
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0372AL044_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   35 , name T0372_D1.pdb
# PARAMETERS: T0372AL044_5-D1.T0372_D1.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:    26        72 - 104         4.57    11.91
  LCS_AVERAGE:     17.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        86 - 93          1.90    12.79
  LONGEST_CONTINUOUS_SEGMENT:     8        88 - 95          1.53    13.26
  LCS_AVERAGE:      4.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        90 - 95          0.55    13.57
  LCS_AVERAGE:      2.90

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:  126
LCS_GDT     D      72     D      72      0    3   26     2    4    4    7    8   10   12   15   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     K      74     K      74      0    3   26     1    2    4    7    8   10   12   15   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     R      78     R      78      0    3   26     0    0    0    3    5    6    7    8   12   16   16   17   18   24   25   26   26   26   26   26 
LCS_GDT     K      79     K      79      5    7   26     3    4    5    7    8   11   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     L      80     L      80      5    7   26     3    4    5    6   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     I      81     I      81      5    7   26     3    4    7    8   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     E      82     E      82      5    7   26     3    4    7    8   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     D      83     D      83      5    7   26     3    4    5    5    7    8   12   15   18   19   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     A      84     A      84      3    7   26     3    3    4    4    7    8    9   10   15   18   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     D      85     D      85      4    7   26     3    4    4    5    9   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     K      86     K      86      4    8   26     3    4    5    6    9   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     E      87     E      87      4    8   26     3    4    5    5    6   11   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     K      88     K      88      4    8   26     3    4    7    8   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     H      89     H      89      3    8   26     3    4    5    7    9   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     N      90     N      90      6    8   26     5    6    6    8   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     F      91     F      91      6    8   26     5    6    6    7   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     C      92     C      92      6    8   26     5    6    7    8   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     M      93     M      93      6    8   26     5    6    7    8   10   12   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     L      94     L      94      6    8   26     5    6    7    8   10   12   14   17   18   19   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     G      95     G      95      6    8   26     3    6    7    8   10   12   14   17   18   19   20   22   24   24   25   26   26   26   26   26 
LCS_GDT     V      96     V      96      4    7   26     3    4    4    5    6   11   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     C      97     C      97      4    7   26     3    4    4    5    7   11   14   17   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     S      98     S      98      4    6   26     1    4    4    7    7    9   14   16   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     M     100     M     100      3    6   26     2    3    3    5    5    7   12   15   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     D     103     D     103      3    5   26     0    0    3    7    8   10   12   15   20   20   22   23   24   24   25   26   26   26   26   26 
