
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0319AL381_1
# Molecule2: number of CA atoms  135 ( 1055),  selected   21 , name T0319.pdb
# PARAMETERS: T0319AL381_1.T0319.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:    21       104 - 124         4.98     4.98
  LCS_AVERAGE:     15.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       107 - 122         1.21     6.27
  LONGEST_CONTINUOUS_SEGMENT:    16       108 - 123         1.87     6.53
  LCS_AVERAGE:     10.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       108 - 122         0.76     6.58
  LCS_AVERAGE:      8.78

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:  135
LCS_GDT     S     104     S     104      4    7   21     0    3    4    5    7    8   10   11   11   11   12   13   15   17   19   19   19   19   20   20 
LCS_GDT     I     105     I     105      4    7   21     3    3    4    5    7    8   10   12   15   17   17   17   18   19   19   19   19   20   20   20 
LCS_GDT     A     106     A     106      4    7   21     3    3    4    5    6    8   10   12   15   17   17   17   18   19   19   19   19   20   20   20 
LCS_GDT     E     107     E     107      4   16   21     3    3    4   14   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     G     108     G     108     15   16   21     2   10   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     E     109     E     109     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     M     110     M     110     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     K     111     K     111     15   16   21     3   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     C     112     C     112     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     R     113     R     113     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     N     114     N     114     15   16   21     5   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     C     115     C     115     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     G     116     G     116     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     H     117     H     117     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     I     118     I     118     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     Y     119     Y     119     15   16   21     9   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     Y     120     Y     120     15   16   21     3   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     I     121     I     121     15   16   21     3   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     K     122     K     122     15   16   21     3   14   15   15   15   16   16   16   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     N     123     N     123      4   16   21     3    3    4    4    4    4   10   11   16   18   18   18   18   19   19   19   19   20   20   20 
LCS_GDT     G     124     G     124      4    4   21     3    3    4    4    7    7   10   13   16   18   18   18   18   18   18   18   19   20   20   20 
LCS_AVERAGE  LCS_A:  11.60  (   8.78   10.48   15.56 )

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     14     15     15     15     16     16     16     16     18     18     18     18     19     19     19     19     20     20     20 
GDT PERCENT_CA   6.67  10.37  11.11  11.11  11.11  11.85  11.85  11.85  11.85  13.33  13.33  13.33  13.33  14.07  14.07  14.07  14.07  14.81  14.81  14.81
GDT RMS_LOCAL    0.35   0.63   0.76   0.76   0.76   1.21   1.21   1.21   1.21   2.55   2.55   2.55   2.55   3.62   3.62   3.62   3.39   4.08   4.08   4.08
GDT RMS_ALL_CA   6.62   6.44   6.58   6.58   6.58   6.27   6.27   6.27   6.27   6.51   6.51   6.51   6.51   5.21   5.21   5.21   5.89   5.32   5.32   5.32

#      Molecule1      Molecule2       DISTANCE
LGA    S     104      S     104         19.998
LGA    I     105      I     105         12.834
LGA    A     106      A     106          9.778
LGA    E     107      E     107          3.460
LGA    G     108      G     108          1.940
LGA    E     109      E     109          0.411
LGA    M     110      M     110          0.530
LGA    K     111      K     111          0.889
LGA    C     112      C     112          0.673
LGA    R     113      R     113          0.502
LGA    N     114      N     114          0.769
LGA    C     115      C     115          0.253
LGA    G     116      G     116          0.446
LGA    H     117      H     117          0.661
LGA    I     118      I     118          0.839
LGA    Y     119      Y     119          0.840
LGA    Y     120      Y     120          1.017
LGA    I     121      I     121          1.290
LGA    K     122      K     122          0.672
LGA    N     123      N     123          7.709
LGA    G     124      G     124          9.016

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  135    4.0     16    1.21    11.852    11.670     1.219

