
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS599_1-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           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    I      12      V      18           #
LGA    P      13      -       -           -
LGA    E      14      -       -           -
LGA    D      15      -       -           -
LGA    F      16      D      19          4.685
LGA    L      17      E      20           #
LGA    V      18      -       -           -
LGA    D      19      -       -           -
LGA    E      20      -       -           -
LGA    L      21      -       -           -
LGA    V      22      L      21           #
LGA    C      23      V      22           #
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    G      24      T      25           #
LGA    T      25      T      26          2.148
LGA    T      26      H      27          4.405
LGA    H      27      S      28          1.563
LGA    S      28      V      29          2.257
LGA    V      29      I      30          2.127
LGA    I      30      R      31          2.103
LGA    R      31      S      32          2.325
LGA    S      32      G      33          2.155
LGA    G      33      N      34          3.510
LGA    N      34      -       -           -
LGA    G      35      -       -           -
LGA    V      36      G      35          3.671
LGA    G      37      V      36          4.618
LGA    L      38      G      37          2.180
LGA    G      39      L      38          3.427
LGA    P      40      G      39          2.174
LGA    N      41      P      40          3.814
LGA    R      42      N      41          2.998
LGA    P      43      R      42          1.967
LGA    F      44      P      43          2.534
LGA    E      45      F      44           -
LGA    -       -      E      45           -
LGA    T      46      T      46          3.197
LGA    R      47      R      47          0.816
LGA    M      48      M      48          4.453
LGA    P      49      P      49          0.500
LGA    M      50      M      50          3.239
LGA    L      51      L      51          4.236
LGA    T      52      T      52          1.966
LGA    Q      53      Q      53          1.951
LGA    N      54      N      54          3.746
LGA    L      55      L      55          2.819
LGA    L      56      L      56          0.766
LGA    G      57      G      57          3.801
LGA    L      58      L      58          2.111
LGA    P      59      P      59          1.112
LGA    L      60      L      60          1.557
LGA    R      61      R      61          1.833
LGA    V      62      V      62          2.297
LGA    A      63      A      63          3.087
LGA    A      64      A      64          3.832
LGA    G      65      G      65          4.757
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    C      66      G      78          2.673
LGA    V      67      L      79          1.360
LGA    K      68      A      80           #
LGA    S      69      A      81           -
LGA    W      70      I      82           #
LGA    N      71      N      83           -
LGA    Y      72      A      84           -
LGA    V      73      Y      85           -
LGA    E      74      Y      86           -
LGA    A      75      N      87           -
LGA    S      76      N      88           -
LGA    I      77      P      89           -
LGA    G      78      Q      90           -
LGA    L      79      V      91           -
LGA    A      80      A      92           -
LGA    A      81      R      93           -
LGA    I      82      E      94           -
LGA    N      83      H      95           -
LGA    A      84      G      96           -
LGA    Y      85      -       -           -
LGA    Y      86      -       -           -
LGA    N      87      -       -           -
LGA    N      88      -       -           -
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     41    2.93    51.22     26.606     1.354

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.288771 * X  +   0.905032 * Y  +  -0.312296 * Z  +   1.412766
  Y_new =  -0.392764 * X  +   0.409466 * Y  +   0.823452 * Z  +  39.787659
  Z_new =   0.873125 * X  +  -0.115130 * Y  +   0.473706 * Z  +  51.007435 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.238419    2.903174  [ DEG:   -13.6604    166.3396 ]