LCS_GDT     L     104     L     104      3    4   26     2    2    3    4    5    7    9   10   12   17   18   18   22   24   25   26   26   26   26   26 
LCS_GDT     E     105     E     105      3    3   18     3    3    3    3    4    4    5    7    7   10   12   16   18   19   19   20   23   24   24   25 
LCS_GDT     A     106     A     106      3    4   10     3    3    3    3    4    5    6    7    7    8   11   13   14   14   15   18   20   22   24   24 
LCS_GDT     I     107     I     107      3    4   10     3    3    3    3    4    5    6    7    7    8   11   13   14   14   15   18   20   22   24   24 
LCS_GDT     P     109     P     109      3    5   10     0    3    3    4    5    5    6    7    7    8   11   13   14   14   15   18   20   22   24   24 
LCS_GDT     E     110     E     110      3    5    9     0    3    3    4    5    5    6    7    7    8   11   13   14   14   15   18   20   22   24   24 
LCS_GDT     R     111     R     111      3    5    9     0    3    3    4    5    5    6    7    7    8   11   13   14   14   15   16   20   22   24   24 
LCS_GDT     F     112     F     112      3    5    9     0    3    3    4    5    5    5    7    7    7    7   13   14   14   15   16   16   22   24   24 
LCS_GDT     I     113     I     113      3    5    9     0    3    3    3    5    5    6    7    7    8   11   13   14   14   15   18   20   22   24   24 
LCS_GDT     D     117     D     117      0    0    9     0    0    0    0    0    0    0    0    0    0    0   10   10   11   13   18   20   22   24   24 
LCS_AVERAGE  LCS_A:   8.36  (   2.90    4.74   17.44 )

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      5      6      7      8     10     12     14     17     20     20     22     23     24     24     25     26     26     26     26     26 
GDT PERCENT_CA   3.97   4.76   5.56   6.35   7.94   9.52  11.11  13.49  15.87  15.87  17.46  18.25  19.05  19.05  19.84  20.63  20.63  20.63  20.63  20.63
GDT RMS_LOCAL    0.25   0.55   0.91   1.20   1.49   1.80   2.33   2.81   3.44   3.44   3.75   3.89   4.07   4.07   4.26   4.57   4.57   4.57   4.57   4.57
GDT RMS_ALL_CA  13.88  13.57  13.49  13.37  13.22  13.21  13.11  12.37  11.57  11.57  11.78  11.76  11.93  11.93  11.99  11.91  11.91  11.91  11.91  11.91

#      Molecule1      Molecule2       DISTANCE
LGA    D      72      D      72         10.622
LGA    K      74      K      74          9.846
LGA    R      78      R      78         10.761
LGA    K      79      K      79          3.643
LGA    L      80      L      80          1.917
LGA    I      81      I      81          2.466
LGA    E      82      E      82          1.805
LGA    D      83      D      83          4.716
LGA    A      84      A      84          5.895
LGA    D      85      D      85          3.516
LGA    K      86      K      86          3.472
LGA    E      87      E      87          3.796
LGA    K      88      K      88          1.972
LGA    H      89      H      89          1.346
LGA    N      90      N      90          2.424
LGA    F      91      F      91          2.484
LGA    C      92      C      92          1.584
LGA    M      93      M      93          1.962
LGA    L      94      L      94          3.361
LGA    G      95      G      95          3.241
LGA    V      96      V      96          3.938
LGA    C      97      C      97          3.094
LGA    S      98      S      98          6.897
LGA    M     100      M     100          9.465
LGA    D     103      D     103         11.105
LGA    L     104      L     104         14.661
LGA    E     105      E     105         16.787
LGA    A     106      A     106         19.608
LGA    I     107      I     107         20.207
LGA    P     109      P     109         21.594
LGA    E     110      E     110         22.170
LGA    R     111      R     111         21.375
LGA    F     112      F     112         22.260
LGA    I     113      I     113         25.096
LGA    D     117      D     117         28.091

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35  126    4.0     17    2.81    11.310    10.089     0.585

