
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0363AL044_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   31 , name T0363_D1.pdb
# PARAMETERS: T0363AL044_3-D1.T0363_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:    17        32 - 52          4.85     8.54
  LCS_AVERAGE:     29.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        38 - 46          0.64    14.01
  LCS_AVERAGE:     13.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        38 - 46          0.64    14.01
  LCS_AVERAGE:     12.06

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:   46
LCS_GDT     I      13     I      13      7    8   11     3    7    7    7    7    8   11   14   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     N      14     N      14      7    8   11     6    7    7    7    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     I      15     I      15      7    8   11     6    7    7    7    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     E      16     E      16      7    8   11     6    7    7    7    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     I      17     I      17      7    8   11     6    7    7    7    7   10   13   16   17   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     A      18     A      18      7    8   11     6    7    7    7    7    8   12   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     Y      19     Y      19      7    8   11     6    7    7    7    7    8    8   14   14   18   20   23   26   27   28   28   28   28   29   29 
LCS_GDT     A      20     A      20      3    8   11     3    3    5    6    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     F      21     F      21      3    4   11     3    4    4    4    5    8   12   13   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     P      22     P      22      3    4   11     3    4    4    4    4    6    9   13   15   20   20   22   26   27   28   28   28   28   29   29 
LCS_GDT     E      23     E      23      3    3   11     3    4    4    4    4    6    7   12   15   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     Q      31     Q      31      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   11   11 
LCS_GDT     V      32     V      32      0    0   17     0    1    1    1    5    8   10   11   15   20   20   22   26   27   28   28   28   28   29   29 
LCS_GDT     D      33     D      33      0    0   17     0    1    1    1    4    8    8   14   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     V      38     V      38      9    9   17     6    8    9    9    9   10   10   13   14   20   21   23   26   27   28   28   28   28   29   29 
LCS_GDT     Q      39     Q      39      9    9   17     6    8    9    9    9   10   12   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     T      40     T      40      9    9   17     6    8    9    9    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     A      41     A      41      9    9   17     6    8    9    9    9   10   12   13   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     I      42     I      42      9    9   17     6    8    9    9    9   10   12   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     T      43     T      43      9    9   17     6    8    9    9    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     Q      44     Q      44      9    9   17     6    8    9    9    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     S      45     S      45      9    9   17     4    8    9    9    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     G      46     G      46      9    9   17     5    7    9    9    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     I      47     I      47      6    8   17     5    5    6    7    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     L      48     L      48      6    8   17     5    5    6    7    7    8    9   13   15   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     S      49     S      49      6    8   17     5    5    6    7    7    8   10   13   15   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     Q      50     Q      50      6    8   17     5    5    6    8    9   10   13   16   18   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     F      51     F      51      6    8   17     3    5    6    7    7    9   13   16   17   20   22   23   26   27   28   28   28   28   29   29 
LCS_GDT     P      52     P      52      0    0   17     0    0    1    1    2    2    3    3    3   11   14   16   17   18   22   23   25   27   29   29 