  Theta =  -1.061577   -2.080016  [ DEG:   -60.8239   -119.1761 ]
  Phi   =  -0.936817    2.204776  [ DEG:   -53.6757    126.3243 ]
 
# 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_1-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS599_1-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   2.93   51.22  26.606
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS599_1-D1
PFRMAT TS                                                                       
TARGET T0321                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       0.724  62.876  68.130  1.00  0.00              
ATOM      2  CA  TRP     2      -0.365  66.923  67.944  1.00  0.00              
ATOM      3  CA  GLU     3      -1.819  69.383  64.854  1.00  0.00              
ATOM      4  CA  ILE     4      -3.336  65.803  63.398  1.00  0.00              
ATOM      5  CA  TYR     5      -4.844  65.180  66.833  1.00  0.00              
ATOM      6  CA  ASP     6      -6.420  68.683  66.836  1.00  0.00              
ATOM      7  CA  ALA     7      -7.856  68.109  63.320  1.00  0.00              
ATOM      8  CA  MET     8      -9.299  64.804  64.427  1.00  0.00              
ATOM      9  CA  ILE     9     -10.974  66.253  67.549  1.00  0.00              
ATOM     10  CA  ASN    10     -12.563  68.922  65.414  1.00  0.00              
ATOM     11  CA  GLY    11     -13.964  66.483  62.883  1.00  0.00              
ATOM     12  CA  ILE    12     -15.449  64.463  65.492  1.00  0.00              
ATOM     13  CA  PRO    13     -17.456  66.702  67.714  1.00  0.00              
ATOM     14  CA  GLU    14     -15.765  67.540  70.989  1.00  0.00              
ATOM     15  CA  ASP    15     -18.081  65.179  72.894  1.00  0.00              
ATOM     16  CA  PHE    16     -16.485  61.839  71.566  1.00  0.00              
ATOM     17  CA  LEU    17     -15.144  60.099  73.899  1.00  0.00              
ATOM     18  CA  VAL    18     -11.332  58.314  73.766  1.00  0.00              
ATOM     19  CA  ASP    19     -11.346  55.273  74.832  1.00  0.00              
ATOM     20  CA  GLU    20      -8.120  54.155  73.447  1.00  0.00              
ATOM     21  CA  LEU    21      -6.016  56.678  71.542  1.00  0.00              
ATOM     22  CA  VAL    22      -3.525  55.673  69.085  1.00  0.00              
ATOM     23  CA  CYS    23      -1.382  58.284  67.544  1.00  0.00              
ATOM     24  CA  GLY    24       0.822  57.626  64.542  1.00  0.00              
ATOM     25  CA  THR    25       1.793  60.886  63.082  1.00  0.00              
ATOM     26  CA  THR    26       0.278  60.875  59.613  1.00  0.00              
ATOM     27  CA  HIS    27      -3.168  58.540  61.381  1.00  0.00              
ATOM     28  CA  SER    28      -4.965  59.581  64.346  1.00  0.00              
ATOM     29  CA  VAL    29      -7.102  56.808  65.848  1.00  0.00              
ATOM     30  CA  ILE    30      -9.712  57.801  68.477  1.00  0.00              
ATOM     31  CA  ARG    31     -11.735  55.070  70.251  1.00  0.00              
ATOM     32  CA  SER    32     -15.139  55.913  71.855  1.00  0.00              
ATOM     33  CA  GLY    33     -15.688  54.336  75.292  1.00  0.00              
ATOM     34  CA  ASN    34     -17.111  50.983  74.394  1.00  0.00              
ATOM     35  CA  GLY    35     -14.991  50.036  71.457  1.00  0.00              
ATOM     36  CA  VAL    36     -11.401  50.949  72.419  1.00  0.00              
ATOM     37  CA  GLY    37     -10.162  52.900  69.083  1.00  0.00              
ATOM     38  CA  LEU    38      -6.730  52.517  67.696  1.00  0.00              
ATOM     39  CA  GLY    39      -5.479  55.224  65.319  1.00  0.00              
ATOM     40  CA  PRO    40      -2.949  54.333  62.642  1.00  0.00              
ATOM     41  CA  ASN    41      -0.853  56.750  60.697  1.00  0.00              
ATOM     42  CA  ARG    42       0.254  55.737  57.179  1.00  0.00              
ATOM     43  CA  PRO    43       3.773  56.583  57.161  1.00  0.00              
ATOM     44  CA  PHE    44       4.164  59.982  55.812  1.00  0.00              
ATOM     45  CA  GLU    45       1.250  61.675  57.407  1.00  0.00              