LGA_LOCAL      RMSD =  1.213  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.266  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  4.976  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.539517 * X  +   0.014793 * Y  +   0.841845 * Z  +  -0.547917
  Y_new =  -0.839186 * X  +  -0.090753 * Y  +  -0.536218 * Z  +   3.994794
  Z_new =   0.068468 * X  +  -0.995764 * Y  +   0.061377 * Z  +  -4.120016 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.509236    1.632356  [ DEG:   -86.4729     93.5271 ]
  Theta =  -0.068521   -3.073071  [ DEG:    -3.9260   -176.0740 ]
  Phi   =  -2.142168    0.999425  [ DEG:  -122.7372     57.2628 ]
 
# 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: T0319AL381_1                                  
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_1.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  135   4.0   16   1.21  11.670     4.98
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_1
REMARK Aligment from pdb entry: 1dx8A
ATOM      1  N   SER   104      11.509  17.787   1.386  1.00  0.00              
ATOM      2  CA  SER   104      12.832  18.103   1.994  1.00  0.00              
ATOM      3  C   SER   104      12.912  17.527   3.411  1.00  0.00              
ATOM      4  O   SER   104      12.345  18.065   4.342  1.00  0.00              
ATOM      5  N   ILE   105      13.607  16.435   3.583  1.00  0.00              
ATOM      6  CA  ILE   105      13.713  15.828   4.942  1.00  0.00              
ATOM      7  C   ILE   105      15.146  15.360   5.205  1.00  0.00              
ATOM      8  O   ILE   105      15.957  15.273   4.304  1.00  0.00              
ATOM      9  N   ALA   106      15.465  15.057   6.440  1.00  0.00              
ATOM     10  CA  ALA   106      16.854  14.591   6.781  1.00  0.00              
ATOM     11  C   ALA   106      17.028  14.441   8.300  1.00  0.00              
ATOM     12  O   ALA   106      17.867  13.694   8.761  1.00  0.00              
ATOM     13  N   GLU   107      16.256  15.150   9.078  1.00  0.00              
ATOM     14  CA  GLU   107      16.395  15.050  10.563  1.00  0.00              
ATOM     15  C   GLU   107      15.913  13.683  11.062  1.00  0.00              
ATOM     16  O   GLU   107      14.983  13.588  11.838  1.00  0.00              
ATOM     17  N   GLY   108      16.542  12.625  10.624  1.00  0.00              
ATOM     18  CA  GLY   108      16.129  11.261  11.072  1.00  0.00              
ATOM     19  C   GLY   108      14.613  11.096  10.937  1.00  0.00              
ATOM     20  O   GLY   108      14.006  10.303  11.627  1.00  0.00              
ATOM     21  N   GLU   109      13.996  11.832  10.053  1.00  0.00              
ATOM     22  CA  GLU   109      12.521  11.695   9.883  1.00  0.00              
ATOM     23  C   GLU   109      12.207  10.416   9.104  1.00  0.00              
ATOM     24  O   GLU   109      12.597  10.263   7.964  1.00  0.00              
ATOM     25  N   MET   110      11.511   9.494   9.708  1.00  0.00              
ATOM     26  CA  MET   110      11.183   8.226   8.994  1.00  0.00              
ATOM     27  C   MET   110       9.748   8.280   8.469  1.00  0.00              
ATOM     28  O   MET   110       8.880   8.879   9.071  1.00  0.00              
ATOM     29  N   LYS   111       9.490   7.662   7.349  1.00  0.00              
ATOM     30  CA  LYS   111       8.109   7.682   6.788  1.00  0.00              
ATOM     31  C   LYS   111       7.544   6.260   6.720  1.00  0.00              
ATOM     32  O   LYS   111       8.163   5.361   6.185  1.00  0.00              
ATOM     33  N   CYS   112       6.374   6.051   7.257  1.00  0.00              
ATOM     34  CA  CYS   112       5.770   4.688   7.222  1.00  0.00              
ATOM     35  C   CYS   112       5.362   4.330   5.795  1.00  0.00              
ATOM     36  O   CYS   112       4.437   4.897   5.248  1.00  0.00              
