
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0304TS599_4
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS599_4.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# 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      -       -           -
LGA    S       2      D      16          1.851
LGA    D       3      R      17          2.221
LGA    T       4      P      18          5.198
LGA    L       5      -       -           -
LGA    P       6      W      19           #
LGA    G       7      W      20           -
LGA    T       8      G      21           -
LGA    T       9      L      22           -
LGA    L      10      P      23           -
LGA    P      11      C      24           -
LGA    D      12      -       -           -
LGA    D      13      -       -           -
LGA    N      14      -       -           -
LGA    H      15      -       -           -
LGA    D      16      -       -           -
LGA    R      17      T      25           #
LGA    P      18      V      26           #
LGA    W      19      T      27          4.822
LGA    W      20      P      28          4.278
LGA    G      21      C      29          2.631
LGA    L      22      F      30          5.194
LGA    P      23      G      31          4.422
LGA    C      24      A      32           #
LGA    T      25      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    V      26      R      47           #
LGA    T      27      A      48          4.071
LGA    P      28      G      49          4.192
LGA    C      29      -       -           -
LGA    F      30      -       -           -
LGA    G      31      -       -           -
LGA    A      32      I      50           #
LGA    R      33      R      51           -
LGA    L      34      -       -           -
LGA    V      35      -       -           -
LGA    Q      36      -       -           -
LGA    E      37      -       -           -
LGA    G      38      -       -           -
LGA    N      39      -       -           -
LGA    R      40      -       -           -
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      -       -           -
LGA    L      44      G      52          1.222
LGA    A      45      L      53          1.850
LGA    D      46      -       -           -
LGA    R      47      F      54          2.679
LGA    A      48      S      55          4.336
LGA    G      49      -       -           -
LGA    I      50      -       -           -
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      -       -           -
LGA    F      54      D      56          3.245
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      A      57          4.899
LGA    D      58      D      58          4.398
LGA    A      59      A      59          4.661
LGA    Y      60      Y      60          3.626
LGA    H      61      H      61          1.119
LGA    L      62      L      62          1.791
LGA    D      63      D      63          2.620
LGA    Q      64      Q      64          2.922
LGA    A      65      A      65          2.262
LGA    F      66      F      66          0.751
LGA    P      67      P      67          1.984
LGA    L      68      L      68          2.281
LGA    L      69      L      69          1.058
LGA    M      70      M      70          0.752
LGA    K      71      K      71          1.545
LGA    Q      72      Q      72          0.962
LGA    L      73      L      73          0.500
LGA    E      74      E      74          1.162
LGA    L      75      L      75          0.947
LGA    M      76      M      76          0.507
LGA    L      77      L      77          0.733
LGA    T      78      T      78          0.842
LGA    S      79      S      79          0.646
LGA    G      80      G      80          1.257
LGA    E      81      E      81          0.966
LGA    L      82      L      82          2.050
LGA    N      83      N      83          3.238
LGA    P      84      P      84          3.096
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    R      85      D     102          3.664
