
#######################################################
#                                                     #
#                        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   25 (  108),  selected   25 , name T0319AL381_2
# Molecule2: number of CA atoms  135 ( 1055),  selected   25 , name T0319.pdb
# PARAMETERS: T0319AL381_2.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:    23       109 - 131         4.31     6.21
  LCS_AVERAGE:     16.27

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       109 - 122         1.06     7.31
  LCS_AVERAGE:      7.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       109 - 121         0.87     7.68
  LCS_AVERAGE:      6.61

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     E     109     E     109     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     M     110     M     110     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     K     111     K     111     13   14   23     5   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     C     112     C     112     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     R     113     R     113     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     N     114     N     114     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     C     115     C     115     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     G     116     G     116     13   14   23     3    3   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     H     117     H     117     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     I     118     I     118     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     Y     119     Y     119     13   14   23     9   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     Y     120     Y     120     13   14   23     5   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     I     121     I     121     13   14   23     5   11   12   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     K     122     K     122      5   14   23     3    5   11   14   14   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     N     123     N     123      4    6   23     3    3    4    4    4    7    7    8   12   17   18   22   22   22   23   23   23   23   23   23 
LCS_GDT     G     124     G     124      4    6   23     3    4    4    4    4    7   10   13   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     I     125     I     125      4    6   23     3    4    4    4    4    7   10   13   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     P     126     P     126      4    6   23     3    4    4    4    5    7    7    8   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     N     127     N     127      4    6   23     3    4    4    4    5    7    7    8    8   12   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     L     128     L     128      4    6   23     3    4    4    4    6    7    7   10   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     L     129     L     129      5    6   23     4    5    5    5    6    7   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     L     130     L     130      5    6   23     4    5    5    9   12   15   16   16   17   18   21   22   22   22   23   23   23   23   23   23 
LCS_GDT     P     131     P     131      5    6   23     4    5    5    5    6    6    7    7    7    9    9   12   17   21   23   23   23   23   23   23 
LCS_GDT     P     132     P     132      5    6   10     4    5    5    5    6    6    7    7    7    9    9    9    9   10   10   11   11   12   14   16 
LCS_GDT     H     133     H     133      5    6   10     3    5    5    5    6    6    7    7    7    9    9    9    9   10   10   11   11   12   12   13 
LCS_AVERAGE  LCS_A:  10.21  (   6.61    7.76   16.27 )

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     11     12     14     14     15     16     16     17     18     21     22     22     22     23     23     23     23     23     23 
GDT PERCENT_CA   6.67   8.15   8.89  10.37  10.37  11.11  11.85  11.85  12.59  13.33  15.56  16.30  16.30  16.30  17.04  17.04  17.04  17.04  17.04  17.04
GDT RMS_LOCAL    0.35   0.54   0.63   1.06   1.06   1.47   1.69   1.69   2.21   2.68   3.53   3.73   3.73   3.73   4.31   4.31   4.31   4.31   4.31   4.31
GDT RMS_ALL_CA   7.99   7.75   7.47   7.31   7.31   6.48   6.48   6.48   6.51   6.45   6.58   6.53   6.53   6.53   6.21   6.21   6.21   6.21   6.21   6.21

#      Molecule1      Molecule2       DISTANCE
LGA    E     109      E     109          0.369
LGA    M     110      M     110          1.051
LGA    K     111      K     111          1.583
LGA    C     112      C     112          1.223
LGA    R     113      R     113          1.286
LGA    N     114      N     114          0.789
LGA    C     115      C     115          0.342
LGA    G     116      G     116          2.611
LGA    H     117      H     117          0.905
LGA    I     118      I     118          1.214
LGA    Y     119      Y     119          1.915
LGA    Y     120      Y     120          0.681
LGA    I     121      I     121          0.961
LGA    K     122      K     122          1.913
LGA    N     123      N     123          8.885
LGA    G     124      G     124          8.482
LGA    I     125      I     125          8.550
LGA    P     126      P     126          7.755
LGA    N     127      N     127          8.384
LGA    L     128      L     128          6.348
LGA    L     129      L     129          3.558
LGA    L     130      L     130          2.765
LGA    P     131      P     131          9.813
LGA    P     132      P     132         14.547
LGA    H     133      H     133         17.394

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25  135    4.0     16    1.69    11.852    11.067     0.893

LGA_LOCAL      RMSD =  1.691  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.484  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  5.850  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.078113 * X  +   0.533643 * Y  +   0.842095 * Z  +  -3.275434
  Y_new =  -0.923187 * X  +   0.280132 * Y  +  -0.263157 * Z  +   3.551310
  Z_new =  -0.376330 * X  +  -0.797967 * Y  +   0.470770 * Z  +  19.613489 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.037791    2.103802  [ DEG:   -59.4610    120.5390 ]
  Theta =   0.385832    2.755761  [ DEG:    22.1065    157.8935 ]
  Phi   =  -1.655207    1.486385  [ DEG:   -94.8364     85.1636 ]
 
