
#######################################################
#                                                     #
#                        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   24 (  118),  selected   19 , name T0342TS239_3_3
# Molecule2: number of CA atoms  169 ( 1343),  selected   19 , name T0342.pdb
# PARAMETERS: T0342TS239_3_3.T0342.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:    12       155 - 170         4.21    15.41
  LCS_AVERAGE:      5.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       155 - 165         1.80    16.75
  LCS_AVERAGE:      4.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       155 - 163         0.75    16.31
  LCS_AVERAGE:      3.43

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:  169
LCS_GDT     E      14     E      14      0    0    7     0    0    1    1    1    2    2    3    3    3    5    6    6    8   10   10   11   11   12   12 
LCS_GDT     E      15     E      15      0    0   10     0    0    0    0    0    2    2    3    3    3    4    4    5    7    7    9   11   11   11   12 
LCS_GDT     E     155     E     155      9   11   12     4    7    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     Y     156     Y     156      9   11   12     5    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     Q     157     Q     157      9   11   12     5    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     E     158     E     158      9   11   12     6    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     K     159     K     159      9   11   12     6    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     L     160     L     160      9   11   12     6    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     K     161     K     161      9   11   12     6    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     A     162     A     162      9   11   12     6    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     I     163     I     163      9   11   12     6    8    9    9   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     E     164     E     164      3   11   12     3    3    3    7    8   10   10   11   11   11   11   11   11   11   11   12   13   14   15   15 
LCS_GDT     P     165     P     165      3   11   12     3    3    3    8   10   10   10   11   11   11   11   11   11   11   11   13   13   14   15   15 
LCS_GDT     G     170     G     170      3    4   12     0    3    3    3    4    4    4    5    6    6    6    6    7   10   11   13   13   14   15   15 
LCS_GDT     K     171     K     171      4    5    6     3    3    4    5    5    5    5    5    6    6    6    6    6    6    8   11   12   14   15   15 
LCS_GDT     V     172     V     172      4    5    6     3    4    4    5    5    5    5    5    6    8    9   11   11   11   11   13   13   14   15   15 
LCS_GDT     S     173     S     173      4    5    6     3    4    4    5    5    5    5    5    6    6    6    6    7    9   11   13   13   14   15   15 
LCS_GDT     E     174     E     174      4    5    6     3    4    4    5    5    5    5    5    6    6    6    6    6    6    7    8   11   12   14   15 
LCS_GDT     E     175     E     175      4    5    6     3    4    4    5    5    5    5    5    6    6    6    6    6    6    7    8    9   12   14   15 
LCS_AVERAGE  LCS_A:   4.68  (   3.43    4.67    5.95 )

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      6      8      9      9     10     10     10     11     11     11     11     11     11     11     11     13     13     14     15     15 
