
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0301AL044_1-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   27 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_1-D2.T0301_D2.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:    21       194 - 219         4.83    10.83
  LCS_AVERAGE:      9.27

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       210 - 217         1.69    15.48
  LCS_AVERAGE:      2.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       212 - 216         0.67    16.74
  LCS_AVERAGE:      1.80

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:  191
LCS_GDT     T     194     T     194      3    5   21     0    3    3    4    4    5    6    8   13   15   17   17   20   20   21   21   21   21   21   22 
LCS_GDT     G     195     G     195      3    5   21     0    3    4    5    5    6    8   11   13   15   17   17   20   20   21   21   21   21   21   22 
LCS_GDT     N     196     N     196      3    5   21     0    3    4    5    5    6    8   11   13   15   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     L     197     L     197      4    5   21     5    5    5    6    6    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     V     198     V     198      4    5   21     5    5    5    6    6    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     D     199     D     199      4    5   21     5    5    5    6    6    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     D     200     D     200      4    5   21     5    5    5    6    6    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     V     203     V     203      4    5   21     4    4    5    5    6    6    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     P     204     P     204      4    5   21     4    4    5    5    6    6    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     G     205     G     205      4    5   21     4    4    5    5    6    6    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     V     206     V     206      4    5   21     4    4    5    5    6    6    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     T     208     T     208      0    5   21     1    3    4    6    6    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     K     210     K     210      0    7   21     5    5    5    6    7    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     T     212     T     212      5    7   21     3    4    5    5    7    7    9   10   13   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     M     213     M     213      5    7   21     3    4    5    5    7    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     I     214     I     214      5    7   21     3    4    5    5    7    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     N     215     N     215      5    7   21     3    4    5    5    7    8    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     A     216     A     216      5    7   21     3    4    5    5    7    7    7    9   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     G     217     G     217      3    7   21     3    3    5    5    7    7    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     I     218     I     218      3    4   21     3    4    5    5    6    7    9   12   14   16   18   18   20   20   21   21   21   21   21   22 
LCS_GDT     P     219     P     219      3    4   21     3    3    3    3    4    4    5    5    5    5    5   10   11   16   21   21   21   21   21   22 
LCS_GDT     T     220     T     220      3    4    7     3    3    3    3    4    4    5    5    5    5    5    5    6    6    8    8   14   16   17   22 
LCS_GDT     E     227     E     227      3    5    6     0    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    8    8    8    8 
LCS_GDT     I     228     I     228      3    5    6     1    3    3    4    4    5    5    5    5    5    5    5    5    5    6   11   13   13   13   16 
LCS_GDT     G     229     G     229      3    5    6     2    3    3    4    4    5    5    5    5    5    5    5    6    7    9   11   13   13   13   14 
LCS_GDT     Y     230     Y     230      3    5    6     0    3    3    4    4    5    5    5    5    5    5    5    6    7    9   11   13   13   13   14 
LCS_GDT     R     231     R     231      3    5    6     2    3    3    3    4    5    5    5    5    5    5    5    5    5    6    6   13   13   15   15 
LCS_AVERAGE  LCS_A:   4.63  (   1.80    2.83    9.27 )

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      5      5      5      6      7      8      9     12     14     16     18     18     20     20     21     21     21     21     21     22 
GDT PERCENT_CA   2.62   2.62   2.62   3.14   3.66   4.19   4.71   6.28   7.33   8.38   9.42   9.42  10.47  10.47  10.99  10.99  10.99  10.99  10.99  11.52
GDT RMS_LOCAL    0.26   0.26   0.26   1.13   1.69   1.87   2.13   3.09   3.71   3.83   4.15   4.15   4.63   4.63   4.83   4.83   4.83   4.83   4.83   5.39
GDT RMS_ALL_CA  12.91  12.91  12.91  12.83  15.48  14.19  13.79  10.60  11.54  11.14  11.01  11.01  10.93  10.93  10.83  10.83  10.83  10.83  10.83  10.46

