
#######################################################
#                                                     #
#                        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 T0303AL242_4-D2
# Molecule2: number of CA atoms   77 (  602),  selected   27 , name T0303_D2.pdb
# PARAMETERS: T0303AL242_4-D2.T0303_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:    14        80 - 93          4.81    17.00
  LCS_AVERAGE:     15.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        80 - 84          1.93    19.71
  LONGEST_CONTINUOUS_SEGMENT:     5        89 - 93          1.81    16.67
  LONGEST_CONTINUOUS_SEGMENT:     5        90 - 94          1.87    17.96
  LCS_AVERAGE:      5.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        81 - 84          0.17    20.73
  LONGEST_CONTINUOUS_SEGMENT:     4        90 - 93          0.89    16.50
  LCS_AVERAGE:      4.28

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:   77
LCS_GDT     S      18     S      18      3    3    4     3    3    4    4    5    6    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     L      19     L      19      3    3    4     3    3    4    4    5    6    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     P      20     P      20      3    3    4     3    3    4    4    5    6    6    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     D      21     D      21      3    3    4     3    3    3    3    3    3    4    4    4    4   10   10   11   12   16   17   18   19   19   20 
LCS_GDT     E      72     E      72      3    4   13     3    3    3    4    4    4    5    6    7    8   10   12   14   14   14   15   15   16   16   16 
LCS_GDT     D      73     D      73      3    4   13     3    3    3    4    4    4    5    6    7    8    9   12   14   14   14   15   15   16   16   16 
LCS_GDT     E      74     E      74      3    4   13     3    3    3    4    4    4    5    8    9    9   10   12   14   14   14   15   15   16   16   16 
LCS_GDT     F      75     F      75      3    4   13     1    3    3    4    4    4    5    7    9   10   10   12   14   14   14   15   15   16   16   17 
LCS_GDT     K      76     K      76      3    4   13     3    3    3    4    4    4    5    8    9   10   10   11   14   14   14   15   15   16   16   17 
LCS_GDT     Y      77     Y      77      3    4   13     3    3    3    4    4    4    5    7    9   10   10   12   14   14   14   15   15   16   18   20 
LCS_GDT     F      78     F      78      3    4   13     3    3    3    4    4    6    6    8    9   10   10   12   14   14   14   15   17   19   19   20 
LCS_GDT     K      79     K      79      3    3   13     3    3    4    4    5    6    8    8    9   10   10   12   14   14   14   17   18   19   19   20 
LCS_GDT     R      80     R      80      3    5   14     3    3    4    4    5    6    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     Q      81     Q      81      4    5   14     4    4    4    4    5    6    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     F      82     F      82      4    5   14     4    4    4    4    4    5    6    7    9   10   11   12   14   16   16   17   18   19   19   20 
LCS_GDT     G      83     G      83      4    5   14     4    4    4    4    4    5    5    7    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     F      84     F      84      4    5   14     4    4    4    4    4    6    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     Y      85     Y      85      3    4   14     3    3    3    3    5    6    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     Y      86     Y      86      3    4   14     3    3    3    3    4    5    8    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     G      87     G      87      3    4   14     3    3    4    4    5    6    6    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     E      88     E      88      3    4   14     3    3    4    4    5    6    6    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     N      89     N      89      3    5   14     3    3    3    4    5    5    6    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     L      90     L      90      4    5   14     3    3    4    4    5    5    6    8    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     C      91     C      91      4    5   14     3    3    4    4    5    5    5    7    9   10   11   13   14   16   16   17   18   19   19   20 
