
#######################################################
#                                                     #
#                        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   96 (   96),  selected   96 , name T0321TS168_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS168_2-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    M       1      L      21           #
LGA    W       2      -       -           -
LGA    E       3      -       -           -
LGA    I       4      -       -           -
LGA    Y       5      V      22           #
LGA    D       6      -       -           -
LGA    A       7      -       -           -
LGA    M       8      C      23           #
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    G      11      -       -           -
LGA    I      12      -       -           -
LGA    P      13      -       -           -
LGA    E      14      -       -           -
LGA    D      15      -       -           -
LGA    F      16      G      24           #
LGA    L      17      T      25          3.096
LGA    V      18      T      26          1.030
LGA    D      19      H      27          0.989
LGA    E      20      S      28          0.852
LGA    L      21      V      29          1.589
LGA    V      22      I      30          2.865
LGA    C      23      R      31          3.217
LGA    G      24      S      32          3.064
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    T      25      G      37           #
LGA    T      26      -       -           -
LGA    H      27      -       -           -
LGA    S      28      -       -           -
LGA    V      29      -       -           -
LGA    I      30      L      38           #
LGA    R      31      G      39           #
LGA    S      32      -       -           -
LGA    G      33      P      40          2.918
LGA    N      34      N      41          0.652
LGA    G      35      R      42           -
LGA    V      36      P      43           -
LGA    G      37      F      44           -
LGA    L      38      E      45           -
LGA    G      39      T      46           -
LGA    P      40      R      47           -
LGA    N      41      M      48           -
LGA    R      42      P      49           -
LGA    P      43      M      50           -
LGA    F      44      L      51           -
LGA    E      45      T      52           -
LGA    T      46      Q      53           -
LGA    R      47      N      54           -
LGA    M      48      L      55           -
LGA    P      49      L      56           -
LGA    M      50      -       -           -
LGA    L      51      -       -           -
LGA    T      52      -       -           -
LGA    Q      53      -       -           -
LGA    N      54      G      57          4.765
LGA    L      55      L      58          4.868
LGA    L      56      P      59          2.769
LGA    G      57      L      60           -
LGA    L      58      -       -           -
LGA    P      59      -       -           -
LGA    L      60      R      61          4.939
LGA    R      61      V      62          2.903
LGA    V      62      A      63          1.919
LGA    A      63      A      64          2.048
LGA    A      64      G      65          2.278
LGA    G      65      C      66          3.308
LGA    C      66      V      67          4.554
LGA    V      67      K      68          3.853
LGA    -       -      S      69           -
LGA    K      68      W      70           #
LGA    S      69      N      71          2.365
LGA    W      70      Y      72          2.467
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    N      71      S      76          1.813
LGA    Y      72      I      77          2.364
LGA    -       -      G      78           -
LGA    V      73      L      79          3.527
LGA    E      74      A      80          2.853
LGA    A      75      A      81          2.263
LGA    S      76      I      82          2.502
LGA    I      77      N      83          2.240
LGA    G      78      A      84          1.523
LGA    L      79      Y      85          1.127
LGA    A      80      Y      86          0.991
LGA    A      81      N      87          2.438
LGA    I      82      N      88          3.426
LGA    N      83      P      89           -
LGA    A      84      Q      90          4.611
LGA    Y      85      V      91          2.834
LGA    -       -      A      92           -
LGA    -       -      R      93           -
LGA    Y      86      E      94          3.778