# 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_2                                  
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_2.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25  135   4.0   16   1.69  11.067     5.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_2
REMARK Aligment from pdb entry: 1yk4A
ATOM      1  N   GLU   109      13.797  12.327   9.291  1.00  0.00              
ATOM      2  CA AGLU   109      12.445  11.876   9.178  1.00  0.00              
ATOM      3  CA BGLU   109      12.432  11.813   9.233  1.00  0.00              
ATOM      4  C   GLU   109      12.321  10.739   8.167  1.00  0.00              
ATOM      5  O   GLU   109      12.966  10.811   7.112  1.00  0.00              
ATOM      6  N   MET   110      11.464   9.753   8.466  1.00  0.00              
ATOM      7  CA  MET   110      11.265   8.607   7.588  1.00  0.00              
ATOM      8  C   MET   110       9.767   8.335   7.448  1.00  0.00              
ATOM      9  O   MET   110       9.038   8.250   8.430  1.00  0.00              
ATOM     10  N   LYS   111       9.321   8.149   6.206  1.00  0.00              
ATOM     11  CA  LYS   111       7.925   7.805   5.950  1.00  0.00              
ATOM     12  C   LYS   111       7.712   6.303   5.978  1.00  0.00              
ATOM     13  O   LYS   111       8.473   5.541   5.369  1.00  0.00              
ATOM     14  N   CYS   112       6.619   5.873   6.639  1.00  0.00              
ATOM     15  CA  CYS   112       6.127   4.507   6.456  1.00  0.00              
ATOM     16  C   CYS   112       5.594   4.388   5.036  1.00  0.00              
ATOM     17  O   CYS   112       4.758   5.206   4.605  1.00  0.00              
ATOM     18  N   ARG   113       6.039   3.381   4.271  1.00  0.00              
ATOM     19  CA  ARG   113       5.583   3.261   2.899  1.00  0.00              
ATOM     20  C  AARG   113       4.047   2.931   2.827  1.00  0.00              
ATOM     21  C  BARG   113       4.158   2.969   2.783  1.00  0.00              
ATOM     22  O  AARG   113       3.497   3.138   1.800  1.00  0.00              
ATOM     23  O  BARG   113       3.467   3.337   1.774  1.00  0.00              
ATOM     24  N  AASN   114       3.539   2.338   3.909  1.00  0.00              
ATOM     25  N  BASN   114       3.518   2.273   3.711  1.00  0.00              
ATOM     26  CA AASN   114       2.276   1.595   3.898  1.00  0.00              
ATOM     27  CA BASN   114       2.128   1.859   3.475  1.00  0.00              
ATOM     28  C  AASN   114       1.145   2.431   4.533  1.00  0.00              
ATOM     29  C  BASN   114       1.092   2.529   4.362  1.00  0.00              
ATOM     30  O  AASN   114      -0.045   2.080   4.336  1.00  0.00              
ATOM     31  O  BASN   114      -0.064   2.057   4.452  1.00  0.00              
ATOM     32  N  ACYS   115       1.487   3.477   5.255  1.00  0.00              
ATOM     33  N  BCYS   115       1.352   3.646   5.029  1.00  0.00              
ATOM     34  CA  CYS   115       0.405   4.388   5.766  1.00  0.00              
ATOM     35  C   CYS   115       0.962   5.818   5.863  1.00  0.00              
ATOM     36  O   CYS   115       2.080   6.088   5.478  1.00  0.00              
ATOM     37  N   GLY   116       0.159   6.718   6.454  1.00  0.00              
ATOM     38  CA  GLY   116       0.562   8.119   6.526  1.00  0.00              
ATOM     39  C   GLY   116       1.547   8.473   7.651  1.00  0.00              
ATOM     40  O   GLY   116       1.946   9.640   7.751  1.00  0.00              
ATOM     41  N   HIS   117       1.944   7.503   8.453  1.00  0.00              
ATOM     42  CA  HIS   117       2.858   7.795   9.559  1.00  0.00              
ATOM     43  C   HIS   117       4.242   8.237   9.046  1.00  0.00              
ATOM     44  O   HIS   117       4.751   7.727   8.023  1.00  0.00              
ATOM     45  N   ILE   118       4.842   9.131   9.834  1.00  0.00              
ATOM     46  CA  ILE   118       6.203   9.618   9.660  1.00  0.00              
ATOM     47  C   ILE   118       6.914   9.453  11.008  1.00  0.00              
ATOM     48  O   ILE   118       6.436   9.991  12.022  1.00  0.00              
ATOM     49  N   TYR   119       8.030   8.700  11.005  1.00  0.00              
ATOM     50  CA  TYR   119       8.898   8.622  12.178  1.00  0.00              
ATOM     51  C   TYR   119       9.897   9.784  12.119  1.00  0.00              
ATOM     52  O   TYR   119      10.752   9.839  11.220  1.00  0.00              