LCS_GDT     N      92     N      92      4    5   14     3    3    4    4    5    5    6    7    9   10   11   12   14   16   16   17   18   19   19   20 
LCS_GDT     I      93     I      93      4    5   14     3    3    4    4    5    5    5    6    6    7    7   12   13   14   14   15   15   18   19   20 
LCS_GDT     S      94     S      94      3    5   13     3    3    3    3    4    5    5    6    6    7    8    9   12   14   15   17   18   19   19   20 
LCS_AVERAGE  LCS_A:   8.53  (   4.28    5.48   15.82 )

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      4      4      4      4      5      6      8      8      9     10     11     13     14     16     16     17     18     19     19     20 
GDT PERCENT_CA   5.19   5.19   5.19   5.19   6.49   7.79  10.39  10.39  11.69  12.99  14.29  16.88  18.18  20.78  20.78  22.08  23.38  24.68  24.68  25.97
GDT RMS_LOCAL    0.17   0.17   0.17   0.17   1.53   2.12   2.67   2.67   3.20   3.55   4.02   4.48   4.64   5.16   5.14   5.42   5.81   5.99   5.99   6.33
GDT RMS_ALL_CA  20.73  20.73  20.73  20.73  13.55  13.22  12.55  12.55  13.44  13.52  17.16  13.92  14.10  14.22  13.87  14.45  13.60  13.78  13.78  13.81

#      Molecule1      Molecule2       DISTANCE
LGA    S      18      S      18          2.362
LGA    L      19      L      19          3.482
LGA    P      20      P      20          7.988
LGA    D      21      D      21         11.835
LGA    E      72      E      72         26.910
LGA    D      73      D      73         26.540
LGA    E      74      E      74         20.081
LGA    F      75      F      75         15.049
LGA    K      76      K      76         14.232
LGA    Y      77      Y      77         12.610
LGA    F      78      F      78          7.447
LGA    K      79      K      79          2.155
LGA    R      80      R      80          2.316
LGA    Q      81      Q      81          1.029
LGA    F      82      F      82          8.548
LGA    G      83      G      83          9.179
LGA    F      84      F      84          3.126
LGA    Y      85      Y      85          2.472
LGA    Y      86      Y      86          3.490
LGA    G      87      G      87          8.960
LGA    E      88      E      88         12.928
LGA    N      89      N      89         15.253
LGA    L      90      L      90         16.614
LGA    C      91      C      91         16.937
LGA    N      92      N      92         11.584
LGA    I      93      I      93          9.988
LGA    S      94      S      94          9.213

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   77    4.0      8    2.67    10.714     9.448     0.289

LGA_LOCAL      RMSD =  2.665  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.554  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 10.840  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.624378 * X  +  -0.754446 * Y  +   0.202394 * Z  + -11.557516
  Y_new =  -0.778824 * X  +   0.581418 * Y  +  -0.235344 * Z  +  77.631699
  Z_new =   0.059879 * X  +  -0.304573 * Y  +  -0.950605 * Z  +  30.457567 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.831528    0.310065  [ DEG:  -162.2346     17.7654 ]
  Theta =  -0.059915   -3.081678  [ DEG:    -3.4329   -176.5672 ]
  Phi   =  -2.246569    0.895024  [ DEG:  -128.7189     51.2811 ]
 
# 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: T0303AL242_4-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0303AL242_4-D2.T0303_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   77   4.0    8   2.67   9.448    10.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0303AL242_4-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     69  N   SER    18     -13.887  84.917  21.055  1.00  0.00              
ATOM     70  CA  SER    18     -13.462  85.856  20.023  1.00  0.00              
ATOM     71  C   SER    18     -12.731  85.118  18.919  1.00  0.00              
ATOM     72  O   SER    18     -12.421  83.934  19.064  1.00  0.00              