LGA_LOCAL      RMSD =  2.807  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.419  Number of atoms =   35 
Std_ALL_ATOMS  RMSD =  9.494  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.461096 * X  +   0.785501 * Y  +  -0.412770 * Z  +  47.527191
  Y_new =   0.854374 * X  +  -0.518637 * Y  +  -0.032563 * Z  +  42.436371
  Z_new =  -0.239656 * X  +  -0.337645 * Y  +  -0.910253 * Z  +  33.156593 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.786390    0.355202  [ DEG:  -159.6484     20.3516 ]
  Theta =   0.242011    2.899581  [ DEG:    13.8662    166.1338 ]
  Phi   =   1.075904   -2.065689  [ DEG:    61.6448   -118.3552 ]
 
# 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: T0372AL044_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_5-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35  126   4.0   17   2.81  10.089     9.49
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_5-D1
REMARK Aligment from pdb entry: 1x7v_A
ATOM      1  N   ASP    72      35.307  60.882   5.771  1.00  0.00              
ATOM      2  CA  ASP    72      35.853  59.667   5.159  1.00  0.00              
ATOM      3  C   ASP    72      35.002  59.114   3.965  1.00  0.00              
ATOM      4  O   ASP    72      35.549  58.692   2.923  1.00  0.00              
ATOM      5  N   LYS    74      33.685  59.102   4.101  1.00  0.00              
ATOM      6  CA  LYS    74      32.773  58.719   3.030  1.00  0.00              
ATOM      7  C   LYS    74      32.997  59.576   1.786  1.00  0.00              
ATOM      8  O   LYS    74      33.011  59.033   0.693  1.00  0.00              
ATOM      9  N   ARG    78      33.144  60.899   1.968  1.00  0.00              
ATOM     10  CA  ARG    78      33.413  61.840   0.871  1.00  0.00              
ATOM     11  C   ARG    78      34.663  61.388   0.137  1.00  0.00              
ATOM     12  O   ARG    78      34.673  61.293  -1.071  1.00  0.00              
ATOM     13  N   LYS    79      36.968  57.534  -4.910  1.00  0.00              
ATOM     14  CA  LYS    79      37.736  56.403  -5.492  1.00  0.00              
ATOM     15  C   LYS    79      36.977  55.581  -6.538  1.00  0.00              
ATOM     16  O   LYS    79      37.590  54.890  -7.381  1.00  0.00              
ATOM     17  N   LEU    80      35.646  55.572  -6.442  1.00  0.00              
ATOM     18  CA  LEU    80      34.887  54.531  -7.081  1.00  0.00              
ATOM     19  C   LEU    80      34.850  54.607  -8.627  1.00  0.00              
ATOM     20  O   LEU    80      35.180  53.617  -9.301  1.00  0.00              
ATOM     21  N   ILE    81      34.435  55.744  -9.188  1.00  0.00              
ATOM     22  CA  ILE    81      34.306  55.828 -10.634  1.00  0.00              
ATOM     23  C   ILE    81      35.666  55.606 -11.308  1.00  0.00              
ATOM     24  O   ILE    81      35.751  54.804 -12.256  1.00  0.00              
ATOM     25  N   GLU    82      36.724  56.294 -10.853  1.00  0.00              
ATOM     26  CA  GLU    82      37.983  56.078 -11.571  1.00  0.00              
ATOM     27  C   GLU    82      38.507  54.656 -11.400  1.00  0.00              
ATOM     28  O   GLU    82      39.153  54.103 -12.334  1.00  0.00              
ATOM     29  N   ASP    83      36.703  51.848 -11.022  1.00  0.00              
ATOM     30  CA  ASP    83      35.887  50.941 -11.829  1.00  0.00              
ATOM     31  C   ASP    83      36.345  50.931 -13.312  1.00  0.00              
ATOM     32  O   ASP    83      36.237  49.896 -13.997  1.00  0.00              
ATOM     33  N   ALA    84      36.889  52.065 -13.778  1.00  0.00              
ATOM     34  CA  ALA    84      37.319  52.245 -15.160  1.00  0.00              
ATOM     35  C   ALA    84      38.653  51.555 -15.430  1.00  0.00              
ATOM     36  O   ALA    84      39.006  51.321 -16.592  1.00  0.00              
ATOM     37  N   ASP    85      39.420  51.270 -14.369  1.00  0.00              
ATOM     38  CA  ASP    85      40.779  50.740 -14.561  1.00  0.00              
ATOM     39  C   ASP    85      40.784  49.368 -15.242  1.00  0.00              