LCS_GDT     E      53     E      53      0    0    3     0    0    0    0    2    2    3    3    3    3    3    7   10   11   22   22   23   25   27   28 
LCS_GDT     L      56     L      56      0    0    3     0    4    4    4    4    6    7   10   13   17   19   21   24   25   28   28   28   28   29   29 
LCS_AVERAGE  LCS_A:  18.33  (  12.06   13.74   29.17 )

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      9     10     13     16     18     20     22     23     26     27     28     28     28     28     29     29 
GDT PERCENT_CA  13.04  17.39  19.57  19.57  19.57  21.74  28.26  34.78  39.13  43.48  47.83  50.00  56.52  58.70  60.87  60.87  60.87  60.87  63.04  63.04
GDT RMS_LOCAL    0.30   0.45   0.64   0.64   0.64   1.53   2.78   3.13   3.59   3.71   3.92   4.04   4.44   4.62   4.95   4.95   4.95   4.95   5.44   5.44
GDT RMS_ALL_CA  14.65  14.34  14.01  14.01  14.01  12.90   7.68   7.38   7.09   7.22   7.38   7.39   7.32   7.36   7.12   7.12   7.12   7.12   6.96   6.96

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      I      13          5.035
LGA    N      14      N      14          3.080
LGA    I      15      I      15          3.640
LGA    E      16      E      16          2.235
LGA    I      17      I      17          3.750
LGA    A      18      A      18          4.000
LGA    Y      19      Y      19          6.232
LGA    A      20      A      20          1.570
LGA    F      21      F      21          5.496
LGA    P      22      P      22          8.762
LGA    E      23      E      23          5.958
LGA    Q      31      Q      31         19.431
LGA    V      32      V      32          9.938
LGA    D      33      D      33          6.792
LGA    V      38      V      38          7.535
LGA    Q      39      Q      39          3.704
LGA    T      40      T      40          2.329
LGA    A      41      A      41          5.341
LGA    I      42      I      42          3.962
LGA    T      43      T      43          2.336
LGA    Q      44      Q      44          3.767
LGA    S      45      S      45          2.630
LGA    G      46      G      46          3.056
LGA    I      47      I      47          2.611
LGA    L      48      L      48          5.580
LGA    S      49      S      49          6.218
LGA    Q      50      Q      50          3.050
LGA    F      51      F      51          3.725
LGA    P      52      P      52         14.815
LGA    E      53      E      53         16.850
LGA    L      56      L      56         10.616

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   46    4.0     16    3.13    33.152    28.436     0.496

LGA_LOCAL      RMSD =  3.127  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.321  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  6.857  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.137521 * X  +  -0.947800 * Y  +  -0.287684 * Z  +  65.506439
  Y_new =   0.980829 * X  +   0.089823 * Y  +   0.172934 * Z  + -21.385586
  Z_new =  -0.138066 * X  +  -0.305951 * Y  +   0.941983 * Z  +  24.449417 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.314046    2.827546  [ DEG:   -17.9935    162.0065 ]
  Theta =   0.138508    3.003085  [ DEG:     7.9359    172.0641 ]
  Phi   =   1.431495   -1.710098  [ DEG:    82.0186    -97.9814 ]
 
# 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: T0363AL044_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL044_3-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   46   4.0   16   3.13  28.436     6.86
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL044_3-D1
REMARK Aligment from pdb entry: 1vjk_A
ATOM      1  N   ILE    13      21.406   5.496   5.106  1.00  0.00              
ATOM      2  CA  ILE    13      21.055   6.786   5.691  1.00  0.00              
ATOM      3  C   ILE    13      20.813   7.796   4.589  1.00  0.00              
ATOM      4  O   ILE    13      21.380   7.692   3.475  1.00  0.00              
ATOM      5  N   ASN    14      19.977   8.776   4.862  1.00  0.00              
ATOM      6  CA  ASN    14      19.692   9.848   3.943  1.00  0.00              
ATOM      7  C   ASN    14      20.496  11.037   4.391  1.00  0.00              
ATOM      8  O   ASN    14      20.273  11.556   5.494  1.00  0.00              
ATOM      9  N   ILE    15      21.422  11.488   3.567  1.00  0.00              
ATOM     10  CA  ILE    15      22.246  12.648   3.869  1.00  0.00              
ATOM     11  C   ILE    15      21.685  13.872   3.190  1.00  0.00              
ATOM     12  O   ILE    15      21.448  13.834   1.981  1.00  0.00              
