
#######################################################
#                                                     #
#                        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   33 (  132),  selected   21 , name T0356AL381_3
# Molecule2: number of CA atoms  469 ( 3688),  selected   21 , name T0356.pdb
# PARAMETERS: T0356AL381_3.T0356.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        85 - 101         4.62     9.73
  LCS_AVERAGE:      3.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        87 - 99          1.64    11.44
  LCS_AVERAGE:      2.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        88 - 98          0.59    12.19
  LCS_AVERAGE:      1.57

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:  469
LCS_GDT     L      85     L      85      3    3   17     3    3    3    3    3    4    4    8   11   14   15   15   16   16   16   16   16   16   18   19 
LCS_GDT     R      86     R      86      3    3   17     3    3    3    3    3    4    5   11   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     E      87     E      87      3   13   17     3    3    3    3    4   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     V      88     V      88     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     G      89     G      89     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     K      90     K      90     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     L      91     L      91     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     L      92     L      92     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     A      93     A      93     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     F      94     F      94     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     L      95     L      95     11   13   17     8   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     K      96     K      96     11   13   17     6   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     E      97     E      97     11   13   17     4   10   11   11   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     P      98     P      98     11   13   17     5   10   11   11   11   12   13   13   13   14   15   15   16   16   16   18   19   19   19   19 
LCS_GDT     E      99     E      99      4   13   17     3    4    5    9   11   12   13   13   13   14   15   15   16   16   17   18   19   19   19   19 
LCS_GDT     P     100     P     100      4    6   17     3    4    5    6    6    6    7    9   11   13   14   15   16   16   17   18   19   19   19   19 
LCS_GDT     P     101     P     101      4    6   17     3    3    5    6    6    6    7    8    9   10   10   12   13   14   17   18   19   19   19   19 
LCS_GDT     K     102     K     102      4    6   14     3    3    5    6    6    6    7    8    9   10   10   12   13   14   17   18   19   19   19   19 
LCS_GDT     G     103     G     103      3    4   12     3    3    3    4    4    5    7    7    9   10   10   12   13   14   17   18   19   19   19   19 
LCS_GDT     F     104     F     104      3    4   12     3    3    3    4    5    5    6    8    9   10   10   10   10   12   14   15   15   15   17   18 
LCS_GDT     R     105     R     105      3    4   12     3    3    3    4    4    5    5    8    9   10   10   12   13   14   15   18   19   19   19   19 
LCS_AVERAGE  LCS_A:   2.37  (   1.57    2.08    3.44 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      8     10     11     11     11     12     13     13     13     14     15     15     16     16     17     18     19     19     19     19 
GDT PERCENT_CA   1.71   2.13   2.35   2.35   2.35   2.56   2.77   2.77   2.77   2.99   3.20   3.20   3.41   3.41   3.62   3.84   4.05   4.05   4.05   4.05
GDT RMS_LOCAL    0.19   0.43   0.59   0.59   0.59   1.32   1.64   1.64   1.64   2.41   2.92   2.92   3.55   3.55   5.38   5.58   5.94   5.94   5.94   5.94
GDT RMS_ALL_CA  12.38  12.16  12.19  12.19  12.19  11.48  11.44  11.44  11.44  11.27  11.48  11.48  10.53  10.53   7.09   7.11   6.82   6.82   6.82   6.82

#      Molecule1      Molecule2       DISTANCE
LGA    L      85      L      85          9.735
LGA    R      86      R      86          7.904