ATOM     40  O   ASP    85      39.942  48.536 -14.985  1.00  0.00              
ATOM     41  N   LYS    86      41.787  49.160 -16.102  1.00  0.00              
ATOM     42  CA  LYS    86      42.054  47.852 -16.688  1.00  0.00              
ATOM     43  C   LYS    86      42.070  46.801 -15.578  1.00  0.00              
ATOM     44  O   LYS    86      42.670  47.028 -14.506  1.00  0.00              
ATOM     45  N   GLU    87      41.429  45.665 -15.832  1.00  0.00              
ATOM     46  CA  GLU    87      41.423  44.554 -14.922  1.00  0.00              
ATOM     47  C   GLU    87      40.510  44.690 -13.705  1.00  0.00              
ATOM     48  O   GLU    87      40.536  43.801 -12.851  1.00  0.00              
ATOM     49  N   LYS    88      39.772  45.805 -13.577  1.00  0.00              
ATOM     50  CA  LYS    88      38.862  45.973 -12.444  1.00  0.00              
ATOM     51  C   LYS    88      37.537  45.320 -12.750  1.00  0.00              
ATOM     52  O   LYS    88      36.769  45.791 -13.611  1.00  0.00              
ATOM     53  N   HIS    89      37.277  44.217 -12.066  1.00  0.00              
ATOM     54  CA  HIS    89      36.036  43.467 -12.232  1.00  0.00              
ATOM     55  C   HIS    89      34.935  43.872 -11.265  1.00  0.00              
ATOM     56  O   HIS    89      33.783  43.604 -11.501  1.00  0.00              
ATOM     57  N   ASN    90      35.299  44.498 -10.165  1.00  0.00              
ATOM     58  CA  ASN    90      34.292  45.009  -9.212  1.00  0.00              
ATOM     59  C   ASN    90      35.003  46.049  -8.368  1.00  0.00              
ATOM     60  O   ASN    90      36.132  45.867  -7.983  1.00  0.00              
ATOM     61  N   PHE    91      34.302  47.125  -8.033  1.00  0.00              
ATOM     62  CA  PHE    91      34.829  48.108  -7.092  1.00  0.00              
ATOM     63  C   PHE    91      33.628  48.843  -6.526  1.00  0.00              
ATOM     64  O   PHE    91      33.103  49.788  -7.150  1.00  0.00              
ATOM     65  N   CYS    92      33.173  48.349  -5.375  1.00  0.00              
ATOM     66  CA  CYS    92      31.937  48.793  -4.773  1.00  0.00              
ATOM     67  C   CYS    92      32.165  49.240  -3.323  1.00  0.00              
ATOM     68  O   CYS    92      32.803  48.553  -2.567  1.00  0.00              
ATOM     69  N   MET    93      31.631  50.416  -2.984  1.00  0.00              
ATOM     70  CA  MET    93      31.693  51.021  -1.667  1.00  0.00              
ATOM     71  C   MET    93      30.402  50.798  -0.878  1.00  0.00              
ATOM     72  O   MET    93      29.325  50.885  -1.403  1.00  0.00              
ATOM     73  N   LEU    94      30.529  50.505   0.407  1.00  0.00              
ATOM     74  CA  LEU    94      29.369  50.190   1.261  1.00  0.00              
ATOM     75  C   LEU    94      29.589  50.843   2.637  1.00  0.00              
ATOM     76  O   LEU    94      30.732  51.044   3.059  1.00  0.00              
ATOM     77  N   GLY    95      28.504  51.102   3.352  1.00  0.00              
ATOM     78  CA  GLY    95      28.611  51.547   4.732  1.00  0.00              
ATOM     79  C   GLY    95      27.915  50.484   5.603  1.00  0.00              
ATOM     80  O   GLY    95      26.868  49.917   5.240  1.00  0.00              
ATOM     81  N   VAL    96      28.540  50.185   6.715  1.00  0.00              
ATOM     82  CA  VAL    96      27.950  49.323   7.748  1.00  0.00              
ATOM     83  C   VAL    96      26.531  49.722   8.176  1.00  0.00              
ATOM     84  O   VAL    96      26.227  50.901   8.302  1.00  0.00              
ATOM     85  N   CYS    97      25.695  48.738   8.413  1.00  0.00              
ATOM     86  CA  CYS    97      24.300  48.995   8.770  1.00  0.00              
ATOM     87  C   CYS    97      24.149  49.589  10.171  1.00  0.00              
ATOM     88  O   CYS    97      23.171  50.304  10.452  1.00  0.00              
ATOM     89  N   SER    98      25.076  49.290  11.076  1.00  0.00              
ATOM     90  CA  SER    98      24.947  49.717  12.481  1.00  0.00              
