
#######################################################
#                                                     #
#                        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 T0321TS599_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS599_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      M       1           -
LGA    W       2      W       2           -
LGA    E       3      E       3           -
LGA    I       4      I       4           -
LGA    Y       5      Y       5           -
LGA    D       6      D       6           -
LGA    A       7      A       7           -
LGA    M       8      M       8           -
LGA    I       9      I       9           -
LGA    N      10      N      10           -
LGA    G      11      G      11           -
LGA    I      12      I      12           -
LGA    P      13      P      13           -
LGA    E      14      E      14           -
LGA    D      15      D      15           -
LGA    F      16      F      16           -
LGA    L      17      L      17           -
LGA    V      18      V      18           -
LGA    D      19      D      19           -
LGA    E      20      E      20           -
LGA    L      21      -       -           -
LGA    V      22      -       -           -
LGA    C      23      L      21           #
LGA    G      24      V      22           #
LGA    -       -      C      23           -
LGA    T      25      G      24          2.971
LGA    T      26      T      25          4.180
LGA    H      27      T      26           -
LGA    -       -      H      27           -
LGA    S      28      S      28           #
LGA    V      29      V      29          3.987
LGA    I      30      I      30           -
LGA    R      31      R      31           #
LGA    S      32      S      32           -
LGA    G      33      -       -           -
LGA    N      34      G      33           #
LGA    G      35      N      34          1.526
LGA    V      36      G      35          3.251
LGA    G      37      V      36          1.904
LGA    L      38      G      37          2.051
LGA    G      39      L      38          2.767
LGA    P      40      G      39          2.063
LGA    N      41      P      40          3.032
LGA    R      42      N      41          2.833
LGA    P      43      R      42          2.029
LGA    F      44      P      43          2.860
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    E      45      T      46          2.384
LGA    T      46      R      47          2.012
LGA    R      47      M      48          5.634
LGA    -       -      P      49           -
LGA    M      48      M      50           #
LGA    P      49      L      51           -
LGA    M      50      T      52           -
LGA    L      51      Q      53           -
LGA    T      52      N      54           -
LGA    Q      53      L      55           -
LGA    N      54      L      56           -
LGA    L      55      G      57           -
LGA    L      56      L      58           -
LGA    G      57      P      59           -
LGA    L      58      L      60           -
LGA    P      59      R      61           -
LGA    L      60      V      62           -
LGA    R      61      A      63           -
LGA    V      62      A      64           -
LGA    A      63      G      65           -
LGA    A      64      C      66           -
LGA    G      65      V      67           -
LGA    C      66      K      68           -
LGA    V      67      S      69          4.634
LGA    K      68      W      70          1.320
LGA    S      69      N      71          2.720
LGA    W      70      Y      72          3.535
LGA    N      71      V      73           -
LGA    -       -      E      74           -
LGA    Y      72      A      75          3.170
LGA    V      73      S      76          2.350
LGA    E      74      I      77          2.953
LGA    A      75      G      78          2.712
LGA    S      76      L      79          1.579
LGA    I      77      A      80          1.644
LGA    G      78      A      81          1.845
LGA    L      79      I      82          1.836
LGA    A      80      N      83          2.050
LGA    A      81      A      84          2.177
LGA    I      82      Y      85          1.308
LGA    N      83      Y      86          0.958
LGA    A      84      N      87          1.245
LGA    Y      85      N      88          1.622
LGA    -       -      P      89           -
LGA    Y      86      Q      90          4.854
LGA    N      87      V      91          3.170
LGA    N      88      A      92          4.682
LGA    P      89      R      93          5.732