#      Molecule1      Molecule2       DISTANCE
LGA    T     194      T     194          9.718
LGA    G     195      G     195         10.946
LGA    N     196      N     196          8.603
LGA    L     197      L     197          3.800
LGA    V     198      V     198          2.755
LGA    D     199      D     199          3.331
LGA    D     200      D     200          2.822
LGA    V     203      V     203          3.226
LGA    P     204      P     204          3.252
LGA    G     205      G     205          3.259
LGA    V     206      V     206          3.590
LGA    T     208      T     208          0.881
LGA    K     210      K     210          3.053
LGA    T     212      T     212          6.799
LGA    M     213      M     213          6.492
LGA    I     214      I     214          6.870
LGA    N     215      N     215          7.277
LGA    A     216      A     216          5.122
LGA    G     217      G     217          3.629
LGA    I     218      I     218          2.373
LGA    P     219      P     219          8.147
LGA    T     220      T     220         11.939
LGA    E     227      E     227         26.550
LGA    I     228      I     228         22.073
LGA    G     229      G     229         21.365
LGA    Y     230      Y     230         17.493
LGA    R     231      R     231         15.877

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  191    4.0     12    3.09     5.759     5.172     0.376

LGA_LOCAL      RMSD =  3.089  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.599  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  9.173  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.581122 * X  +   0.659186 * Y  +   0.477254 * Z  +  71.953972
  Y_new =  -0.452256 * X  +   0.225965 * Y  +  -0.862789 * Z  +  39.905556
  Z_new =  -0.676580 * X  +  -0.717227 * Y  +   0.166808 * Z  +  39.879768 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.342286    1.799307  [ DEG:   -76.9073    103.0927 ]
  Theta =   0.743109    2.398484  [ DEG:    42.5770    137.4230 ]
  Phi   =  -2.480258    0.661335  [ DEG:  -142.1083     37.8917 ]
 