LGA    E      87      E      87          3.366
LGA    V      88      V      88          0.844
LGA    G      89      G      89          1.249
LGA    K      90      K      90          1.103
LGA    L      91      L      91          1.113
LGA    L      92      L      92          0.970
LGA    A      93      A      93          0.975
LGA    F      94      F      94          0.679
LGA    L      95      L      95          1.091
LGA    K      96      K      96          0.681
LGA    E      97      E      97          1.106
LGA    P      98      P      98          1.120
LGA    E      99      E      99          3.498
LGA    P     100      P     100          9.714
LGA    P     101      P     101         14.950
LGA    K     102      K     102         20.432
LGA    G     103      G     103         20.991
LGA    F     104      F     104         25.087
LGA    R     105      R     105         27.374

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  469    4.0     13    1.64     2.772     2.595     0.749

LGA_LOCAL      RMSD =  1.635  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.437  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  6.737  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.852803 * X  +   0.351949 * Y  +   0.385822 * Z  +  76.881325
  Y_new =   0.083391 * X  +  -0.637539 * Y  +   0.765892 * Z  + 109.093826
  Z_new =   0.515531 * X  +   0.685329 * Y  +   0.514346 * Z  +  58.732140 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.926969   -2.214623  [ DEG:    53.1114   -126.8886 ]
  Theta =  -0.541627   -2.599965  [ DEG:   -31.0330   -148.9670 ]
  Phi   =   3.044118   -0.097475  [ DEG:   174.4151     -5.5849 ]
 
# 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: T0356AL381_3                                  
REMARK     2: T0356.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL381_3.T0356.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  469   4.0   13   1.64   2.595     6.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL381_3
REMARK Aligment from pdb entry: 1om2A
ATOM      1  N   LEU    85      68.990  84.434  68.453  1.00  0.00              
ATOM      2  CA  LEU    85      68.584  85.612  67.711  1.00  0.00              
ATOM      3  C   LEU    85      67.881  85.228  66.412  1.00  0.00              
ATOM      4  O   LEU    85      67.182  86.062  65.842  1.00  0.00              
ATOM      5  N   ARG    86      68.041  83.982  65.945  1.00  0.00              
ATOM      6  CA  ARG    86      67.380  83.543  64.721  1.00  0.00              
ATOM      7  C   ARG    86      65.965  83.047  65.023  1.00  0.00              
ATOM      8  O   ARG    86      65.009  83.474  64.379  1.00  0.00              
ATOM      9  N   GLU    87      65.825  82.144  66.000  1.00  0.00              
ATOM     10  CA  GLU    87      64.537  81.589  66.397  1.00  0.00              
ATOM     11  C   GLU    87      64.049  80.479  65.461  1.00  0.00              
ATOM     12  O   GLU    87      62.937  79.983  65.627  1.00  0.00              
ATOM     13  N   VAL    88      66.124  77.420  64.615  1.00  0.00              
ATOM     14  CA  VAL    88      67.288  76.558  64.697  1.00  0.00              
ATOM     15  C   VAL    88      67.372  75.550  63.564  1.00  0.00              
ATOM     16  O   VAL    88      68.392  75.472  62.898  1.00  0.00              
ATOM     17  N   GLY    89      66.308  74.774  63.374  1.00  0.00              
ATOM     18  CA  GLY    89      66.233  73.702  62.389  1.00  0.00              
ATOM     19  C   GLY    89      66.601  74.154  60.979  1.00  0.00              
ATOM     20  O   GLY    89      67.290  73.421  60.268  1.00  0.00              
ATOM     21  N   LYS    90      66.173  75.352  60.565  1.00  0.00              
ATOM     22  CA  LYS    90      66.535  75.849  59.242  1.00  0.00              
ATOM     23  C   LYS    90      68.048  75.996  59.186  1.00  0.00              
ATOM     24  O   LYS    90      68.696  75.523  58.253  1.00  0.00              
ATOM     25  N   LEU    91      68.606  76.645  60.208  1.00  0.00              
ATOM     26  CA  LEU    91      70.036  76.841  60.281  1.00  0.00              
ATOM     27  C   LEU    91      70.763  75.494  60.371  1.00  0.00              
