761 * X  +  -0.646938 * Y  +  -0.410280 * Z  +  18.372618
  Z_new =  -0.623432 * X  +  -0.752977 * Y  +   0.210615 * Z  + -15.359486 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.298056    1.843536  [ DEG:   -74.3731    105.6269 ]
  Theta =   0.673125    2.468468  [ DEG:    38.5672    141.4328 ]
  Phi   =   2.176549   -0.965044  [ DEG:   124.7071    -55.2929 ]
 
# 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_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_5-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   3.37   41.38  28.578
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_5-D2
PFRMAT TS
TARGET T0316
MODEL 5
PARENT N/A
ATOM    220  CA  GLY   220      36.656  24.152  -7.137  1.00 25.00           C
ATOM    221  CA  ARG   221      37.221  24.086 -10.943  1.00 25.00           C
ATOM    222  CA  MET   222      38.557  21.769 -13.667  1.00 25.00           C
ATOM    223  CA  MET   223      41.122  23.925 -15.555  1.00 25.00           C
ATOM    224  CA  THR   224      43.876  26.137 -16.844  1.00 25.00           C
ATOM    225  CA  VAL   225      42.923  28.991 -14.592  1.00 25.00           C
ATOM    226  CA  ASP   226      39.881  28.533 -12.286  1.00 25.00           C
ATOM    227  CA  GLY   227      41.795  25.385 -11.306  1.00 25.00           C
ATOM    228  CA  ARG   228      44.461  23.160 -12.857  1.00 25.00           C
ATOM    229  CA  ASP   229      44.753  21.752 -16.362  1.00 25.00           C
ATOM    230  CA  MET   230      44.362  20.389 -19.898  1.00 25.00           C
ATOM    231  CA  GLY   231      43.753  22.276 -23.094  1.00 25.00           C
ATOM    232  CA  GLU   232      43.271  23.696 -26.528  1.00 25.00           C
ATOM    233  CA  HIS   233      43.983  20.130 -27.621  1.00 25.00           C
ATOM    234  CA  ALA   234      42.609  18.961 -31.018  1.00 25.00           C
ATOM    235  CA  GLY   235      40.870  16.348 -28.899  1.00 25.00           C
ATOM    236  CA  LEU   236      43.341  14.859 -26.406  1.00 25.00           C
ATOM    237  CA  MET   237      41.064  17.299 -24.587  1.00 25.00           C
ATOM    238  CA  TYR   238      39.169  20.034 -22.741  1.00 25.00           C
ATOM    239  CA  TYR   239      39.477  20.569 -19.042  1.00 25.00           C
ATOM    240  CA  THR   240      36.667  22.792 -17.751  1.00 25.00           C
ATOM    241  CA  ILE   241      34.410  24.583 -15.197  1.00 25.00           C
ATOM    242  CA  GLY   242      33.231  28.114 -14.667  1.00 25.00           C
ATOM    243  CA  GLN   243      31.968  27.902 -18.230  1.00 25.00           C
ATOM    244  CA  ARG   244      34.676  26.202 -20.284  1.00 25.00           C
ATOM    245  CA  GLY   245      36.692  27.449 -23.228  1.00 25.00           C
ATOM    246  CA  GLY   246      38.990  24.624 -24.054  1.00 25.00           C
ATOM    247  CA  LEU   247      40.247  24.775 -20.499  1.00 25.00           C
ATOM    248  CA  GLY   248      40.465  28.480 -19.667  1.00 25.00           C
ATOM    249  CA  ILE   249      38.300  26.993 -16.885  1.00 25.00           C
ATOM    250  CA  GLY   250      37.545  30.539 -15.602  1.00 25.00           C
ATOM    251  CA  GLY   251      35.540  31.068 -18.790  1.00 25.00           C
ATOM    252  CA  GLN   252      37.878  32.506 -21.426  1.00 25.00           C
ATOM    253  CA  HIS   253      39.746  33.721 -24.502  1.00 25.00           C
ATOM    254  CA  GLY   254      42.191  32.307 -27.081  1.00 25.00           C
ATOM    255  CA  GLY   255      39.292  30.481 -28.664  1.00 25.00           C
ATOM    256  CA  ASP   256      36.733  33.268 -28.926  1.00 25.00           C
ATOM    257  CA  ASN   257      33.606  32.844 -26.793  1.00 25.00           C
ATOM    258  CA  ALA   258      32.989  29.096 -26.232  1.00 25.00           C
ATOM    259  CA  PRO   259      31.368  27.568 -23.194  1.00 25.00           C
ATOM    260  CA  TRP   260      28.507  26.473 -20.948  1.00 25.00           C
ATOM    261  CA  PHE   261      29.558  23.964 -18.237  1.00 25.00           C
ATOM    262  CA  VAL   262      28.615  21.250 -15.744  1.00 25.00           C
ATOM    263  CA  VAL   263      28.862  17.463 -16.245  1.00 25.00           C
ATOM    264  CA  GLY   264      31.843  15.363 -15.161  1.00 25.00           C
ATOM    265  CA  LYS   265      35.472  14.209 -15.404  1.00 25.00           C
ATOM    266  CA  ASP   266      39.071  14.932 -16.224  1.00 25.00           C
ATOM    267  CA  LEU   267      41.722  17.567 -15.643  1.00 25.00           C
ATOM    268  CA  SER   268      45.344  16.696 -16.549  1.00 25.00           C
ATOM    269  CA  LYS   269      48.213  17.327 -18.862  1.00 25.00           C
ATOM    270  CA  ASN   270      46.349  15.908 -21.851  1.00 25.00           C
ATOM    271  CA  ILE   271      43.475  13.595 -20.976  1.00 25.00           C
ATOM    272  CA  LEU   272      41.717  16.847 -20.032  1.00 25.00           C
ATOM    273  CA  TYR   273      38.308  15.738 -21.266  1.00 25.00           C
ATOM    274  CA  VAL   274      35.949  15.510 -24.235  1.00 25.00           C
ATOM    275  CA  GLY   275      32.609  13.772 -24.538  1.00 25.00           C
ATOM    276  CA  GLN   276      30.209  15.318 -27.011  1.00 25.00           C
ATOM    277  CA  GLY   277      27.895  12.511 -28.010  1.00 25.00           C
ATOM    278  CA  PHE   278      24.516  11.595 -26.480  1.00 25.00           C
ATOM    279  CA  TYR   279      21.004  12.769 -25.562  1.00 25.00           C
ATOM    280  CA  HIS   280      20.512  15.250 -22.700  1.00 25.00           C
ATOM    281  CA  ASP   281      19.580  12.583 -20.120  1.00 25.00           C
ATOM    282  CA  SER   282      23.180  11.737 -21.116  1.00 25.00           C
ATOM    283  CA  LEU   283      24.437  14.892 -19.345  1.00 25.00           C
TER
END