# 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: T0301AL044_1-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_1-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  191   4.0   12   3.09   5.172     9.17
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_1-D2
REMARK Aligment from pdb entry: 2azp_A
ATOM    281  N   THR   194      92.531   2.917   5.484  1.00  0.00              
ATOM    282  CA  THR   194      93.020   1.578   5.786  1.00  0.00              
ATOM    283  C   THR   194      93.385   1.488   7.256  1.00  0.00              
ATOM    284  O   THR   194      93.828   2.464   7.857  1.00  0.00              
ATOM    285  N   GLY   195      93.197   0.309   7.833  1.00  0.00              
ATOM    286  CA  GLY   195      93.484   0.108   9.245  1.00  0.00              
ATOM    287  C   GLY   195      94.666  -0.814   9.501  1.00  0.00              
ATOM    288  O   GLY   195      94.969  -1.691   8.699  1.00  0.00              
ATOM    289  N   ASN   196      95.316  -0.602  10.640  1.00  0.00              
ATOM    290  CA  ASN   196      96.458  -1.403  11.059  1.00  0.00              
ATOM    291  C   ASN   196      97.354  -1.849   9.912  1.00  0.00              
ATOM    292  O   ASN   196      97.553  -3.040   9.684  1.00  0.00              
ATOM    293  N   LEU   197      97.895  -0.874   9.194  1.00  0.00              
ATOM    294  CA  LEU   197      98.786  -1.138   8.078  1.00  0.00              
ATOM    295  C   LEU   197     100.207  -1.212   8.619  1.00  0.00              
ATOM    296  O   LEU   197     100.690  -0.265   9.239  1.00  0.00              
ATOM    297  N   VAL   198     100.870  -2.342   8.395  1.00  0.00              
ATOM    298  CA  VAL   198     102.236  -2.528   8.870  1.00  0.00              
ATOM    299  C   VAL   198     103.247  -2.128   7.811  1.00  0.00              
ATOM    300  O   VAL   198     103.079  -2.434   6.633  1.00  0.00              
ATOM    301  N   ASP   199     104.298  -1.441   8.239  1.00  0.00              
ATOM    302  CA  ASP   199     105.340  -0.997   7.322  1.00  0.00              
ATOM    303  C   ASP   199     106.720  -1.215   7.924  1.00  0.00              
ATOM    304  O   ASP   199     106.950  -0.914   9.096  1.00  0.00              
ATOM    305  N   ASP   200     107.634  -1.747   7.120  1.00  0.00              
ATOM    306  CA  ASP   200     108.997  -1.966   7.575  1.00  0.00              
ATOM    307  C   ASP   200     109.738  -0.656   7.371  1.00  0.00              
ATOM    308  O   ASP   200     109.992  -0.252   6.236  1.00  0.00              
ATOM    309  N   VAL   203     110.078   0.011   8.467  1.00  0.00              
ATOM    310  CA  VAL   203     110.776   1.288   8.383  1.00  0.00              
ATOM    311  C   VAL   203     112.251   1.171   8.756  1.00  0.00              
ATOM    312  O   VAL   203     112.596   0.756   9.860  1.00  0.00              
ATOM    313  N   PRO   204     113.144   1.532   7.827  1.00  0.00              
ATOM    314  CA  PRO   204     114.585   1.464   8.078  1.00  0.00              
ATOM    315  C   PRO   204     114.995   2.251   9.320  1.00  0.00              
ATOM    316  O   PRO   204     114.601   3.407   9.494  1.00  0.00              
ATOM    317  N   GLY   205     115.784   1.616  10.181  1.00  0.00              
ATOM    318  CA  GLY   205     116.247   2.272  11.389  1.00  0.00              
ATOM    319  C   GLY   205     115.292   2.153  12.558  1.00  0.00              
ATOM    320  O   GLY   205     115.648   2.472  13.694  1.00  0.00              
ATOM    321  N   VAL   206     114.075   1.696  12.288  1.00  0.00              
ATOM    322  CA  VAL   206     113.079   1.545  13.340  1.00  0.00              
ATOM    323  C   VAL   206     112.548   0.120  13.381  1.00  0.00              
ATOM    324  O   VAL   206     112.417  -0.475  14.450  1.00  0.00              
ATOM    325  N   THR   208     112.242  -0.422  12.208  1.00  0.00              
ATOM    326  CA  THR   208     111.707  -1.766  12.131  1.00  0.00              
ATOM    327  C   THR   208     110.252  -1.712  11.713  1.00  0.00              
ATOM    328  O   THR   208     109.831  -0.784  11.018  1.00  0.00              
ATOM    329  N   LYS   210     109.477  -2.700  12.145  1.00  0.00              
ATOM    330  CA  LYS   210     108.063  -2.768  11.809  1.00  0.00              
ATOM    331  C   LYS   210     107.215  -1.748  12.557  1.00  0.00              
ATOM    332  O   LYS   210     107.232  -1.681  13.787  1.00  0.00              
