
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0381AL242_2-D2
# Molecule2: number of CA atoms  176 ( 1314),  selected   19 , name T0381_D2.pdb
# PARAMETERS: T0381AL242_2-D2.T0381_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:    19        90 - 108         1.55     1.55
  LCS_AVERAGE:     10.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        90 - 108         1.55     1.55
  LCS_AVERAGE:     10.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        91 - 106         1.00     1.72
  LONGEST_CONTINUOUS_SEGMENT:    16        92 - 107         0.91     1.61
  LONGEST_CONTINUOUS_SEGMENT:    16        93 - 108         0.89     1.58
  LCS_AVERAGE:      8.70

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:  176
LCS_GDT     L      90     L      90      3   19   19     0    3   14   14   15   17   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     S      91     S      91     16   19   19     7    9   15   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L      92     L      92     16   19   19     7    9   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     P      93     P      93     16   19   19     7   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E      94     E      94     16   19   19     7   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V      95     V      95     16   19   19     7    9   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     A      96     A      96     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q      97     Q      97     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     P      98     P      98     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H      99     H      99     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     100     L     100     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     E     101     E     101     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     102     K     102     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     103     L     103     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     S     104     S     104     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H     105     H     105     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     106     K     106     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     V     107     V     107     16   19   19     9   12   16   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_GDT     H     108     H     108     16   19   19     3    3   14   17   18   18   18   19   19   19   19   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  10.10  (   8.70   10.80   10.80 )

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      9     12     16     17     18     18     18     19     19     19     19     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   5.11   6.82   9.09   9.66  10.23  10.23  10.23  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80  10.80
GDT RMS_LOCAL    0.19   0.42   0.91   1.01   1.12   1.12   1.12   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55
GDT RMS_ALL_CA   2.00   1.76   1.61   1.69   1.64   1.64   1.64   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55   1.55

#      Molecule1      Molecule2       DISTANCE
LGA    L      90      L      90          3.694
LGA    S      91      S      91          3.452
LGA    L      92      L      92          2.685
LGA    P      93      P      93          1.773
LGA    E      94      E      94          1.179
LGA    V      95      V      95          1.767
LGA    A      96      A      96          0.156
LGA    Q      97      Q      97          0.840
LGA    P      98      P      98          0.846
LGA    H      99      H      99          0.499
LGA    L     100      L     100          0.416
LGA    E     101      E     101          0.334
LGA    K     102      K     102          0.696
LGA    L     103      L     103          0.488
LGA    S     104      S     104          0.118
LGA    H     105      H     105          0.633
LGA    K     106      K     106          0.603
LGA    V     107      V     107          0.951
LGA    H     108      H     108          1.692

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  176    4.0     19    1.55     9.517    10.170     1.151

LGA_LOCAL      RMSD =  1.550  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.584  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  1.550  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.464985 * X  +   0.784210 * Y  +  -0.410858 * Z  +   2.112241
  Y_new =   0.657739 * X  +   0.004632 * Y  +   0.753232 * Z  +   3.301332
  Z_new =   0.592595 * X  +  -0.620478 * Y  +  -0.513652 * Z  +  11.774314 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.262279    0.879314  [ DEG:  -129.6190     50.3810 ]
  Theta =  -0.634276   -2.507316  [ DEG:   -36.3414   -143.6586 ]
  Phi   =   0.955425   -2.186168  [ DEG:    54.7418   -125.2582 ]
 