ATOM     46  CA  THR    46      -0.537  63.073  54.096  1.00  0.00              
ATOM     47  CA  ARG    47      -3.696  62.514  54.007  1.00  0.00              
ATOM     48  CA  MET    48      -6.366  64.763  56.014  1.00  0.00              
ATOM     49  CA  PRO    49      -9.403  64.739  54.177  1.00  0.00              
ATOM     50  CA  MET    50      -9.744  61.024  53.426  1.00  0.00              
ATOM     51  CA  LEU    51      -8.965  60.098  57.005  1.00  0.00              
ATOM     52  CA  THR    52     -11.459  62.400  58.677  1.00  0.00              
ATOM     53  CA  GLN    53     -14.360  61.283  56.462  1.00  0.00              
ATOM     54  CA  ASN    54     -13.557  57.685  57.259  1.00  0.00              
ATOM     55  CA  LEU    55     -13.344  58.086  60.941  1.00  0.00              
ATOM     56  CA  LEU    56     -16.427  60.117  61.745  1.00  0.00              
ATOM     57  CA  GLY    57     -18.659  57.877  59.703  1.00  0.00              
ATOM     58  CA  LEU    58     -17.305  54.584  60.733  1.00  0.00              
ATOM     59  CA  PRO    59     -18.165  52.195  63.505  1.00  0.00              
ATOM     60  CA  LEU    60     -15.625  51.323  66.110  1.00  0.00              
ATOM     61  CA  ARG    61     -15.363  47.706  64.913  1.00  0.00              
ATOM     62  CA  VAL    62     -14.606  48.764  61.384  1.00  0.00              
ATOM     63  CA  ALA    63     -11.881  51.083  62.645  1.00  0.00              
ATOM     64  CA  ALA    64     -10.199  48.459  64.770  1.00  0.00              
ATOM     65  CA  GLY    65     -10.290  45.997  61.995  1.00  0.00              
ATOM     66  CA  CYS    66      -8.742  48.536  59.565  1.00  0.00              
ATOM     67  CA  VAL    67      -6.050  49.466  62.003  1.00  0.00              
ATOM     68  CA  LYS    68      -5.066  45.846  62.454  1.00  0.00              
ATOM     69  CA  SER    69      -5.007  45.238  58.691  1.00  0.00              
ATOM     70  CA  TRP    70      -2.577  48.006  57.912  1.00  0.00              
ATOM     71  CA  ASN    71      -0.078  46.891  60.571  1.00  0.00              
ATOM     72  CA  TYR    72      -0.021  43.256  59.483  1.00  0.00              
ATOM     73  CA  VAL    73       0.689  44.211  55.857  1.00  0.00              
ATOM     74  CA  GLU    74       3.573  46.424  56.742  1.00  0.00              
ATOM     75  CA  ALA    75       5.136  43.826  59.029  1.00  0.00              
ATOM     76  CA  SER    76       4.780  41.024  56.504  1.00  0.00              
ATOM     77  CA  ILE    77       6.393  43.003  53.703  1.00  0.00              
ATOM     78  CA  GLY    78       9.317  43.985  55.851  1.00  0.00              
ATOM     79  CA  LEU    79      10.216  40.689  57.398  1.00  0.00              
ATOM     80  CA  ALA    80      10.031  38.855  54.187  1.00  0.00              
ATOM     81  CA  ALA    81      12.210  41.347  52.295  1.00  0.00              
ATOM     82  CA  ILE    82      14.849  41.184  55.231  1.00  0.00              
ATOM     83  CA  ASN    83      14.782  37.326  55.293  1.00  0.00              
ATOM     84  CA  ALA    84      15.280  37.014  51.589  1.00  0.00              
ATOM     85  CA  TYR    85      18.306  39.429  51.920  1.00  0.00              
ATOM     86  CA  TYR    86      19.884  37.478  54.727  1.00  0.00              
ATOM     87  CA  ASN    87      19.462  34.102  52.929  1.00  0.00              
ATOM     88  CA  ASN    88      21.176  35.323  49.819  1.00  0.00              
ATOM     89  CA  PRO    89      24.074  36.788  51.394  1.00  0.00              
ATOM     90  CA  GLN    90      24.621  33.818  53.806  1.00  0.00              
ATOM     91  CA  VAL    91      24.167  35.909  56.929  1.00  0.00              
ATOM     92  CA  ALA    92      21.879  33.980  59.272  1.00  0.00              
ATOM     93  CA  ARG    93      21.690  36.321  62.278  1.00  0.00              
ATOM     94  CA  GLU    94      18.207  37.747  61.762  1.00  0.00              
ATOM     95  CA  HIS    95      19.071  41.418  61.216  1.00  0.00              
ATOM     96  CA  GLY    96      18.028  42.221  58.411  1.00  0.00              
TER                                                                             
END