ATOM    333  N   THR   212     106.472  -0.958  11.790  1.00  0.00              
ATOM    334  CA  THR   212     105.591   0.071  12.326  1.00  0.00              
ATOM    335  C   THR   212     104.218  -0.102  11.691  1.00  0.00              
ATOM    336  O   THR   212     104.116  -0.325  10.487  1.00  0.00              
ATOM    337  N   MET   213     103.162  -0.006  12.490  1.00  0.00              
ATOM    338  CA  MET   213     101.819  -0.143  11.938  1.00  0.00              
ATOM    339  C   MET   213     100.929   1.006  12.394  1.00  0.00              
ATOM    340  O   MET   213     101.114   1.557  13.479  1.00  0.00              
ATOM    341  N   ILE   214      99.964   1.369  11.558  1.00  0.00              
ATOM    342  CA  ILE   214      99.066   2.448  11.914  1.00  0.00              
ATOM    343  C   ILE   214      97.933   2.586  10.925  1.00  0.00              
ATOM    344  O   ILE   214      97.846   1.829   9.956  1.00  0.00              
ATOM    345  N   ASN   215      97.057   3.553  11.168  1.00  0.00              
ATOM    346  CA  ASN   215      95.933   3.786  10.281  1.00  0.00              
ATOM    347  C   ASN   215      96.258   4.877   9.282  1.00  0.00              
ATOM    348  O   ASN   215      97.060   5.767   9.559  1.00  0.00              
ATOM    349  N   ALA   216      95.632   4.794   8.116  1.00  0.00              
ATOM    350  CA  ALA   216      95.798   5.788   7.072  1.00  0.00              
ATOM    351  C   ALA   216      94.428   6.442   6.976  1.00  0.00              
ATOM    352  O   ALA   216      93.458   5.800   6.571  1.00  0.00              
ATOM    353  N   GLY   217      94.341   7.713   7.360  1.00  0.00              
ATOM    354  CA  GLY   217      93.063   8.407   7.333  1.00  0.00              
ATOM    355  C   GLY   217      93.120   9.795   6.711  1.00  0.00              
ATOM    356  O   GLY   217      94.158  10.451   6.703  1.00  0.00              
ATOM    357  N   ILE   218      91.980  10.235   6.195  1.00  0.00              
ATOM    358  CA  ILE   218      91.871  11.544   5.579  1.00  0.00              
ATOM    359  C   ILE   218      91.140  12.501   6.511  1.00  0.00              
ATOM    360  O   ILE   218      90.100  12.156   7.078  1.00  0.00              
ATOM    361  N   PRO   219      91.697  13.699   6.667  1.00  0.00              
ATOM    362  CA  PRO   219      91.087  14.712   7.510  1.00  0.00              
ATOM    363  C   PRO   219      91.245  16.087   6.887  1.00  0.00              
ATOM    364  O   PRO   219      91.130  17.104   7.565  1.00  0.00              
ATOM    365  N   THR   220      91.492  16.116   5.582  1.00  0.00              
ATOM    366  CA  THR   220      91.695  17.376   4.887  1.00  0.00              
ATOM    367  C   THR   220      93.073  17.305   4.261  1.00  0.00              
ATOM    368  O   THR   220      93.458  18.143   3.442  1.00  0.00              
ATOM    369  N   GLU   227      93.811  16.283   4.691  1.00  0.00              
ATOM    370  CA  GLU   227      95.155  15.947   4.223  1.00  0.00              
ATOM    371  C   GLU   227      95.273  14.481   4.632  1.00  0.00              
ATOM    372  O   GLU   227      94.506  14.018   5.481  1.00  0.00              
ATOM    373  N   ILE   228      96.217  13.754   4.042  1.00  0.00              
ATOM    374  CA  ILE   228      96.409  12.351   4.392  1.00  0.00              
ATOM    375  C   ILE   228      97.348  12.210   5.580  1.00  0.00              
ATOM    376  O   ILE   228      98.415  12.832   5.627  1.00  0.00              
ATOM    377  N   GLY   229      96.937  11.389   6.541  1.00  0.00              
ATOM    378  CA  GLY   229      97.724  11.148   7.736  1.00  0.00              
ATOM    379  C   GLY   229      97.935   9.665   7.969  1.00  0.00              
ATOM    380  O   GLY   229      97.122   8.828   7.568  1.00  0.00              
ATOM    381  N   TYR   230      99.043   9.351   8.621  1.00  0.00              
ATOM    382  CA  TYR   230      99.356   7.988   9.001  1.00  0.00              
ATOM    383  C   TYR   230      99.427   8.098  10.517  1.00  0.00              
ATOM    384  O   TYR   230     100.320   8.757  11.051  1.00  0.00              
ATOM    385  N   ARG   231      98.466   7.494  11.207  1.00  0.00              
ATOM    386  CA  ARG   231      98.438   7.537  12.664  1.00  0.00              
ATOM    387  C   ARG   231      99.114   6.284  13.197  1.00  0.00              
ATOM    388  O   ARG   231      98.546   5.192  13.168  1.00  0.00              
END