ATOM     53  N   TYR   120       9.771  10.712  13.072  1.00  0.00              
ATOM     54  CA  TYR   120      10.722  11.812  13.191  1.00  0.00              
ATOM     55  C   TYR   120      11.620  11.473  14.382  1.00  0.00              
ATOM     56  O   TYR   120      11.107  11.282  15.509  1.00  0.00              
ATOM     57  N   ILE   121      12.932  11.349  14.155  1.00  0.00              
ATOM     58  CA  ILE   121      13.849  11.030  15.244  1.00  0.00              
ATOM     59  C   ILE   121      13.723  11.998  16.418  1.00  0.00              
ATOM     60  O   ILE   121      13.943  11.609  17.576  1.00  0.00              
ATOM     61  N   LYS   122      13.387  13.275  16.150  1.00  0.00              
ATOM     62  CA  LYS   122      13.201  14.247  17.219  1.00  0.00              
ATOM     63  C   LYS   122      11.899  14.063  18.014  1.00  0.00              
ATOM     64  O   LYS   122      11.748  14.655  19.101  1.00  0.00              
ATOM     65  N   ASN   123      10.953  13.286  17.474  1.00  0.00              
ATOM     66  CA  ASN   123       9.732  12.924  18.191  1.00  0.00              
ATOM     67  C   ASN   123       9.822  11.589  18.937  1.00  0.00              
ATOM     68  O   ASN   123       9.151  11.410  19.965  1.00  0.00              
ATOM     69  N   GLY   124      10.591  10.634  18.392  1.00  0.00              
ATOM     70  CA  GLY   124      10.498   9.279  18.923  1.00  0.00              
ATOM     71  C   GLY   124       9.102   8.684  18.693  1.00  0.00              
ATOM     72  O   GLY   124       8.352   9.111  17.817  1.00  0.00              
ATOM     73  N   ILE   125       8.799   7.655  19.508  1.00  0.00              
ATOM     74  CA  ILE   125       7.518   6.943  19.476  1.00  0.00              
ATOM     75  C   ILE   125       7.147   6.701  20.952  1.00  0.00              
ATOM     76  O   ILE   125       7.173   5.565  21.460  1.00  0.00              
ATOM     77  N   PRO   126       6.859   7.797  21.665  1.00  0.00              
ATOM     78  CA  PRO   126       6.808   7.706  23.142  1.00  0.00              
ATOM     79  C   PRO   126       5.672   6.833  23.651  1.00  0.00              
ATOM     80  O   PRO   126       5.815   6.243  24.748  1.00  0.00              
ATOM     81  N   ASN   127       4.550   6.766  22.950  1.00  0.00              
ATOM     82  CA  ASN   127       3.442   5.975  23.473  1.00  0.00              
ATOM     83  C   ASN   127       3.794   4.487  23.548  1.00  0.00              
ATOM     84  O   ASN   127       3.212   3.730  24.338  1.00  0.00              
ATOM     85  N   LEU   128       4.759   4.057  22.718  1.00  0.00              
ATOM     86  CA  LEU   128       5.200   2.678  22.665  1.00  0.00              
ATOM     87  C   LEU   128       6.606   2.494  23.288  1.00  0.00              
ATOM     88  O   LEU   128       7.240   1.464  23.094  1.00  0.00              
ATOM     89  N   LEU   129       7.085   3.475  24.040  1.00  0.00              
ATOM     90  CA  LEU   129       8.313   3.337  24.823  1.00  0.00              
ATOM     91  C   LEU   129       9.619   3.736  24.145  1.00  0.00              
ATOM     92  O   LEU   129      10.691   3.342  24.620  1.00  0.00              
ATOM     93  N   LEU   130       9.540   4.533  23.073  1.00  0.00              
ATOM     94  CA  LEU   130      10.725   5.039  22.370  1.00  0.00              
ATOM     95  C   LEU   130      10.818   6.551  22.640  1.00  0.00              
ATOM     96  O   LEU   130       9.971   7.339  22.190  1.00  0.00              
ATOM     97  N   PRO   131      11.853   6.955  23.373  1.00  0.00              
ATOM     98  CA  PRO   131      11.977   8.359  23.749  1.00  0.00              
ATOM     99  C   PRO   131      12.244   9.259  22.543  1.00  0.00              
ATOM    100  O   PRO   131      12.922   8.873  21.567  1.00  0.00              
ATOM    101  N   PRO   132      11.806  10.519  22.634  1.00  0.00              
ATOM    102  CA  PRO   132      12.242  11.524  21.646  1.00  0.00              
ATOM    103  C   PRO   132      13.759  11.541  21.549  1.00  0.00              
ATOM    104  O   PRO   132      14.473  11.415  22.557  1.00  0.00              
ATOM    105  N   HIS   133      14.261  11.751  20.313  1.00  0.00              
ATOM    106  CA  HIS   133      15.666  11.794  20.032  1.00  0.00              
ATOM    107  C   HIS   133      16.260  10.418  19.657  1.00  0.00              
ATOM    108  O   HIS   133      17.447  10.322  19.292  1.00  0.00              
END