LGA    Q      90      E      94          2.617
LGA    V      91      -       -           -
LGA    A      92      -       -           -
LGA    R      93      -       -           -
LGA    E      94      H      95          3.366
LGA    H      95      G      96          2.928
LGA    G      96      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   96   96    5.0     41    2.98     7.32     27.844     1.332

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.850477 * X  +  -0.349971 * Y  +   0.392695 * Z  +  -8.579700
  Y_new =  -0.391792 * X  +   0.076677 * Y  +   0.916853 * Z  +  50.634136
  Z_new =  -0.350982 * X  +  -0.933617 * Y  +  -0.071904 * Z  +  58.085369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.647661    1.493932  [ DEG:   -94.4040     85.5960 ]
  Theta =   0.358620    2.782973  [ DEG:    20.5474    159.4526 ]
  Phi   =  -0.431694    2.709899  [ DEG:   -24.7342    155.2658 ]
 
# 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: T0321TS599_2-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS599_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   41   2.98    7.32  27.844
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS599_2-D1
PFRMAT TS                                                                       
TARGET T0321                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -7.494  78.551  64.138  1.00  0.00              
ATOM      2  CA  TRP     2      -6.968  81.051  67.470  1.00  0.00              
ATOM      3  CA  GLU     3     -10.425  80.595  68.326  1.00  0.00              
ATOM      4  CA  ILE     4      -9.446  76.924  67.551  1.00  0.00              
ATOM      5  CA  TYR     5      -6.780  76.919  70.232  1.00  0.00              
ATOM      6  CA  ASP     6      -9.233  78.333  72.767  1.00  0.00              
ATOM      7  CA  ALA     7     -11.832  75.655  71.909  1.00  0.00              
ATOM      8  CA  MET     8      -9.286  72.917  72.251  1.00  0.00              
ATOM      9  CA  ILE     9      -7.999  74.222  75.562  1.00  0.00              
ATOM     10  CA  ASN    10     -11.576  74.368  76.888  1.00  0.00              
ATOM     11  CA  GLY    11     -12.417  70.800  75.783  1.00  0.00              
ATOM     12  CA  ILE    12      -9.216  69.332  77.632  1.00  0.00              
ATOM     13  CA  PRO    13      -8.930  70.824  80.641  1.00  0.00              
ATOM     14  CA  GLU    14      -5.402  72.162  80.792  1.00  0.00              
ATOM     15  CA  ASP    15      -3.878  69.453  83.012  1.00  0.00              
ATOM     16  CA  PHE    16      -5.276  66.519  81.218  1.00  0.00              
ATOM     17  CA  LEU    17      -2.901  63.572  80.700  1.00  0.00              
ATOM     18  CA  VAL    18      -2.202  61.833  77.490  1.00  0.00              
ATOM     19  CA  ASP    19      -2.892  58.172  78.205  1.00  0.00              
ATOM     20  CA  GLU    20      -2.243  56.840  74.753  1.00  0.00              
ATOM     21  CA  LEU    21      -0.940  59.123  72.138  1.00  0.00              
ATOM     22  CA  VAL    22      -1.289  58.180  68.354  1.00  0.00              
ATOM     23  CA  CYS    23       0.448  60.290  65.708  1.00  0.00              
ATOM     24  CA  GLY    24      -0.513  59.896  62.108  1.00  0.00              
ATOM     25  CA  THR    25       0.815  62.459  59.761  1.00  0.00              
ATOM     26  CA  THR    26      -1.272  65.590  60.439  1.00  0.00              
ATOM     27  CA  HIS    27      -3.694  63.733  62.905  1.00  0.00              
ATOM     28  CA  SER    28      -3.048  63.688  65.816  1.00  0.00              
ATOM     29  CA  VAL    29      -5.235  61.230  68.714  1.00  0.00              
ATOM     30  CA  ILE    30      -5.213  61.735  71.894  1.00  0.00              
ATOM     31  CA  ARG    31      -6.638  59.251  74.489  1.00  0.00              
ATOM     32  CA  SER    32      -7.994  60.638  77.945  1.00  0.00              
ATOM     33  CA  GLY    33      -7.956  58.246  80.899  1.00  0.00              
ATOM     34  CA  ASN    34     -11.461  56.814  80.386  1.00  0.00              
ATOM     35  CA  GLY    35     -11.328  56.209  76.748  1.00  0.00              
ATOM     36  CA  VAL    36      -7.814  54.794  76.118  1.00  0.00              
ATOM     37  CA  GLY    37      -6.842  56.753  73.096  1.00  0.00              
ATOM     38  CA  LEU    38      -4.823  55.109  70.215  1.00  0.00              
ATOM     39  CA  GLY    39      -2.974  57.253  67.534  1.00  0.00              
ATOM     40  CA  PRO    40      -2.269  55.370  64.057  1.00  0.00              