LGA    H      86      T     103          4.564
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    Q      87      C     107           #
LGA    H      88      -       -           -
LGA    T      89      -       -           -
LGA    V      90      -       -           -
LGA    T      91      -       -           -
LGA    L      92      -       -           -
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      D     108          4.631
LGA    D     108      Y     109          2.637
LGA    Y     109      V     110           #
LGA    V     110      Y     111           #
LGA    Y     111      L     112           #
LGA    L     112      A     113           -
LGA    A     113      V     114           -
LGA    V     114      Y     115           -
LGA    Y     115      P     116           -
LGA    P     116      T     117           -
LGA    T     117      P     118           -
LGA    P     118      E     119           -
LGA    E     119      M     120           -
LGA    M     120      K     121           -
LGA    K     121      N     122           -
LGA    N     122      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  107    5.0     47    2.98    59.57     29.747     1.525

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.267344 * X  +  -0.765807 * Y  +  -0.584864 * Z  +  42.322029
  Y_new =   0.920423 * X  +   0.382601 * Y  +  -0.080239 * Z  +  19.563633
  Z_new =   0.285217 * X  +  -0.516871 * Y  +   0.807153 * Z  +  38.998447 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.569571    2.572021  [ DEG:   -32.6340    147.3660 ]
  Theta =  -0.289233   -2.852360  [ DEG:   -16.5718   -163.4282 ]
  Phi   =   1.288117   -1.853476  [ DEG:    73.8036   -106.1964 ]
 
# 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: T0304TS599_4                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_4.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  107   5.0   47   2.98   59.57  29.747
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_4
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      28.195  15.310  41.044  1.00  0.00              
ATOM      2  CA  SER     2      28.958  15.143  44.889  1.00  0.00              
ATOM      3  CA  ASP     3      32.451  17.339  45.761  1.00  0.00              
ATOM      4  CA  THR     4      28.788  16.768  47.104  1.00  0.00              
ATOM      5  CA  LEU     5      27.514  20.074  45.608  1.00  0.00              
ATOM      6  CA  PRO     6      28.872  20.400  42.119  1.00  0.00              
ATOM      7  CA  GLY     7      25.727  20.489  40.078  1.00  0.00              
ATOM      8  CA  THR     8      26.793  22.880  37.383  1.00  0.00              
ATOM      9  CA  THR     9      26.664  21.566  33.837  1.00  0.00              
ATOM     10  CA  LEU    10      29.553  22.631  31.610  1.00  0.00              
ATOM     11  CA  PRO    11      28.685  24.433  28.429  1.00  0.00              
ATOM     12  CA  ASP    12      29.307  22.553  25.153  1.00  0.00              
ATOM     13  CA  ASP    13      31.221  25.334  23.381  1.00  0.00              
ATOM     14  CA  ASN    14      28.765  28.108  23.968  1.00  0.00              
ATOM     15  CA  HIS    15      30.746  31.070  24.799  1.00  0.00              
ATOM     16  CA  ASP    16      29.676  31.833  28.392  1.00  0.00              
ATOM     17  CA  ARG    17      32.658  30.604  30.386  1.00  0.00              
ATOM     18  CA  PRO    18      35.288  30.409  27.612  1.00  0.00              
ATOM     19  CA  TRP    19      37.603  27.708  28.837  1.00  0.00              
ATOM     20  CA  TRP    20      35.852  26.024  31.688  1.00  0.00              
ATOM     21  CA  GLY    21      38.448  25.374  34.311  1.00  0.00              
ATOM     22  CA  LEU    22      36.884  23.007  36.796  1.00  0.00              
ATOM     23  CA  PRO    23      37.164  24.195  40.420  1.00  0.00              
ATOM     24  CA  CYS    24      33.637  23.890  41.828  1.00  0.00              