ATOM     91  C   SER    98      25.945  50.709  13.021  1.00  0.00              
ATOM     92  O   SER    98      25.689  51.282  14.100  1.00  0.00              
ATOM     93  N   MET   100      27.091  50.899  12.351  1.00  0.00              
ATOM     94  CA  MET   100      28.109  51.852  12.794  1.00  0.00              
ATOM     95  C   MET   100      28.490  52.681  11.581  1.00  0.00              
ATOM     96  O   MET   100      29.104  52.158  10.651  1.00  0.00              
ATOM     97  N   ASP   103      28.159  53.976  11.608  1.00  0.00              
ATOM     98  CA  ASP   103      28.395  54.871  10.472  1.00  0.00              
ATOM     99  C   ASP   103      29.895  55.046  10.136  1.00  0.00              
ATOM    100  O   ASP   103      30.240  55.405   9.026  1.00  0.00              
ATOM    101  N   LEU   104      32.101  52.710   9.812  1.00  0.00              
ATOM    102  CA  LEU   104      32.634  51.500   9.150  1.00  0.00              
ATOM    103  C   LEU   104      32.159  51.418   7.717  1.00  0.00              
ATOM    104  O   LEU   104      30.963  51.510   7.440  1.00  0.00              
ATOM    105  N   GLU   105      33.191  49.501   3.725  1.00  0.00              
ATOM    106  CA  GLU   105      33.737  48.274   3.118  1.00  0.00              
ATOM    107  C   GLU   105      33.874  48.507   1.659  1.00  0.00              
ATOM    108  O   GLU   105      32.879  48.867   1.011  1.00  0.00              
ATOM    109  N   ALA   106      35.087  48.308   1.113  1.00  0.00              
ATOM    110  CA  ALA   106      35.236  48.303  -0.344  1.00  0.00              
ATOM    111  C   ALA   106      35.363  46.834  -0.745  1.00  0.00              
ATOM    112  O   ALA   106      36.231  46.141  -0.222  1.00  0.00              
ATOM    113  N   ILE   107      34.500  46.377  -1.637  1.00  0.00              
ATOM    114  CA  ILE   107      34.571  45.023  -2.202  1.00  0.00              
ATOM    115  C   ILE   107      35.092  45.209  -3.606  1.00  0.00              
ATOM    116  O   ILE   107      34.489  45.888  -4.447  1.00  0.00              
ATOM    117  N   PRO   109      36.225  44.574  -3.877  1.00  0.00              
ATOM    118  CA  PRO   109      36.960  44.761  -5.121  1.00  0.00              
ATOM    119  C   PRO   109      37.283  43.379  -5.729  1.00  0.00              
ATOM    120  O   PRO   109      37.540  42.440  -4.980  1.00  0.00              
ATOM    121  N   GLU   110      37.278  43.285  -7.051  1.00  0.00              
ATOM    122  CA  GLU   110      37.802  42.111  -7.760  1.00  0.00              
ATOM    123  C   GLU   110      38.779  42.615  -8.823  1.00  0.00              
ATOM    124  O   GLU   110      38.506  43.571  -9.582  1.00  0.00              
ATOM    125  N   ARG   111      39.906  41.937  -8.931  1.00  0.00              
ATOM    126  CA  ARG   111      40.948  42.360  -9.845  1.00  0.00              
ATOM    127  C   ARG   111      41.349  41.137 -10.638  1.00  0.00              
ATOM    128  O   ARG   111      41.427  40.050 -10.087  1.00  0.00              
ATOM    129  N   PHE   112      41.591  41.299 -11.925  1.00  0.00              
ATOM    130  CA  PHE   112      41.941  40.154 -12.777  1.00  0.00              
ATOM    131  C   PHE   112      43.177  39.415 -12.240  1.00  0.00              
ATOM    132  O   PHE   112      43.230  38.197 -12.275  1.00  0.00              
ATOM    133  N   ILE   113      44.176  40.139 -11.774  1.00  0.00              
ATOM    134  CA  ILE   113      45.398  39.536 -11.267  1.00  0.00              
ATOM    135  C   ILE   113      46.111  40.538 -10.388  1.00  0.00              
ATOM    136  O   ILE   113      45.667  41.690 -10.257  1.00  0.00              
ATOM    137  N   ASP   117      47.225  40.112  -9.796  1.00  0.00              
ATOM    138  CA  ASP   117      48.030  40.979  -8.943  1.00  0.00              
ATOM    139  C   ASP   117      48.558  42.216  -9.659  1.00  0.00              
ATOM    140  O   ASP   117      48.645  43.281  -9.046  1.00  0.00              
END