LGA    N      87      H      95          4.618
LGA    N      88      G      96           -
LGA    P      89      -       -           -
LGA    Q      90      -       -           -
LGA    V      91      -       -           -
LGA    A      92      -       -           -
LGA    R      93      -       -           -
LGA    E      94      -       -           -
LGA    H      95      -       -           -
LGA    G      96      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   96   96    5.0     39    2.97    10.26     24.697     1.272

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.685730 * X  +  -0.338097 * Y  +   0.644566 * Z  +  -2.408300
  Y_new =   0.305281 * X  +  -0.937508 * Y  +  -0.166978 * Z  +  48.434113
  Z_new =   0.660740 * X  +   0.082272 * Y  +   0.746092 * Z  +  68.745636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.109827   -3.031766  [ DEG:     6.2926   -173.7074 ]
  Theta =  -0.721805   -2.419788  [ DEG:   -41.3564   -138.6436 ]
  Phi   =   2.722744   -0.418848  [ DEG:   156.0018    -23.9982 ]
 
# 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: T0321TS168_2-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS168_2-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   96   96   5.0   39   2.97   10.26  24.697
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS168_2-D1
PFRMAT TS
TARGET T0321
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1     -14.465  67.582  61.986  1.00 25.00           C
ATOM      2  CA  TRP     2     -10.879  67.828  63.201  1.00 25.00           C
ATOM      3  CA  GLU     3      -9.802  70.728  60.944  1.00 25.00           C
ATOM      4  CA  ILE     4      -6.643  68.808  59.942  1.00 25.00           C
ATOM      5  CA  TYR     5      -8.751  65.715  59.134  1.00 25.00           C
ATOM      6  CA  ASP     6     -11.112  67.849  57.003  1.00 25.00           C
ATOM      7  CA  ALA     7      -8.117  69.341  55.137  1.00 25.00           C
ATOM      8  CA  MET     8      -6.730  65.829  54.503  1.00 25.00           C
ATOM      9  CA  ILE     9     -10.139  64.696  53.174  1.00 25.00           C
ATOM     10  CA  ASN    10     -10.276  67.742  50.857  1.00 25.00           C
ATOM     11  CA  GLY    11      -7.955  70.200  49.152  1.00 25.00           C
ATOM     12  CA  ILE    12      -4.174  70.806  49.014  1.00 25.00           C
ATOM     13  CA  PRO    13      -1.063  72.118  50.801  1.00 25.00           C
ATOM     14  CA  GLU    14       0.849  68.891  49.888  1.00 25.00           C
ATOM     15  CA  ASP    15       1.739  65.484  51.350  1.00 25.00           C
ATOM     16  CA  PHE    16       1.626  63.805  54.764  1.00 25.00           C
ATOM     17  CA  LEU    17       3.589  62.132  57.531  1.00 25.00           C
ATOM     18  CA  VAL    18       3.569  60.850  61.128  1.00 25.00           C
ATOM     19  CA  ASP    19       0.548  59.581  63.029  1.00 25.00           C
ATOM     20  CA  GLU    20      -2.777  57.808  62.395  1.00 25.00           C
ATOM     21  CA  LEU    21      -4.634  59.415  65.363  1.00 25.00           C
ATOM     22  CA  VAL    22      -7.842  57.606  64.281  1.00 25.00           C
ATOM     23  CA  CYS    23      -8.560  57.520  68.025  1.00 25.00           C
ATOM     24  CA  GLY    24     -11.501  55.203  68.892  1.00 25.00           C
ATOM     25  CA  THR    25     -12.520  51.754  67.652  1.00 25.00           C
ATOM     26  CA  THR    26     -12.622  48.707  65.366  1.00 25.00           C
ATOM     27  CA  HIS    27      -9.292  48.399  63.616  1.00 25.00           C
ATOM     28  CA  SER    28      -5.877  46.817  63.636  1.00 25.00           C
ATOM     29  CA  VAL    29      -2.284  46.372  64.757  1.00 25.00           C
ATOM     30  CA  ILE    30       0.523  48.682  65.760  1.00 25.00           C
ATOM     31  CA  ARG    31       4.018  48.204  64.233  1.00 25.00           C
ATOM     32  CA  SER    32       3.583  51.958  63.560  1.00 25.00           C
ATOM     33  CA  GLY    33       4.784  55.100  61.785  1.00 25.00           C
ATOM     34  CA  ASN    34       2.017  56.364  59.454  1.00 25.00           C
ATOM     35  CA  GLY    35      -0.476  54.229  61.389  1.00 25.00           C
ATOM     36  CA  VAL    36       0.548  54.572  65.007  1.00 25.00           C
ATOM     37  CA  GLY    37       0.177  53.949  68.792  1.00 25.00           C
ATOM     38  CA  LEU    38      -0.605  50.431  69.988  1.00 25.00           C
ATOM     39  CA  GLY    39      -2.098  47.031  70.828  1.00 25.00           C