GDT PERCENT_CA   3.55   4.73   5.33   5.33   5.92   5.92   5.92   6.51   6.51   6.51   6.51   6.51   6.51   6.51   6.51   7.69   7.69   8.28   8.88   8.88
GDT RMS_LOCAL    0.42   0.58   0.75   0.75   1.21   1.21   1.21   1.80   1.80   1.80   1.80   1.80   1.80   1.80   1.80   5.39   5.39   5.65   6.15   6.15
GDT RMS_ALL_CA  15.78  16.25  16.31  16.31  17.00  17.00  17.00  16.75  16.75  16.75  16.75  16.75  16.75  16.75  16.75  19.53  19.53  19.74  18.96  18.96

#      Molecule1      Molecule2       DISTANCE
LGA    E      14      E      14         38.422
LGA    E      15      E      15         43.665
LGA    E     155      E     155          2.509
LGA    Y     156      Y     156          1.021
LGA    Q     157      Q     157          0.911
LGA    E     158      E     158          0.486
LGA    K     159      K     159          0.721
LGA    L     160      L     160          1.042
LGA    K     161      K     161          0.782
LGA    A     162      A     162          1.106
LGA    I     163      I     163          0.994
LGA    E     164      E     164          3.861
LGA    P     165      P     165          3.175
LGA    G     170      G     170         16.219
LGA    K     171      K     171         14.993
LGA    V     172      V     172         12.739
LGA    S     173      S     173         17.765
LGA    E     174      E     174         22.866
LGA    E     175      E     175         22.479

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  169    4.0     11    1.80     6.065     5.691     0.579

LGA_LOCAL      RMSD =  1.801  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.881  Number of atoms =   19 
Std_ALL_ATOMS  RMSD = 12.025  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.610705 * X  +  -0.592766 * Y  +   0.525041 * Z  +  26.111750
  Y_new =   0.345495 * X  +  -0.796072 * Y  +  -0.496893 * Z  +  79.214737
  Z_new =   0.712512 * X  +  -0.122057 * Y  +   0.690963 * Z  +   6.981903 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.174844    2.966749  [ DEG:   -10.0178    169.9822 ]
  Theta =  -0.793071   -2.348521  [ DEG:   -45.4396   -134.5604 ]
  Phi   =   2.626753   -0.514840  [ DEG:   150.5018    -29.4982 ]
 
# 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: T0342TS239_3_3                                
REMARK     2: T0342.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0342TS239_3_3.T0342.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  169   4.0   11   1.80   5.691    12.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS239_3_3
REMARK PARENT number 3
PFRMAT TS
TARGET T0342
PARENT 2g0q_A
ATOM      1  N   VAL     9      37.489  92.987  -6.520  1.00  9.99
ATOM      2  CA  VAL     9      38.257  92.293  -7.532  1.00  9.99
ATOM      3  C   VAL     9      39.441  93.133  -7.997  1.00  9.99
ATOM      4  O   VAL     9      39.288  94.291  -8.396  1.00  9.99
ATOM      5  CB  VAL     9      37.376  91.951  -8.719  1.00  9.99
ATOM      6  N   THR    10      40.611  92.572  -7.887  1.00  9.99
ATOM      7  CA  THR    10      41.834  93.184  -8.363  1.00  9.99
ATOM      8  C   THR    10      42.777  92.081  -8.858  1.00  9.99
ATOM      9  O   THR    10      43.977  92.285  -9.032  1.00  9.99
ATOM     10  CB  THR    10      42.471  94.006  -7.239  1.00  9.99
ATOM     11  N   GLY    11      42.191  90.925  -9.112  1.00  9.99
ATOM     12  CA  GLY    11      42.906  89.760  -9.568  1.00  9.99
ATOM     13  C   GLY    11      43.099  89.778 -11.083  1.00  9.99