ATOM     41  CA  ASN    41       0.184  57.107  61.827  1.00  0.00              
ATOM     42  CA  ARG    42      -0.383  56.792  58.008  1.00  0.00              
ATOM     43  CA  PRO    43       3.215  57.390  56.881  1.00  0.00              
ATOM     44  CA  PHE    44       3.351  61.191  56.344  1.00  0.00              
ATOM     45  CA  GLU    45       0.948  61.378  53.451  1.00  0.00              
ATOM     46  CA  THR    46      -1.974  63.485  54.650  1.00  0.00              
ATOM     47  CA  ARG    47      -2.771  65.603  52.229  1.00  0.00              
ATOM     48  CA  MET    48      -6.432  65.246  50.638  1.00  0.00              
ATOM     49  CA  PRO    49      -6.316  66.984  47.502  1.00  0.00              
ATOM     50  CA  MET    50      -2.877  65.781  46.277  1.00  0.00              
ATOM     51  CA  LEU    51      -3.987  62.162  46.806  1.00  0.00              
ATOM     52  CA  THR    52      -7.051  62.197  44.996  1.00  0.00              
ATOM     53  CA  GLN    53      -5.666  63.733  41.795  1.00  0.00              
ATOM     54  CA  ASN    54      -2.844  61.229  41.797  1.00  0.00              
ATOM     55  CA  LEU    55      -5.158  58.353  42.169  1.00  0.00              
ATOM     56  CA  LEU    56      -7.532  59.116  39.361  1.00  0.00              
ATOM     57  CA  GLY    57      -4.787  59.389  36.856  1.00  0.00              
ATOM     58  CA  LEU    58      -3.229  56.083  37.670  1.00  0.00              
ATOM     59  CA  PRO    59      -3.065  52.662  36.237  1.00  0.00              
ATOM     60  CA  LEU    60      -4.905  49.827  37.778  1.00  0.00              
ATOM     61  CA  ARG    61      -1.874  48.343  39.489  1.00  0.00              
ATOM     62  CA  VAL    62      -0.983  51.589  41.070  1.00  0.00              
ATOM     63  CA  ALA    63      -4.476  52.092  42.261  1.00  0.00              
ATOM     64  CA  ALA    64      -4.659  48.559  43.880  1.00  0.00              
ATOM     65  CA  GLY    65      -1.360  49.148  45.629  1.00  0.00              
ATOM     66  CA  CYS    66      -2.526  52.479  47.174  1.00  0.00              
ATOM     67  CA  VAL    67      -5.867  50.954  48.290  1.00  0.00              
ATOM     68  CA  LYS    68      -4.015  48.175  49.991  1.00  0.00              
ATOM     69  CA  SER    69      -1.683  50.588  51.776  1.00  0.00              
ATOM     70  CA  TRP    70      -4.356  52.715  53.355  1.00  0.00              
ATOM     71  CA  ASN    71      -6.586  49.848  54.302  1.00  0.00              
ATOM     72  CA  TYR    72      -3.885  48.052  56.318  1.00  0.00              
ATOM     73  CA  VAL    73      -3.110  51.155  58.371  1.00  0.00              
ATOM     74  CA  GLU    74      -6.771  51.787  59.132  1.00  0.00              
ATOM     75  CA  ALA    75      -7.117  48.250  60.505  1.00  0.00              
ATOM     76  CA  SER    76      -4.313  48.552  62.332  1.00  0.00              
ATOM     77  CA  ILE    77      -5.086  51.660  64.250  1.00  0.00              
ATOM     78  CA  GLY    78      -8.292  50.295  65.042  1.00  0.00              
ATOM     79  CA  LEU    79      -7.118  46.984  66.439  1.00  0.00              
ATOM     80  CA  ALA    80      -4.635  48.498  68.881  1.00  0.00              
ATOM     81  CA  ALA    81      -7.341  50.794  70.181  1.00  0.00              
ATOM     82  CA  ILE    82      -9.886  48.010  70.653  1.00  0.00              
ATOM     83  CA  ASN    83      -7.438  45.899  72.567  1.00  0.00              
ATOM     84  CA  ALA    84      -6.697  48.726  74.965  1.00  0.00              
ATOM     85  CA  TYR    85     -10.401  49.399  75.533  1.00  0.00              
ATOM     86  CA  TYR    86     -11.092  45.781  76.215  1.00  0.00              
ATOM     87  CA  ASN    87      -8.260  45.511  78.760  1.00  0.00              
ATOM     88  CA  ASN    88      -9.256  48.519  80.626  1.00  0.00              
ATOM     89  CA  PRO    89     -12.819  47.439  81.062  1.00  0.00              
ATOM     90  CA  GLN    90     -12.126  43.875  81.861  1.00  0.00              
ATOM     91  CA  VAL    91     -14.235  42.649  78.980  1.00  0.00              
ATOM     92  CA  ALA    92     -13.859  38.882  78.682  1.00  0.00              
ATOM     93  CA  ARG    93     -10.605  37.989  80.570  1.00  0.00              
ATOM     94  CA  GLU    94      -8.456  37.003  77.651  1.00  0.00              
ATOM     95  CA  HIS    95      -5.861  39.602  78.056  1.00  0.00              
ATOM     96  CA  GLY    96      -5.998  41.453  74.510  1.00  0.00              
TER                                                                             
END