ATOM     25  CA  THR    25      34.219  22.006  45.083  1.00  0.00              
ATOM     26  CA  VAL    26      37.312  20.060  44.254  1.00  0.00              
ATOM     27  CA  THR    27      38.685  17.266  46.475  1.00  0.00              
ATOM     28  CA  PRO    28      40.423  14.636  44.323  1.00  0.00              
ATOM     29  CA  CYS    29      39.321  11.310  45.765  1.00  0.00              
ATOM     30  CA  PHE    30      35.700  12.314  45.173  1.00  0.00              
ATOM     31  CA  GLY    31      36.247  13.646  41.662  1.00  0.00              
ATOM     32  CA  ALA    32      37.704  10.356  40.418  1.00  0.00              
ATOM     33  CA  ARG    33      34.738   8.524  41.889  1.00  0.00              
ATOM     34  CA  LEU    34      32.253  10.842  40.140  1.00  0.00              
ATOM     35  CA  VAL    35      33.941  10.392  36.754  1.00  0.00              
ATOM     36  CA  GLN    36      34.004   6.628  37.278  1.00  0.00              
ATOM     37  CA  GLU    37      30.305   6.474  38.218  1.00  0.00              
ATOM     38  CA  GLY    38      29.142   8.178  35.110  1.00  0.00              
ATOM     39  CA  ASN    39      28.169  11.533  36.496  1.00  0.00              
ATOM     40  CA  ARG    40      29.004  13.723  33.456  1.00  0.00              
ATOM     41  CA  LEU    41      30.401  17.190  34.096  1.00  0.00              
ATOM     42  CA  HIS    42      30.792  18.500  30.580  1.00  0.00              
ATOM     43  CA  TYR    43      33.422  21.299  30.750  1.00  0.00              
ATOM     44  CA  LEU    44      35.825  19.505  33.142  1.00  0.00              
ATOM     45  CA  ALA    45      35.707  16.239  31.275  1.00  0.00              
ATOM     46  CA  ASP    46      36.391  17.714  27.812  1.00  0.00              
ATOM     47  CA  ARG    47      39.407  19.920  28.493  1.00  0.00              
ATOM     48  CA  ALA    48      41.223  17.145  30.291  1.00  0.00              
ATOM     49  CA  GLY    49      40.396  14.311  27.821  1.00  0.00              
ATOM     50  CA  ILE    50      38.683  12.115  30.381  1.00  0.00              
ATOM     51  CA  ARG    51      35.985  10.464  28.196  1.00  0.00              
ATOM     52  CA  GLY    52      38.448   9.616  25.419  1.00  0.00              
ATOM     53  CA  LEU    53      41.647   8.373  26.939  1.00  0.00              
ATOM     54  CA  PHE    54      44.101  11.289  26.972  1.00  0.00              
ATOM     55  CA  SER    55      46.942  11.205  24.561  1.00  0.00              
ATOM     56  CA  ASP    56      50.449  10.792  25.982  1.00  0.00              
ATOM     57  CA  ALA    57      51.252  14.354  24.837  1.00  0.00              
ATOM     58  CA  ASP    58      48.354  15.695  26.949  1.00  0.00              
ATOM     59  CA  ALA    59      49.574  13.725  30.005  1.00  0.00              
ATOM     60  CA  TYR    60      53.077  15.177  29.469  1.00  0.00              
ATOM     61  CA  HIS    61      51.582  18.705  29.203  1.00  0.00              
ATOM     62  CA  LEU    62      49.845  18.299  32.581  1.00  0.00              
ATOM     63  CA  ASP    63      53.073  17.095  34.195  1.00  0.00              
ATOM     64  CA  GLN    64      54.998  20.096  32.780  1.00  0.00              
ATOM     65  CA  ALA    65      52.364  22.516  34.062  1.00  0.00              
ATOM     66  CA  PHE    66      52.247  21.143  37.643  1.00  0.00              
ATOM     67  CA  PRO    67      56.037  21.192  38.184  1.00  0.00              
ATOM     68  CA  LEU    68      56.115  24.707  36.853  1.00  0.00              
ATOM     69  CA  LEU    69      53.278  25.794  39.212  1.00  0.00              
ATOM     70  CA  MET    70      54.853  24.351  42.329  1.00  0.00              
ATOM     71  CA  LYS    71      58.271  25.935  41.535  1.00  0.00              
ATOM     72  CA  GLN    72      56.637  29.268  40.987  1.00  0.00              
ATOM     73  CA  LEU    73      54.735  29.110  44.172  1.00  0.00              
ATOM     74  CA  GLU    74      57.814  28.278  46.209  1.00  0.00              