ATOM     14  O   GLY    11      43.899  89.005 -11.617  1.00  9.99
ATOM     15  N   PRO    12      42.363  90.682 -11.759  1.00  9.99
ATOM     16  CA  PRO    12      42.413  90.845 -13.224  1.00  9.99
ATOM     17  C   PRO    12      41.887  89.586 -13.912  1.00  9.99
ATOM     18  O   PRO    12      42.629  88.638 -14.174  1.00  9.99
ATOM     19  CB  PRO    12      43.850  91.208 -13.698  1.00  9.99
ATOM     20  N   ASP    13      40.598  89.545 -14.144  1.00  9.99
ATOM     21  CA  ASP    13      40.006  88.398 -14.763  1.00  9.99
ATOM     22  C   ASP    13      39.596  88.628 -16.211  1.00  9.99
ATOM     23  O   ASP    13      38.431  88.865 -16.527  1.00  9.99
ATOM     24  CB  ASP    13      38.895  87.764 -13.898  1.00  9.99
ATOM     25  N   GLU    14      40.591  88.663 -17.059  1.00  9.99
ATOM     26  CA  GLU    14      40.423  88.762 -18.454  1.00  9.99
ATOM     27  C   GLU    14      40.816  87.476 -19.095  1.00  9.99
ATOM     28  O   GLU    14      40.000  86.771 -19.681  1.00  9.99
ATOM     29  CB  GLU    14      41.231  89.899 -19.004  1.00  9.99
ATOM     30  N   GLU    15      42.064  87.163 -18.950  1.00  9.99
ATOM     31  CA  GLU    15      42.614  85.894 -19.414  1.00  9.99
ATOM     32  C   GLU    15      42.652  84.915 -18.260  1.00  9.99
ATOM     33  O   GLU    15      42.886  83.718 -18.418  1.00  9.99
ATOM     34  CB  GLU    15      43.977  86.068 -20.096  1.00  9.99
ATOM    637  N   GLU   155      17.610  85.052  14.156  1.00  9.99
ATOM    638  CA  GLU   155      18.470  86.215  14.303  1.00  9.99
ATOM    639  C   GLU   155      17.716  87.489  13.908  1.00  9.99
ATOM    640  O   GLU   155      17.887  88.542  14.531  1.00  9.99
ATOM    641  CB  GLU   155      19.753  86.056  13.480  1.00  9.99
ATOM    642  N   TYR   156      16.878  87.372  12.880  1.00  9.99
ATOM    643  CA  TYR   156      16.010  88.464  12.446  1.00  9.99
ATOM    644  C   TYR   156      14.845  88.574  13.398  1.00  9.99
ATOM    645  O   TYR   156      14.408  89.661  13.749  1.00  9.99
ATOM    646  CB  TYR   156      15.458  88.214  11.036  1.00  9.99
ATOM    647  N   GLN   157      14.352  87.427  13.817  1.00  9.99
ATOM    648  CA  GLN   157      13.212  87.344  14.708  1.00  9.99
ATOM    649  C   GLN   157      13.501  88.051  16.033  1.00  9.99
ATOM    650  O   GLN   157      12.624  88.631  16.600  1.00  9.99
ATOM    651  CB  GLN   157      12.750  85.867  14.942  1.00  9.99
ATOM    652  N   GLU   158      14.752  88.020  16.483  1.00  9.99
ATOM    653  CA  GLU   158      15.180  88.704  17.722  1.00  9.99
ATOM    654  C   GLU   158      14.764  90.185  17.773  1.00  9.99
ATOM    655  O   GLU   158      14.343  90.672  18.826  1.00  9.99
ATOM    656  CB  GLU   158      16.687  88.581  17.907  1.00  9.99
ATOM    657  N   LYS   159      14.845  90.888  16.647  1.00  9.99
ATOM    658  CA  LYS   159      14.460  92.285  16.644  1.00  9.99
ATOM    659  C   LYS   159      12.925  92.394  16.689  1.00  9.99
ATOM    660  O   LYS   159      12.379  93.356  17.218  1.00  9.99
ATOM    661  CB  LYS   159      15.044  93.083  15.431  1.00  9.99
ATOM    662  N   LEU   160      12.250  91.389  16.139  1.00  9.99
ATOM    663  CA  LEU   160      10.803  91.318  16.176  1.00  9.99
ATOM    664  C   LEU   160      10.297  90.899  17.501  1.00  9.99
ATOM    665  O   LEU   160       9.276  91.373  17.930  1.00  9.99
ATOM    666  CB  LEU   160      10.217  90.433  15.089  1.00  9.99
ATOM    667  N   LYS   161      11.034  90.020  18.154  1.00  9.99
ATOM    668  CA  LYS   161      10.673  89.504  19.453  1.00  9.99