ATOM     28  O   LEU    91      71.812  75.330  59.765  1.00  0.00              
ATOM     29  N   LEU    92      70.235  74.510  61.102  1.00  0.00              
ATOM     30  CA  LEU    92      70.902  73.216  61.202  1.00  0.00              
ATOM     31  C   LEU    92      71.001  72.550  59.830  1.00  0.00              
ATOM     32  O   LEU    92      72.038  71.973  59.501  1.00  0.00              
ATOM     33  N   ALA    93      69.951  72.651  59.010  1.00  0.00              
ATOM     34  CA  ALA    93      69.980  72.094  57.666  1.00  0.00              
ATOM     35  C   ALA    93      71.029  72.843  56.842  1.00  0.00              
ATOM     36  O   ALA    93      71.771  72.236  56.068  1.00  0.00              
ATOM     37  N   PHE    94      71.097  74.166  57.019  1.00  0.00              
ATOM     38  CA  PHE    94      72.044  75.025  56.320  1.00  0.00              
ATOM     39  C   PHE    94      73.491  74.733  56.730  1.00  0.00              
ATOM     40  O   PHE    94      74.396  74.812  55.903  1.00  0.00              
ATOM     41  N   LEU    95      73.704  74.358  57.993  1.00  0.00              
ATOM     42  CA  LEU    95      75.021  74.031  58.524  1.00  0.00              
ATOM     43  C   LEU    95      75.412  72.619  58.096  1.00  0.00              
ATOM     44  O   LEU    95      76.598  72.363  57.912  1.00  0.00              
ATOM     45  N   LYS    96      74.452  71.702  57.940  1.00  0.00              
ATOM     46  CA  LYS    96      74.762  70.328  57.560  1.00  0.00              
ATOM     47  C   LYS    96      75.114  70.215  56.075  1.00  0.00              
ATOM     48  O   LYS    96      75.834  69.299  55.683  1.00  0.00              
ATOM     49  N   GLU    97      74.589  71.129  55.251  1.00  0.00              
ATOM     50  CA  GLU    97      74.774  71.121  53.807  1.00  0.00              
ATOM     51  C   GLU    97      75.931  71.999  53.335  1.00  0.00              
ATOM     52  O   GLU    97      76.471  71.751  52.259  1.00  0.00              
ATOM     53  N   PRO    98      76.317  73.018  54.115  1.00  0.00              
ATOM     54  CA  PRO    98      77.398  73.906  53.711  1.00  0.00              
ATOM     55  C   PRO    98      78.757  73.257  53.976  1.00  0.00              
ATOM     56  O   PRO    98      79.688  73.451  53.195  1.00  0.00              
ATOM     57  N   GLU    99      78.859  72.454  55.041  1.00  0.00              
ATOM     58  CA  GLU    99      80.073  71.708  55.381  1.00  0.00              
ATOM     59  C   GLU    99      79.757  70.695  56.484  1.00  0.00              
ATOM     60  O   GLU    99      78.907  70.994  57.315  1.00  0.00              
ATOM     61  N   PRO   100      80.407  69.518  56.536  1.00  0.00              
ATOM     62  CA  PRO   100      80.168  68.529  57.583  1.00  0.00              
ATOM     63  C   PRO   100      80.611  69.140  58.923  1.00  0.00              
ATOM     64  O   PRO   100      81.803  69.387  59.094  1.00  0.00              
ATOM     65  N   PRO   101      79.693  69.426  59.865  1.00  0.00              
ATOM     66  CA  PRO   101      80.014  70.074  61.125  1.00  0.00              
ATOM     67  C   PRO   101      80.228  69.089  62.288  1.00  0.00              
ATOM     68  O   PRO   101      79.257  68.547  62.813  1.00  0.00              
ATOM     69  N   LYS   102      81.472  68.849  62.746  1.00  0.00              
ATOM     70  CA  LYS   102      81.726  67.972  63.882  1.00  0.00              
ATOM     71  C   LYS   102      81.312  68.683  65.179  1.00  0.00              
ATOM     72  O   LYS   102      80.795  68.060  66.102  1.00  0.00              
ATOM     73  N   GLY   103      81.536  70.002  65.232  1.00  0.00              
ATOM     74  CA  GLY   103      81.206  70.870  66.355  1.00  0.00              
ATOM     75  C   GLY   103      79.723  70.761  66.670  1.00  0.00              
ATOM     76  O   GLY   103      79.355  70.591  67.825  1.00  0.00              
ATOM     77  N   PHE   104      78.884  70.843  65.637  1.00  0.00              
ATOM     78  CA  PHE   104      77.436  70.693  65.747  1.00  0.00              
ATOM     79  C   PHE   104      77.102  69.474  66.610  1.00  0.00              
ATOM     80  O   PHE   104      76.268  69.559  67.505  1.00  0.00              
