
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0349TS168_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS168_2-D1.T0349_D1.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.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    R       2      S      14          4.841
LGA    E       3      -       -           -
LGA    L       4      -       -           -
LGA    L       5      A      15          4.330
LGA    R       6      V      16          3.446
LGA    T       7      G      17          2.355
LGA    N       8      A      18          1.675
LGA    D       9      L      19          2.657
LGA    A      10      L      20          5.102
LGA    V      11      D      21          4.190
LGA    -       -      G      22           -
LGA    L      12      A      23           #
LGA    L      13      D      24           -
LGA    S      14      I      25           #
LGA    A      15      G      26          2.192
LGA    V      16      H      27           #
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    G      17      L      49          3.931
LGA    A      18      V      50          4.439
LGA    L      19      H      51          2.421
LGA    L      20      E      52          2.299
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      D      53          2.760
LGA    H      27      D      54          2.501
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    P      45      L      55          2.105
LGA    R      46      A      56          4.129
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    R      47      L      61          3.024
LGA    V      48      L      62          0.984
LGA    L      49      T      63          2.511
LGA    -       -      D      64           -
LGA    V      50      A      65          3.207
LGA    H      51      G      66          5.342
LGA    E      52      L      67          4.727
LGA    D      53      -       -           -
LGA    D      54      -       -           -
LGA    L      55      A      68          0.825
LGA    A      56      H      69          1.987
LGA    G      57      E      70          2.121
LGA    A      58      -       -           -
LGA    R      59      L      71          2.608
LGA    R      60      R      72          2.410
LGA    L      61      -       -           -
LGA    L      62      -       -           -
LGA    T      63      -       -           -
LGA    D      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    L      67      -       -           -
LGA    A      68      -       -           -
LGA    H      69      -       -           -
LGA    E      70      -       -           -
LGA    L      71      -       -           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   57   57    5.0     28    3.27     3.57     28.859     0.832

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.136762 * X  +  -0.025379 * Y  +  -0.990279 * Z  +   2.844171
  Y_new =  -0.482578 * X  +  -0.874735 * Y  +  -0.044229 * Z  +   6.040390
  Z_new =  -0.865109 * X  +   0.483936 * Y  +  -0.131878 * Z  +   3.037667 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.836848   -1.304745  [ DEG:   105.2436    -74.7564 ]
  Theta =   1.045368    2.096224  [ DEG:    59.8952    120.1048 ]
  Phi   =  -1.294638    1.846954  [ DEG:   -74.1773    105.8227 ]
 
# 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: T0349TS168_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS168_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   57   57   5.0   28   3.27    3.57  28.859
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS168_2-D1
PFRMAT TS
TARGET T0349
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1     -12.900  -4.271  11.857  1.00 25.00           C
ATOM      2  CA  ARG     2     -10.044  -2.054  10.648  1.00 25.00           C
ATOM      3  CA  GLU     3      -7.079  -0.922  12.711  1.00 25.00           C
ATOM      4  CA  LEU     4      -8.180   2.746  12.652  1.00 25.00           C
ATOM      5  CA  LEU     5      -4.547   3.869  13.106  1.00 25.00           C
ATOM      6  CA  ARG     6      -3.455   1.583  10.234  1.00 25.00           C