ATOM    669  C   LYS   161      10.459  90.605  20.462  1.00  9.99
ATOM    670  O   LYS   161       9.647  90.459  21.383  1.00  9.99
ATOM    671  CB  LYS   161      11.705  88.495  19.954  1.00  9.99
ATOM    672  N   ALA   162      11.178  91.717  20.316  1.00  9.99
ATOM    673  CA  ALA   162      10.948  92.801  21.232  1.00  9.99
ATOM    674  C   ALA   162       9.633  93.505  20.881  1.00  9.99
ATOM    675  O   ALA   162       8.902  93.902  21.754  1.00  9.99
ATOM    676  CB  ALA   162      12.110  93.808  21.325  1.00  9.99
ATOM    677  N   ILE   163       9.331  93.567  19.577  1.00  9.99
ATOM    678  CA  ILE   163       8.158  94.266  19.016  1.00  9.99
ATOM    679  C   ILE   163       6.820  93.785  19.631  1.00  9.99
ATOM    680  O   ILE   163       5.857  94.571  19.751  1.00  9.99
ATOM    681  CB  ILE   163       8.161  94.254  17.425  1.00  9.99
ATOM    682  N   GLU   164       6.767  92.512  20.055  1.00  9.99
ATOM    683  CA  GLU   164       5.567  91.955  20.719  1.00  9.99
ATOM    684  C   GLU   164       5.132  92.784  21.941  1.00  9.99
ATOM    685  O   GLU   164       3.953  92.770  22.305  1.00  9.99
ATOM    686  CB  GLU   164       5.722  90.472  21.145  1.00  9.99
ATOM    687  N   PRO   165       6.079  93.500  22.570  1.00  9.99
ATOM    688  CA  PRO   165       5.783  94.339  23.749  1.00  9.99
ATOM    689  C   PRO   165       4.701  95.371  23.426  1.00  9.99
ATOM    690  O   PRO   165       3.801  95.614  24.222  1.00  9.99
ATOM    691  CB  PRO   165       7.054  95.050  24.267  1.00  9.99
ATOM    692  N   GLY   170       4.796  95.950  22.241  1.00  9.99
ATOM    693  CA  GLY   170       3.865  96.954  21.780  1.00  9.99
ATOM    694  C   GLY   170       2.530  96.309  21.464  1.00  9.99
ATOM    695  O   GLY   170       1.468  96.901  21.651  1.00  9.99
ATOM    696  N   LYS   171       2.599  95.075  21.024  1.00  9.99
ATOM    697  CA  LYS   171       1.436  94.353  20.589  1.00  9.99
ATOM    698  C   LYS   171       0.602  93.889  21.769  1.00  9.99
ATOM    699  O   LYS   171      -0.623  94.032  21.755  1.00  9.99
ATOM    700  CB  LYS   171       1.846  93.160  19.727  1.00  9.99
ATOM    701  N   VAL   172       1.254  93.349  22.801  1.00  9.99
ATOM    702  CA  VAL   172       0.530  92.840  23.964  1.00  9.99
ATOM    703  C   VAL   172       1.463  92.316  25.051  1.00  9.99
ATOM    704  O   VAL   172       1.251  92.571  26.244  1.00  9.99
ATOM    705  CB  VAL   172      -0.428  91.703  23.534  1.00  9.99
ATOM    706  N   SER   173       2.490  91.606  24.659  1.00  9.99
ATOM    707  CA  SER   173       3.315  90.915  25.627  1.00  9.99
ATOM    708  C   SER   173       4.790  90.998  25.263  1.00  9.99
ATOM    709  O   SER   173       5.195  90.497  24.220  1.00  9.99
ATOM    710  CB  SER   173       2.856  89.459  25.672  1.00  9.99
ATOM    711  N   GLU   174       5.605  91.652  26.110  1.00  9.99
ATOM    712  CA  GLU   174       7.055  91.755  25.897  1.00  9.99
ATOM    713  C   GLU   174       7.716  90.385  25.966  1.00  9.99
ATOM    714  O   GLU   174       7.488  89.621  26.913  1.00  9.99
ATOM    715  CB  GLU   174       7.538  92.633  27.069  1.00  9.99
ATOM    716  N   GLU   175       8.525  90.066  24.982  1.00  9.99
ATOM    717  CA  GLU   175       9.169  88.766  24.929  1.00  9.99
ATOM    718  C   GLU   175      10.670  88.907  24.700  1.00  9.99
ATOM    719  O   GLU   175      11.478  88.507  25.551  1.00  9.99
ATOM    720  CB  GLU   175       8.550  87.881  23.823  1.00  9.99
TER
END