ATOM     81  N   ARG   105      77.776  68.353  66.352  1.00  0.00              
ATOM     82  CA  ARG   105      77.579  67.110  67.093  1.00  0.00              
ATOM     83  C   ARG   105      77.877  67.302  68.584  1.00  0.00              
ATOM     84  O   ARG   105      77.213  66.722  69.440  1.00  0.00              
ATOM     85  N   ASP   106      78.871  68.137  68.889  1.00  0.00              
ATOM     86  CA  ASP   106      79.272  68.474  70.240  1.00  0.00              
ATOM     87  C   ASP   106      78.244  69.443  70.820  1.00  0.00              
ATOM     88  O   ASP   106      77.950  69.371  72.006  1.00  0.00              
ATOM     89  N   LEU   107      77.651  70.322  70.002  1.00  0.00              
ATOM     90  CA  LEU   107      76.601  71.217  70.454  1.00  0.00              
ATOM     91  C   LEU   107      75.456  70.329  70.949  1.00  0.00              
ATOM     92  O   LEU   107      74.882  70.566  72.011  1.00  0.00              
ATOM     93  N   PHE   108      75.158  69.279  70.182  1.00  0.00              
ATOM     94  CA  PHE   108      74.100  68.339  70.532  1.00  0.00              
ATOM     95  C   PHE   108      74.402  67.513  71.770  1.00  0.00              
ATOM     96  O   PHE   108      73.474  67.002  72.391  1.00  0.00              
ATOM     97  N   ASP   109      75.680  67.368  72.111  1.00  0.00              
ATOM     98  CA  ASP   109      76.099  66.600  73.270  1.00  0.00              
ATOM     99  C   ASP   109      76.204  67.526  74.478  1.00  0.00              
ATOM    100  O   ASP   109      76.098  67.069  75.613  1.00  0.00              
ATOM    101  N   LYS   110      76.390  68.831  74.238  1.00  0.00              
ATOM    102  CA  LYS   110      76.473  69.802  75.314  1.00  0.00              
ATOM    103  C   LYS   110      75.088  70.057  75.912  1.00  0.00              
ATOM    104  O   LYS   110      74.955  70.196  77.125  1.00  0.00              
ATOM    105  N   LEU   111      74.070  70.127  75.046  1.00  0.00              
ATOM    106  CA  LEU   111      72.682  70.376  75.409  1.00  0.00              
ATOM    107  C   LEU   111      72.160  69.427  76.510  1.00  0.00              
ATOM    108  O   LEU   111      71.878  69.899  77.611  1.00  0.00              
ATOM    109  N   PRO   112      72.009  68.114  76.272  1.00  0.00              
ATOM    110  CA  PRO   112      71.519  67.163  77.256  1.00  0.00              
ATOM    111  C   PRO   112      72.643  66.702  78.190  1.00  0.00              
ATOM    112  O   PRO   112      73.800  66.612  77.786  1.00  0.00              
ATOM    113  N   GLN   113      72.284  66.389  79.440  1.00  0.00              
ATOM    114  CA  GLN   113      73.191  65.920  80.471  1.00  0.00              
ATOM    115  C   GLN   113      72.666  64.606  81.062  1.00  0.00              
ATOM    116  O   GLN   113      73.410  63.634  81.185  1.00  0.00              
ATOM    117  N   PHE   114      71.378  64.578  81.427  1.00  0.00              
ATOM    118  CA  PHE   114      70.722  63.418  82.018  1.00  0.00              
ATOM    119  C   PHE   114      70.805  62.232  81.065  1.00  0.00              
ATOM    120  O   PHE   114      71.135  61.122  81.476  1.00  0.00              
ATOM    121  N   LYS   115      70.502  62.488  79.790  1.00  0.00              
ATOM    122  CA  LYS   115      70.524  61.480  78.737  1.00  0.00              
ATOM    123  C   LYS   115      71.826  60.676  78.768  1.00  0.00              
ATOM    124  O   LYS   115      71.798  59.445  78.765  1.00  0.00              
ATOM    125  N   GLN   116      72.963  61.380  78.816  1.00  0.00              
ATOM    126  CA  GLN   116      74.270  60.748  78.857  1.00  0.00              
ATOM    127  C   GLN   116      74.420  59.843  80.080  1.00  0.00              
ATOM    128  O   GLN   116      75.026  58.775  79.990  1.00  0.00              
ATOM    129  N   VAL   117      73.856  60.263  81.215  1.00  0.00              
ATOM    130  CA  VAL   117      73.916  59.486  82.446  1.00  0.00              
ATOM    131  C   VAL   117      73.158  58.163  82.296  1.00  0.00              
ATOM    132  O   VAL   117      73.637  57.144  82.790  1.00  0.00              
END