ATOM     73  N   LEU    19     -12.473  85.819  17.816  1.00  0.00              
ATOM     74  CA  LEU    19     -11.708  85.256  16.706  1.00  0.00              
ATOM     75  C   LEU    19     -10.275  85.726  16.935  1.00  0.00              
ATOM     76  O   LEU    19     -10.027  86.927  17.052  1.00  0.00              
ATOM     77  N   PRO    20      -9.339  84.788  17.005  1.00  0.00              
ATOM     78  CA  PRO    20      -7.946  85.142  17.239  1.00  0.00              
ATOM     79  C   PRO    20      -7.325  85.948  16.088  1.00  0.00              
ATOM     80  O   PRO    20      -6.332  86.646  16.286  1.00  0.00              
ATOM     81  N   ASP    21      -7.915  85.871  14.896  1.00  0.00              
ATOM     82  CA  ASP    21      -7.382  86.606  13.749  1.00  0.00              
ATOM     83  C   ASP    21      -8.071  87.957  13.550  1.00  0.00              
ATOM     84  O   ASP    21      -7.800  88.656  12.573  1.00  0.00              
ATOM     85  N   GLU    72      -8.939  88.334  14.484  1.00  0.00              
ATOM     86  CA  GLU    72      -9.679  89.581  14.354  1.00  0.00              
ATOM     87  C   GLU    72      -9.752  90.498  15.574  1.00  0.00              
ATOM     88  O   GLU    72      -9.419  91.680  15.489  1.00  0.00              
ATOM     89  N   ASP    73     -10.198  89.956  16.701  1.00  0.00              
ATOM     90  CA  ASP    73     -10.387  90.749  17.910  1.00  0.00              
ATOM     91  C   ASP    73      -9.173  91.056  18.773  1.00  0.00              
ATOM     92  O   ASP    73      -9.251  91.884  19.677  1.00  0.00              
ATOM     93  N   GLU    74      -8.057  90.394  18.506  1.00  0.00              
ATOM     94  CA  GLU    74      -6.856  90.611  19.293  1.00  0.00              
ATOM     95  C   GLU    74      -5.660  90.948  18.422  1.00  0.00              
ATOM     96  O   GLU    74      -5.709  90.815  17.202  1.00  0.00              
ATOM     97  N   PHE    75      -4.580  91.383  19.057  1.00  0.00              
ATOM     98  CA  PHE    75      -3.370  91.749  18.335  1.00  0.00              
ATOM     99  C   PHE    75      -2.169  91.033  18.961  1.00  0.00              
ATOM    100  O   PHE    75      -1.602  91.496  19.952  1.00  0.00              
ATOM    101  N   LYS    76      -1.791  89.871  18.395  1.00  0.00              
ATOM    102  CA  LYS    76      -0.672  89.029  18.839  1.00  0.00              
ATOM    103  C   LYS    76       0.671  89.724  18.604  1.00  0.00              
ATOM    104  O   LYS    76       0.762  90.640  17.796  1.00  0.00              
ATOM    105  N   TYR    77       1.732  89.284  19.296  1.00  0.00              
ATOM    106  CA  TYR    77       1.764  88.189  20.273  1.00  0.00              
ATOM    107  C   TYR    77       1.119  88.559  21.605  1.00  0.00              
ATOM    108  O   TYR    77       0.756  89.717  21.842  1.00  0.00              
ATOM    109  N   PHE    78       0.994  87.565  22.478  1.00  0.00              
ATOM    110  CA  PHE    78       0.406  87.763  23.794  1.00  0.00              
ATOM    111  C   PHE    78       1.477  87.588  24.866  1.00  0.00              
ATOM    112  O   PHE    78       2.595  87.178  24.574  1.00  0.00              
ATOM    113  N   LYS    79       1.122  87.897  26.110  1.00  0.00              
ATOM    114  CA  LYS    79       2.051  87.765  27.229  1.00  0.00              
ATOM    115  C   LYS    79       1.295  87.841  28.550  1.00  0.00              
ATOM    116  O   LYS    79       0.245  88.478  28.634  1.00  0.00              
ATOM    117  N   ARG    80       1.831  87.191  29.579  1.00  0.00              
ATOM    118  CA  ARG    80       1.203  87.234  30.893  1.00  0.00              
ATOM    119  C   ARG    80       1.598  88.532  31.578  1.00  0.00              
ATOM    120  O   ARG    80       2.768  88.908  31.589  1.00  0.00              
ATOM    121  N   GLN    81       0.612  89.215  32.143  1.00  0.00              
ATOM    122  CA  GLN    81       0.851  90.473  32.831  1.00  0.00              
ATOM    123  C   GLN    81       1.286  90.189  34.266  1.00  0.00              
ATOM    124  O   GLN    81       1.259  89.042  34.716  1.00  0.00              