ATOM     37  N   ARG   113       6.019   3.382   5.195  1.00  0.00              
ATOM     38  CA  ARG   113       5.631   2.986   3.814  1.00  0.00              
ATOM     39  C   ARG   113       4.255   2.309   3.840  1.00  0.00              
ATOM     40  O   ARG   113       3.646   2.075   2.815  1.00  0.00              
ATOM     41  N   ASN   114       3.769   1.980   5.010  1.00  0.00              
ATOM     42  CA  ASN   114       2.447   1.302   5.111  1.00  0.00              
ATOM     43  C   ASN   114       1.289   2.310   5.119  1.00  0.00              
ATOM     44  O   ASN   114       0.255   2.064   4.531  1.00  0.00              
ATOM     45  N   CYS   115       1.428   3.428   5.791  1.00  0.00              
ATOM     46  CA  CYS   115       0.290   4.397   5.821  1.00  0.00              
ATOM     47  C   CYS   115       0.722   5.798   5.358  1.00  0.00              
ATOM     48  O   CYS   115      -0.046   6.522   4.758  1.00  0.00              
ATOM     49  N   GLY   116       1.936   6.187   5.626  1.00  0.00              
ATOM     50  CA  GLY   116       2.395   7.540   5.190  1.00  0.00              
ATOM     51  C   GLY   116       2.638   8.426   6.416  1.00  0.00              
ATOM     52  O   GLY   116       2.641   9.637   6.329  1.00  0.00              
ATOM     53  N   HIS   117       2.849   7.829   7.555  1.00  0.00              
ATOM     54  CA  HIS   117       3.101   8.627   8.786  1.00  0.00              
ATOM     55  C   HIS   117       4.576   9.024   8.846  1.00  0.00              
ATOM     56  O   HIS   117       5.424   8.382   8.260  1.00  0.00              
ATOM     57  N   ILE   118       4.890  10.076   9.545  1.00  0.00              
ATOM     58  CA  ILE   118       6.314  10.507   9.631  1.00  0.00              
ATOM     59  C   ILE   118       6.782  10.509  11.091  1.00  0.00              
ATOM     60  O   ILE   118       6.377  11.338  11.881  1.00  0.00              
ATOM     61  N   TYR   119       7.642   9.595  11.448  1.00  0.00              
ATOM     62  CA  TYR   119       8.145   9.555  12.849  1.00  0.00              
ATOM     63  C   TYR   119       9.170  10.673  13.060  1.00  0.00              
ATOM     64  O   TYR   119      10.133  10.794  12.330  1.00  0.00              
ATOM     65  N   TYR   120       8.971  11.485  14.060  1.00  0.00              
ATOM     66  CA  TYR   120       9.936  12.588  14.325  1.00  0.00              
ATOM     67  C   TYR   120      10.843  12.207  15.503  1.00  0.00              
ATOM     68  O   TYR   120      10.386  12.128  16.627  1.00  0.00              
ATOM     69  N   ILE   121      12.103  11.980  15.216  1.00  0.00              
ATOM     70  CA  ILE   121      13.060  11.602  16.285  1.00  0.00              
ATOM     71  C   ILE   121      13.312  12.775  17.232  1.00  0.00              
ATOM     72  O   ILE   121      12.895  12.767  18.373  1.00  0.00              
ATOM     73  N   LYS   122      13.988  13.781  16.764  1.00  0.00              
ATOM     74  CA  LYS   122      14.275  14.968  17.625  1.00  0.00              
ATOM     75  C   LYS   122      13.002  15.432  18.346  1.00  0.00              
ATOM     76  O   LYS   122      13.057  16.026  19.403  1.00  0.00              
ATOM     77  N   ASN   123      11.856  15.159  17.781  1.00  0.00              
ATOM     78  CA  ASN   123      10.584  15.580  18.435  1.00  0.00              
ATOM     79  C   ASN   123      10.036  14.446  19.303  1.00  0.00              
ATOM     80  O   ASN   123       9.443  14.676  20.340  1.00  0.00              
ATOM     81  N   GLY   124      10.235  13.225  18.894  1.00  0.00              
ATOM     82  CA  GLY   124       9.735  12.079  19.701  1.00  0.00              
ATOM     83  C   GLY   124       8.307  11.730  19.286  1.00  0.00              
ATOM     84  O   GLY   124       7.583  12.547  18.752  1.00  0.00              
END