ATOM      7  CA  THR     7      -6.214   3.024   8.004  1.00 25.00           C
ATOM      8  CA  ASN     8      -5.095   6.581   8.876  1.00 25.00           C
ATOM      9  CA  ASP     9      -1.472   5.675   8.030  1.00 25.00           C
ATOM     10  CA  ALA    10      -2.597   4.203   4.678  1.00 25.00           C
ATOM     11  CA  VAL    11      -4.576   7.392   3.915  1.00 25.00           C
ATOM     12  CA  LEU    12      -1.511   9.527   4.759  1.00 25.00           C
ATOM     13  CA  LEU    13       0.657   7.367   2.456  1.00 25.00           C
ATOM     14  CA  SER    14      -1.909   7.754  -0.362  1.00 25.00           C
ATOM     15  CA  ALA    15      -1.933  11.548   0.146  1.00 25.00           C
ATOM     16  CA  VAL    16       1.894  11.615   0.013  1.00 25.00           C
ATOM     17  CA  GLY    17       1.842   9.567  -3.222  1.00 25.00           C
ATOM     18  CA  ALA    18      -0.714  11.983  -4.739  1.00 25.00           C
ATOM     19  CA  LEU    19       1.478  14.963  -3.750  1.00 25.00           C
ATOM     20  CA  LEU    20       4.526  13.284  -5.350  1.00 25.00           C
ATOM     21  CA  ASP    21       2.527  12.657  -8.557  1.00 25.00           C
ATOM     22  CA  GLY    22       2.715  16.354  -9.544  1.00 25.00           C
ATOM     23  CA  ALA    23       2.444  19.069  -6.869  1.00 25.00           C
ATOM     24  CA  ASP    24      -1.381  18.828  -6.398  1.00 25.00           C
ATOM     25  CA  ILE    25      -0.816  19.323  -2.660  1.00 25.00           C
ATOM     26  CA  GLY    26       2.538  20.113  -1.046  1.00 25.00           C
ATOM     27  CA  HIS    27       3.479  17.904   1.878  1.00 25.00           C
ATOM     28  CA  LEU    28       4.359  17.978   5.593  1.00 25.00           C
ATOM     29  CA  VAL    29       4.390  15.439   8.405  1.00 25.00           C
ATOM     45  CA  PRO    45       6.949  11.244   0.220  1.00 25.00           C
ATOM     46  CA  ARG    46       5.415  10.185   3.568  1.00 25.00           C
ATOM     47  CA  ARG    47       3.739  10.103   6.989  1.00 25.00           C
ATOM     48  CA  VAL    48       4.220   6.978   9.054  1.00 25.00           C
ATOM     49  CA  LEU    49       6.719   6.522  11.951  1.00 25.00           C
ATOM     50  CA  VAL    50       4.799   4.063  14.118  1.00 25.00           C
ATOM     51  CA  HIS    51       8.117   2.272  14.651  1.00 25.00           C
ATOM     52  CA  GLU    52       9.991  -0.715  13.093  1.00 25.00           C
ATOM     53  CA  ASP    53       8.247  -3.199  10.758  1.00 25.00           C
ATOM     54  CA  ASP    54       5.307  -0.781  10.340  1.00 25.00           C
ATOM     55  CA  LEU    55       7.734   2.069   9.531  1.00 25.00           C
ATOM     56  CA  ALA    56       9.494  -0.134   6.938  1.00 25.00           C
ATOM     57  CA  GLY    57       6.118  -1.012   5.358  1.00 25.00           C
ATOM     58  CA  ALA    58       5.194   2.700   5.207  1.00 25.00           C
ATOM     59  CA  ARG    59       8.553   3.495   3.550  1.00 25.00           C
ATOM     60  CA  ARG    60       7.973   0.711   0.984  1.00 25.00           C
ATOM     61  CA  LEU    61       4.477   2.089   0.243  1.00 25.00           C
ATOM     62  CA  LEU    62       5.933   5.600  -0.225  1.00 25.00           C
ATOM     63  CA  THR    63       8.585   4.208  -2.612  1.00 25.00           C
ATOM     64  CA  ASP    64       5.870   2.386  -4.606  1.00 25.00           C
ATOM     65  CA  ALA    65       3.823   5.616  -4.818  1.00 25.00           C
ATOM     66  CA  GLY    66       0.848   3.277  -5.266  1.00 25.00           C
ATOM     67  CA  LEU    67      -1.863   1.217  -3.611  1.00 25.00           C
ATOM     68  CA  ALA    68      -2.499   0.085  -7.171  1.00 25.00           C
ATOM     69  CA  HIS    69      -4.739  -1.581  -9.738  1.00 25.00           C
ATOM     70  CA  GLU    70      -6.590  -4.826  -9.149  1.00 25.00           C
ATOM     71  CA  LEU    71      -4.233  -5.240  -6.179  1.00 25.00           C
ATOM     72  CA  ARG    72      -3.215  -8.500  -7.790  1.00 25.00           C
TER
END