ATOM     13  N   GLU    16      21.443  14.940   3.962  1.00  0.00              
ATOM     14  CA  GLU    16      20.938  16.200   3.409  1.00  0.00              
ATOM     15  C   GLU    16      22.026  17.239   3.564  1.00  0.00              
ATOM     16  O   GLU    16      22.476  17.527   4.687  1.00  0.00              
ATOM     17  N   ILE    17      22.459  17.800   2.446  1.00  0.00              
ATOM     18  CA  ILE    17      23.465  18.864   2.448  1.00  0.00              
ATOM     19  C   ILE    17      22.801  20.210   2.427  1.00  0.00              
ATOM     20  O   ILE    17      21.747  20.393   1.793  1.00  0.00              
ATOM     21  N   ALA    18      23.451  21.172   3.093  1.00  0.00              
ATOM     22  CA  ALA    18      22.928  22.521   3.184  1.00  0.00              
ATOM     23  C   ALA    18      23.911  23.554   2.707  1.00  0.00              
ATOM     24  O   ALA    18      25.122  23.388   2.837  1.00  0.00              
ATOM     25  N   TYR    19      23.370  24.656   2.189  1.00  0.00              
ATOM     26  CA  TYR    19      24.163  25.831   1.836  1.00  0.00              
ATOM     27  C   TYR    19      25.324  25.437   0.910  1.00  0.00              
ATOM     28  O   TYR    19      25.093  24.726  -0.077  1.00  0.00              
ATOM     29  N   ALA    20      26.555  25.878   1.196  1.00  0.00              
ATOM     30  CA  ALA    20      27.618  25.649   0.196  1.00  0.00              
ATOM     31  C   ALA    20      27.956  24.186   0.030  1.00  0.00              
ATOM     32  O   ALA    20      28.527  23.794  -0.985  1.00  0.00              
ATOM     33  N   PHE    21      27.578  23.357   1.001  1.00  0.00              
ATOM     34  CA  PHE    21      27.883  21.917   0.918  1.00  0.00              
ATOM     35  C   PHE    21      27.051  21.214  -0.129  1.00  0.00              
ATOM     36  O   PHE    21      27.429  20.129  -0.575  1.00  0.00              
ATOM     37  N   PRO    22      25.963  21.845  -0.563  1.00  0.00              
ATOM     38  CA  PRO    22      25.218  21.352  -1.726  1.00  0.00              
ATOM     39  C   PRO    22      26.076  21.433  -2.976  1.00  0.00              
ATOM     40  O   PRO    22      25.971  20.556  -3.846  1.00  0.00              
ATOM     41  N   GLU    23      26.894  22.487  -3.112  1.00  0.00              
ATOM     42  CA  GLU    23      27.797  22.565  -4.242  1.00  0.00              
ATOM     43  C   GLU    23      28.949  21.633  -4.129  1.00  0.00              
ATOM     44  O   GLU    23      29.354  21.066  -5.132  1.00  0.00              
ATOM     45  N   GLN    31      29.500  21.463  -2.923  1.00  0.00              
ATOM     46  CA  GLN    31      30.611  20.522  -2.769  1.00  0.00              
ATOM     47  C   GLN    31      30.187  19.084  -3.048  1.00  0.00              
ATOM     48  O   GLN    31      30.950  18.314  -3.629  1.00  0.00              
ATOM     49  N   VAL    32      26.962  -1.688  11.827  1.00  0.00              
ATOM     50  CA  VAL    32      27.738  -1.125  12.924  1.00  0.00              
ATOM     51  C   VAL    32      28.277   0.266  12.639  1.00  0.00              
ATOM     52  O   VAL    32      28.995   0.851  13.468  1.00  0.00              
ATOM     53  N   ASP    33      27.947   0.813  11.478  1.00  0.00              
ATOM     54  CA  ASP    33      28.474   2.117  11.116  1.00  0.00              
ATOM     55  C   ASP    33      28.136   3.171  12.126  1.00  0.00              
ATOM     56  O   ASP    33      27.020   3.218  12.669  1.00  0.00              
ATOM     57  N   VAL    38      29.116   4.046  12.340  1.00  0.00              
ATOM     58  CA  VAL    38      28.997   5.172  13.245  1.00  0.00              
ATOM     59  C   VAL    38      29.039   6.488  12.473  1.00  0.00              
ATOM     60  O   VAL    38      29.446   6.541  11.301  1.00  0.00              
ATOM     61  N   GLN    39      28.668   7.584  13.125  1.00  0.00              
ATOM     62  CA  GLN    39      28.768   8.906  12.506  1.00  0.00              
ATOM     63  C   GLN    39      30.157   9.150  11.883  1.00  0.00              
ATOM     64  O   GLN    39      30.266   9.632  10.734  1.00  0.00              
ATOM     65  N   THR    40      31.230   8.791  12.602  1.00  0.00              
ATOM     66  CA  THR    40      32.563   9.015  12.040  1.00  0.00              
ATOM     67  C   THR    40      32.784   8.250  10.710  1.00  0.00              
ATOM     68  O   THR    40      33.507   8.733   9.822  1.00  0.00              