ATOM     40  CA  PRO    40      -4.944  45.787  68.545  1.00 25.00           C
ATOM     41  CA  ASN    41      -8.058  43.641  69.005  1.00 25.00           C
ATOM     42  CA  ARG    42     -11.711  43.624  70.003  1.00 25.00           C
ATOM     43  CA  PRO    43     -14.752  45.726  70.843  1.00 25.00           C
ATOM     44  CA  PHE    44     -16.790  47.322  73.612  1.00 25.00           C
ATOM     45  CA  GLU    45     -16.951  47.433  77.389  1.00 25.00           C
ATOM     46  CA  THR    46     -15.335  50.272  79.354  1.00 25.00           C
ATOM     47  CA  ARG    47     -14.059  53.407  77.676  1.00 25.00           C
ATOM     48  CA  MET    48     -17.352  53.292  75.681  1.00 25.00           C
ATOM     49  CA  PRO    49     -20.138  51.178  74.218  1.00 25.00           C
ATOM     50  CA  MET    50     -20.867  54.266  72.075  1.00 25.00           C
ATOM     51  CA  LEU    51     -17.423  53.967  70.427  1.00 25.00           C
ATOM     52  CA  THR    52     -18.066  50.262  69.701  1.00 25.00           C
ATOM     53  CA  GLN    53     -21.463  51.127  68.159  1.00 25.00           C
ATOM     54  CA  ASN    54     -19.816  53.811  65.978  1.00 25.00           C
ATOM     55  CA  LEU    55     -17.167  51.292  64.836  1.00 25.00           C
ATOM     56  CA  LEU    56     -19.910  48.762  63.971  1.00 25.00           C
ATOM     57  CA  GLY    57     -21.002  47.071  60.699  1.00 25.00           C
ATOM     58  CA  LEU    58     -19.279  44.006  62.253  1.00 25.00           C
ATOM     59  CA  PRO    59     -15.952  45.743  62.627  1.00 25.00           C
ATOM     60  CA  LEU    60     -15.872  44.824  58.908  1.00 25.00           C
ATOM     61  CA  ARG    61     -16.648  48.039  56.976  1.00 25.00           C
ATOM     62  CA  VAL    62     -14.743  50.095  59.584  1.00 25.00           C
ATOM     63  CA  ALA    63     -11.750  47.722  59.307  1.00 25.00           C
ATOM     64  CA  ALA    64     -11.818  48.043  55.491  1.00 25.00           C
ATOM     65  CA  GLY    65     -11.909  51.860  55.790  1.00 25.00           C
ATOM     66  CA  CYS    66      -8.932  51.767  58.198  1.00 25.00           C
ATOM     67  CA  VAL    67      -6.997  49.537  55.759  1.00 25.00           C
ATOM     68  CA  LYS    68      -7.768  51.959  52.894  1.00 25.00           C
ATOM     69  CA  SER    69      -4.200  53.153  52.644  1.00 25.00           C
ATOM     70  CA  TRP    70      -2.128  51.557  55.384  1.00 25.00           C
ATOM     71  CA  ASN    71      -4.187  52.866  58.325  1.00 25.00           C
ATOM     72  CA  TYR    72      -5.638  52.941  61.875  1.00 25.00           C
ATOM     73  CA  VAL    73      -3.005  52.189  64.554  1.00 25.00           C
ATOM     74  CA  GLU    74      -4.793  54.529  67.003  1.00 25.00           C
ATOM     75  CA  ALA    75      -8.126  52.788  66.272  1.00 25.00           C
ATOM     76  CA  SER    76      -6.501  49.372  66.874  1.00 25.00           C
ATOM     77  CA  ILE    77      -5.054  50.618  70.194  1.00 25.00           C
ATOM     78  CA  GLY    78      -8.502  51.920  71.236  1.00 25.00           C
ATOM     79  CA  LEU    79     -10.072  48.541  70.352  1.00 25.00           C
ATOM     80  CA  ALA    80      -7.400  46.732  72.414  1.00 25.00           C
ATOM     81  CA  ALA    81      -8.078  49.059  75.380  1.00 25.00           C
ATOM     82  CA  ILE    82     -11.836  48.379  75.085  1.00 25.00           C
ATOM     83  CA  ASN    83     -11.174  44.608  75.020  1.00 25.00           C
ATOM     84  CA  ALA    84      -8.967  44.916  78.135  1.00 25.00           C
ATOM     85  CA  TYR    85     -11.716  46.899  79.916  1.00 25.00           C
ATOM     86  CA  TYR    86     -13.946  43.804  79.578  1.00 25.00           C
ATOM     87  CA  ASN    87     -12.209  40.586  80.635  1.00 25.00           C
ATOM     88  CA  ASN    88     -15.698  39.085  80.221  1.00 25.00           C
ATOM     89  CA  PRO    89     -17.591  39.881  76.951  1.00 25.00           C
ATOM     90  CA  GLN    90     -21.272  39.337  77.861  1.00 25.00           C
ATOM     91  CA  VAL    91     -21.759  37.206  74.717  1.00 25.00           C
ATOM     92  CA  ALA    92     -18.670  35.128  75.616  1.00 25.00           C
ATOM     93  CA  ARG    93     -20.016  34.619  79.166  1.00 25.00           C
ATOM     94  CA  GLU    94     -23.398  33.512  77.751  1.00 25.00           C
ATOM     95  CA  HIS    95     -21.638  31.043  75.410  1.00 25.00           C
ATOM     96  CA  GLY    96     -21.322  27.273  75.931  1.00 25.00           C
TER
END