# 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: T0381AL242_2-D2                               
REMARK     2: T0381_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381AL242_2-D2.T0381_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  176   4.0   19   1.55  10.170     1.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL242_2-D2
REMARK Aligment from pdb entry: 1r7j_A
ATOM    285  N   LEU    90      21.136  28.088  24.435  1.00  0.00              
ATOM    286  CA  LEU    90      21.481  28.517  25.785  1.00  0.00              
ATOM    287  C   LEU    90      20.492  29.534  26.330  1.00  0.00              
ATOM    288  O   LEU    90      20.209  29.543  27.527  1.00  0.00              
ATOM    289  N   SER    91      19.969  30.388  25.459  1.00  0.00              
ATOM    290  CA  SER    91      19.001  31.390  25.886  1.00  0.00              
ATOM    291  C   SER    91      17.706  30.673  26.261  1.00  0.00              
ATOM    292  O   SER    91      17.039  31.040  27.230  1.00  0.00              
ATOM    293  N   LEU    92      17.360  29.639  25.500  1.00  0.00              
ATOM    294  CA  LEU    92      16.153  28.870  25.783  1.00  0.00              
ATOM    295  C   LEU    92      16.286  28.211  27.147  1.00  0.00              
ATOM    296  O   LEU    92      15.329  28.175  27.926  1.00  0.00              
ATOM    297  N   PRO    93      17.470  27.683  27.433  1.00  0.00              
ATOM    298  CA  PRO    93      17.713  27.022  28.708  1.00  0.00              
ATOM    299  C   PRO    93      17.550  28.011  29.852  1.00  0.00              
ATOM    300  O   PRO    93      16.942  27.695  30.877  1.00  0.00              
ATOM    301  N   GLU    94      18.095  29.209  29.677  1.00  0.00              
ATOM    302  CA  GLU    94      17.998  30.245  30.696  1.00  0.00              
ATOM    303  C   GLU    94      16.537  30.577  30.983  1.00  0.00              
ATOM    304  O   GLU    94      16.122  30.638  32.145  1.00  0.00              
ATOM    305  N   VAL    95      15.755  30.795  29.929  1.00  0.00              
ATOM    306  CA  VAL    95      14.341  31.125  30.099  1.00  0.00              
ATOM    307  C   VAL    95      13.570  29.965  30.707  1.00  0.00              
ATOM    308  O   VAL    95      12.651  30.169  31.499  1.00  0.00              
ATOM    309  N   ALA    96      13.934  28.746  30.332  1.00  0.00              
ATOM    310  CA  ALA    96      13.258  27.576  30.871  1.00  0.00              
ATOM    311  C   ALA    96      13.546  27.462  32.364  1.00  0.00              
ATOM    312  O   ALA    96      12.632  27.245  33.161  1.00  0.00              
ATOM    313  N   GLN    97      14.812  27.608  32.745  1.00  0.00              
ATOM    314  CA  GLN    97      15.188  27.524  34.155  1.00  0.00              
ATOM    315  C   GLN    97      14.435  28.565  34.973  1.00  0.00              
ATOM    316  O   GLN    97      14.000  28.284  36.091  1.00  0.00              
ATOM    317  N   PRO    98      14.283  29.768  34.426  1.00  0.00              
ATOM    318  CA  PRO    98      13.585  30.814  35.156  1.00  0.00              
ATOM    319  C   PRO    98      12.105  30.491  35.302  1.00  0.00              
ATOM    320  O   PRO    98      11.521  30.728  36.361  1.00  0.00              
ATOM    321  N   HIS    99      11.498  29.942  34.253  1.00  0.00              
ATOM    322  CA  HIS    99      10.083  29.589  34.313  1.00  0.00              
ATOM    323  C   HIS    99       9.887  28.453  35.311  1.00  0.00              
ATOM    324  O   HIS    99       8.858  28.386  35.985  1.00  0.00              
ATOM    325  N   LEU   100      10.871  27.563  35.414  1.00  0.00              
ATOM    326  CA  LEU   100      10.781  26.465  36.364  1.00  0.00              
ATOM    327  C   LEU   100      10.791  27.035  37.783  1.00  0.00              
ATOM    328  O   LEU   100      10.102  26.524  38.659  1.00  0.00              
ATOM    329  N   GLU   101      11.563  28.095  38.003  1.00  0.00              
ATOM    330  CA  GLU   101      11.618  28.718  39.323  1.00  0.00              
ATOM    331  C   GLU   101      10.255  29.335  39.635  1.00  0.00              
ATOM    332  O   GLU   101       9.792  29.294  40.777  1.00  0.00              
ATOM    333  N   LYS   102       9.611  29.903  38.621  1.00  0.00              
ATOM    334  CA  LYS   102       8.300  30.525  38.802  1.00  0.00              
ATOM    335  C   LYS   102       7.297  29.451  39.204  1.00  0.00              
ATOM    336  O   LYS   102       6.539  29.613  40.163  1.00  0.00              
ATOM    337  N   LEU   103       7.305  28.349  38.467  1.00  0.00              
ATOM    338  CA  LEU   103       6.410  27.233  38.733  1.00  0.00              
ATOM    339  C   LEU   103       6.656  26.677  40.133  1.00  0.00              
ATOM    340  O   LEU   103       5.711  26.466  40.899  1.00  0.00              
ATOM    341  N   SER   104       7.919  26.453  40.479  1.00  0.00              
ATOM    342  CA  SER   104       8.223  25.916  41.796  1.00  0.00              
ATOM    343  C   SER   104       7.811  26.851  42.926  1.00  0.00              
ATOM    344  O   SER   104       7.388  26.388  43.982  1.00  0.00              
ATOM    345  N   HIS   105       7.916  28.159  42.710  1.00  0.00              
ATOM    346  CA  HIS   105       7.536  29.119  43.745  1.00  0.00              
ATOM    347  C   HIS   105       6.042  29.034  44.057  1.00  0.00              
ATOM    348  O   HIS   105       5.628  29.230  45.200  1.00  0.00              
ATOM    349  N   LYS   106       5.237  28.744  43.041  1.00  0.00              
ATOM    350  CA  LYS   106       3.791  28.632  43.223  1.00  0.00              
ATOM    351  C   LYS   106       3.451  27.344  43.967  1.00  0.00              
ATOM    352  O   LYS   106       2.529  27.314  44.783  1.00  0.00              
ATOM    353  N   VAL   107       4.200  26.284  43.690  1.00  0.00              
ATOM    354  CA  VAL   107       3.962  24.989  44.319  1.00  0.00              
ATOM    355  C   VAL   107       4.742  24.807  45.611  1.00  0.00              
ATOM    356  O   VAL   107       4.546  23.828  46.328  1.00  0.00              
ATOM    357  N   HIS   108       5.624  25.754  45.906  1.00  0.00              
ATOM    358  CA  HIS   108       6.449  25.682  47.106  1.00  0.00              
ATOM    359  C   HIS   108       7.275  26.951  47.256  1.00  0.00              
ATOM    360  O   HIS   108       8.517  26.858  47.167  1.00  0.00              
END