ATOM     69  N   ALA    41      32.170   7.067  10.580  1.00  0.00              
ATOM     70  CA  ALA    41      32.317   6.277   9.337  1.00  0.00              
ATOM     71  C   ALA    41      31.581   6.952   8.218  1.00  0.00              
ATOM     72  O   ALA    41      32.067   6.965   7.080  1.00  0.00              
ATOM     73  N   ILE    42      30.430   7.529   8.521  1.00  0.00              
ATOM     74  CA  ILE    42      29.688   8.279   7.507  1.00  0.00              
ATOM     75  C   ILE    42      30.473   9.505   7.028  1.00  0.00              
ATOM     76  O   ILE    42      30.543   9.756   5.811  1.00  0.00              
ATOM     77  N   THR    43      31.103  10.228   7.954  1.00  0.00              
ATOM     78  CA  THR    43      31.920  11.373   7.573  1.00  0.00              
ATOM     79  C   THR    43      33.043  10.928   6.640  1.00  0.00              
ATOM     80  O   THR    43      33.312  11.587   5.602  1.00  0.00              
ATOM     81  N   GLN    44      33.713   9.809   6.965  1.00  0.00              
ATOM     82  CA  GLN    44      34.749   9.314   6.049  1.00  0.00              
ATOM     83  C   GLN    44      34.226   8.943   4.682  1.00  0.00              
ATOM     84  O   GLN    44      34.924   9.168   3.669  1.00  0.00              
ATOM     85  N   SER    45      33.024   8.391   4.622  1.00  0.00              
ATOM     86  CA  SER    45      32.442   8.032   3.342  1.00  0.00              
ATOM     87  C   SER    45      32.064   9.277   2.539  1.00  0.00              
ATOM     88  O   SER    45      32.242   9.278   1.315  1.00  0.00              
ATOM     89  N   GLY    46      31.564  10.341   3.196  1.00  0.00              
ATOM     90  CA  GLY    46      31.272  11.591   2.481  1.00  0.00              
ATOM     91  C   GLY    46      32.548  12.128   1.832  1.00  0.00              
ATOM     92  O   GLY    46      32.535  12.512   0.643  1.00  0.00              
ATOM     93  N   ILE    47      33.640  12.105   2.589  1.00  0.00              
ATOM     94  CA  ILE    47      34.940  12.558   2.080  1.00  0.00              
ATOM     95  C   ILE    47      35.451  11.690   0.921  1.00  0.00              
ATOM     96  O   ILE    47      36.089  12.216  -0.021  1.00  0.00              
ATOM     97  N   LEU    48      35.174  10.391   0.974  1.00  0.00              
ATOM     98  CA  LEU    48      35.578   9.480  -0.083  1.00  0.00              
ATOM     99  C   LEU    48      34.782   9.733  -1.360  1.00  0.00              
ATOM    100  O   LEU    48      35.334   9.652  -2.468  1.00  0.00              
ATOM    101  N   SER    49      33.488  10.016  -1.234  1.00  0.00              
ATOM    102  CA  SER    49      32.653  10.247  -2.400  1.00  0.00              
ATOM    103  C   SER    49      32.884  11.618  -3.016  1.00  0.00              
ATOM    104  O   SER    49      32.709  11.817  -4.217  1.00  0.00              
ATOM    105  N   GLN    50      33.196  12.580  -2.160  1.00  0.00              
ATOM    106  CA  GLN    50      33.257  13.980  -2.561  1.00  0.00              
ATOM    107  C   GLN    50      34.519  14.588  -2.009  1.00  0.00              
ATOM    108  O   GLN    50      34.527  15.142  -0.881  1.00  0.00              
ATOM    109  N   PHE    51      35.585  14.519  -2.806  1.00  0.00              
ATOM    110  CA  PHE    51      36.923  14.859  -2.315  1.00  0.00              
ATOM    111  C   PHE    51      37.054  16.285  -1.800  1.00  0.00              
ATOM    112  O   PHE    51      37.934  16.551  -0.986  1.00  0.00              
ATOM    113  N   PRO    52      32.999  19.158  12.801  1.00  0.00              
ATOM    114  CA  PRO    52      32.928  19.239  14.241  1.00  0.00              
ATOM    115  C   PRO    52      32.227  18.033  14.823  1.00  0.00              
ATOM    116  O   PRO    52      31.496  17.279  14.145  1.00  0.00              
ATOM    117  N   GLU    53      32.463  17.841  16.113  1.00  0.00              
ATOM    118  CA  GLU    53      31.757  16.828  16.863  1.00  0.00              
ATOM    119  C   GLU    53      30.686  17.525  17.672  1.00  0.00              
ATOM    120  O   GLU    53      30.999  18.410  18.503  1.00  0.00              
ATOM    121  N   LEU    56      29.435  17.143  17.447  1.00  0.00              
ATOM    122  CA  LEU    56      28.297  17.855  18.003  1.00  0.00              
ATOM    123  C   LEU    56      28.257  19.281  17.496  1.00  0.00              
ATOM    124  O   LEU    56      28.691  19.584  16.368  1.00  0.00              
END