ATOM    125  N   PHE    82       1.690  91.233  34.981  1.00  0.00              
ATOM    126  CA  PHE    82       2.134  91.083  36.362  1.00  0.00              
ATOM    127  C   PHE    82       1.003  90.608  37.268  1.00  0.00              
ATOM    128  O   PHE    82       1.249  89.973  38.294  1.00  0.00              
ATOM    129  N   GLY    83      -0.234  90.916  36.888  1.00  0.00              
ATOM    130  CA  GLY    83      -1.396  90.519  37.678  1.00  0.00              
ATOM    131  C   GLY    83      -1.905  89.127  37.308  1.00  0.00              
ATOM    132  O   GLY    83      -3.011  88.741  37.686  1.00  0.00              
ATOM    133  N   PHE    84      -1.097  88.380  36.562  1.00  0.00              
ATOM    134  CA  PHE    84      -1.475  87.029  36.171  1.00  0.00              
ATOM    135  C   PHE    84      -2.336  86.886  34.925  1.00  0.00              
ATOM    136  O   PHE    84      -2.528  85.779  34.429  1.00  0.00              
ATOM    137  N   TYR    85      -2.857  87.996  34.414  1.00  0.00              
ATOM    138  CA  TYR    85      -3.703  87.946  33.231  1.00  0.00              
ATOM    139  C   TYR    85      -2.908  87.755  31.939  1.00  0.00              
ATOM    140  O   TYR    85      -1.692  87.945  31.904  1.00  0.00              
ATOM    141  N   TYR    86      -3.603  87.355  30.881  1.00  0.00              
ATOM    142  CA  TYR    86      -2.980  87.198  29.576  1.00  0.00              
ATOM    143  C   TYR    86      -3.367  88.465  28.826  1.00  0.00              
ATOM    144  O   TYR    86      -4.523  88.891  28.866  1.00  0.00              
ATOM    145  N   GLY    87      -2.401  89.076  28.157  1.00  0.00              
ATOM    146  CA  GLY    87      -2.678  90.311  27.439  1.00  0.00              
ATOM    147  C   GLY    87      -2.117  90.292  26.027  1.00  0.00              
ATOM    148  O   GLY    87      -1.191  89.540  25.730  1.00  0.00              
ATOM    149  N   GLU    88      -2.684  91.128  25.164  1.00  0.00              
ATOM    150  CA  GLU    88      -2.216  91.235  23.791  1.00  0.00              
ATOM    151  C   GLU    88      -1.566  92.611  23.652  1.00  0.00              
ATOM    152  O   GLU    88      -1.572  93.398  24.602  1.00  0.00              
ATOM    153  N   ASN    89      -1.009  92.897  22.482  1.00  0.00              
ATOM    154  CA  ASN    89      -0.328  94.167  22.234  1.00  0.00              
ATOM    155  C   ASN    89      -1.123  95.432  22.563  1.00  0.00              
ATOM    156  O   ASN    89      -0.537  96.486  22.812  1.00  0.00              
ATOM    157  N   LEU    90      -2.448  95.340  22.559  1.00  0.00              
ATOM    158  CA  LEU    90      -3.278  96.506  22.847  1.00  0.00              
ATOM    159  C   LEU    90      -3.803  96.537  24.276  1.00  0.00              
ATOM    160  O   LEU    90      -4.778  97.230  24.575  1.00  0.00              
ATOM    161  N   CYS    91      -3.145  95.786  25.154  1.00  0.00              
ATOM    162  CA  CYS    91      -3.535  95.755  26.551  1.00  0.00              
ATOM    163  C   CYS    91      -4.870  95.105  26.862  1.00  0.00              
ATOM    164  O   CYS    91      -5.428  95.318  27.942  1.00  0.00              
ATOM    165  N   ASN    92      -5.392  94.312  25.932  1.00  0.00              
ATOM    166  CA  ASN    92      -6.668  93.640  26.156  1.00  0.00              
ATOM    167  C   ASN    92      -6.521  92.453  27.098  1.00  0.00              
ATOM    168  O   ASN    92      -5.546  91.710  27.039  1.00  0.00              
ATOM    169  N   ILE    93      -7.506  92.281  27.965  1.00  0.00              
ATOM    170  CA  ILE    93      -7.500  91.162  28.888  1.00  0.00              
ATOM    171  C   ILE    93      -8.037  89.984  28.078  1.00  0.00              
ATOM    172  O   ILE    93      -9.181  90.015  27.637  1.00  0.00              
ATOM    173  N   SER    94      -7.213  88.962  27.871  1.00  0.00              
ATOM    174  CA  SER    94      -7.634  87.796  27.098  1.00  0.00              
ATOM    175  C   SER    94      -8.085  86.691  28.047  1.00  0.00              
ATOM    176  O   SER    94      -7.322  86.267  28.905  1.00  0.00              
END