ATOM     75  CA  LEU    75      59.831  31.086  44.607  1.00  0.00              
ATOM     76  CA  MET    76      57.062  33.585  45.348  1.00  0.00              
ATOM     77  CA  LEU    77      56.690  32.473  49.022  1.00  0.00              
ATOM     78  CA  THR    78      60.434  32.800  49.574  1.00  0.00              
ATOM     79  CA  SER    79      60.488  36.261  47.911  1.00  0.00              
ATOM     80  CA  GLY    80      57.715  37.872  49.828  1.00  0.00              
ATOM     81  CA  GLU    81      55.152  37.889  47.004  1.00  0.00              
ATOM     82  CA  LEU    82      52.953  35.917  49.319  1.00  0.00              
ATOM     83  CA  ASN    83      49.289  35.721  48.491  1.00  0.00              
ATOM     84  CA  PRO    84      47.175  33.894  50.992  1.00  0.00              
ATOM     85  CA  ARG    85      46.310  30.876  48.791  1.00  0.00              
ATOM     86  CA  HIS    86      49.993  30.342  47.992  1.00  0.00              
ATOM     87  CA  GLN    87      51.300  30.438  51.572  1.00  0.00              
ATOM     88  CA  HIS    88      49.587  27.176  52.294  1.00  0.00              
ATOM     89  CA  THR    89      51.261  25.096  49.677  1.00  0.00              
ATOM     90  CA  VAL    90      49.993  24.070  46.307  1.00  0.00              
ATOM     91  CA  THR    91      51.155  20.733  45.097  1.00  0.00              
ATOM     92  CA  LEU    92      50.480  19.358  41.770  1.00  0.00              
ATOM     93  CA  TYR    93      51.374  15.659  41.236  1.00  0.00              
ATOM     94  CA  ALA    94      51.448  14.187  37.890  1.00  0.00              
ATOM     95  CA  LYS    95      51.094  10.575  38.462  1.00  0.00              
ATOM     96  CA  GLY    96      48.374  10.197  40.909  1.00  0.00              
ATOM     97  CA  LEU    97      48.372  11.860  44.359  1.00  0.00              
ATOM     98  CA  THR    98      44.840  12.750  45.497  1.00  0.00              
ATOM     99  CA  CYS    99      44.087  15.530  47.916  1.00  0.00              
ATOM    100  CA  LYS   100      41.246  15.129  50.402  1.00  0.00              
ATOM    101  CA  ALA   101      39.174  18.306  50.540  1.00  0.00              
ATOM    102  CA  ASP   102      39.167  18.717  54.270  1.00  0.00              
ATOM    103  CA  THR   103      42.817  18.340  55.213  1.00  0.00              
ATOM    104  CA  LEU   104      44.466  20.355  52.409  1.00  0.00              
ATOM    105  CA  SER   105      41.944  23.128  53.031  1.00  0.00              
ATOM    106  CA  SER   106      41.938  23.460  56.825  1.00  0.00              
ATOM    107  CA  CYS   107      45.716  23.632  57.194  1.00  0.00              
ATOM    108  CA  ASP   108      46.111  25.587  53.952  1.00  0.00              
ATOM    109  CA  TYR   109      47.646  22.944  51.613  1.00  0.00              
ATOM    110  CA  VAL   110      46.431  22.140  48.177  1.00  0.00              
ATOM    111  CA  TYR   111      47.356  18.817  46.644  1.00  0.00              
ATOM    112  CA  LEU   112      46.219  17.994  43.211  1.00  0.00              
ATOM    113  CA  ALA   113      46.708  14.656  41.788  1.00  0.00              
ATOM    114  CA  VAL   114      46.503  14.099  37.998  1.00  0.00              
ATOM    115  CA  TYR   115      45.729  10.771  36.669  1.00  0.00              
ATOM    116  CA  PRO   116      45.952   8.077  34.180  1.00  0.00              
ATOM    117  CA  THR   117      43.510   8.548  31.353  1.00  0.00              
ATOM    118  CA  PRO   118      40.999   5.662  31.565  1.00  0.00              
ATOM    119  CA  GLU   119      40.923   4.122  28.115  1.00  0.00              
ATOM    120  CA  MET   120      36.746   4.670  27.815  1.00  0.00              
ATOM    121  CA  LYS   121      33.019   6.148  29.105  1.00  0.00              
ATOM    122  CA  ASN   122      31.966   8.977  32.039  1.00  0.00              
TER                                                                             
END
