
#######################################################
#                                                     #
#                        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 T0304AL381_3-D1
# Molecule2: number of CA atoms  101 (  799),  selected   21 , name T0304_D1.pdb
# PARAMETERS: T0304AL381_3-D1.T0304_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:    21        97 - 117         4.47     4.47
  LCS_AVERAGE:     20.79

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       106 - 117         1.86     7.02
  LCS_AVERAGE:     10.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       108 - 115         0.88     6.90
  LONGEST_CONTINUOUS_SEGMENT:     8       109 - 116         0.99     6.72
  LONGEST_CONTINUOUS_SEGMENT:     8       110 - 117         0.75     6.56
  LCS_AVERAGE:      6.84

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:  101
LCS_GDT     L      97     L      97      7    8   21     5    6    7   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     T      98     T      98      7    8   21     5    6    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     C      99     C      99      7    8   21     5    6    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     K     100     K     100      7    8   21     5    6    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     A     101     A     101      7    8   21     5    6    7   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     D     102     D     102      7    8   21     3    6    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     T     103     T     103      7    8   21     1    6    8   10   13   16   16   16   17   18   18   18   20   20   20   20   20   21   21   21 
LCS_GDT     L     104     L     104      3    8   21     0    3    4    5    8   11   11   15   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     S     105     S     105      3    4   21     3    3    3    3    4    5    6    6    8   12   15   19   20   20   20   20   20   21   21   21 
LCS_GDT     S     106     S     106      3   12   21     3    3    3    3    4    5    6    9   12   14   15   19   20   20   20   20   20   21   21   21 
LCS_GDT     C     107     C     107      7   12   21     3    6    7    9   11   11   11   12   16   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     D     108     D     108      8   12   21     3    6    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     Y     109     Y     109      8   12   21     3    6    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     V     110     V     110      8   12   21     3    7    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     Y     111     Y     111      8   12   21     3    7    8   10   11   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     L     112     L     112      8   12   21     4    7    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     A     113     A     113      8   12   21     4    7    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     V     114     V     114      8   12   21     4    7    8   10   11   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     Y     115     Y     115      8   12   21     4    7    8   10   13   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     P     116     P     116      8   12   21     3    7    8   10   12   16   16   16   17   18   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     T     117     T     117      8   12   21     3    7    8   10   11   11   11   11   12   12   12   12   13   14   16   20   20   21   21   21 
LCS_AVERAGE  LCS_A:  12.54  (   6.84   10.00   20.79 )

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      7      8     10     13     16     16     16     17     18     18     19     20     20     20     20     20     21     21     21 
GDT PERCENT_CA   4.95   6.93   7.92   9.90  12.87  15.84  15.84  15.84  16.83  17.82  17.82  18.81  19.80  19.80  19.80  19.80  19.80  20.79  20.79  20.79
GDT RMS_LOCAL    0.29   0.66   0.75   1.18   1.82   2.10   2.10   2.10   2.46   2.95   2.95   3.85   3.93   3.93   3.93   3.93   3.93   4.47   4.47   4.47
GDT RMS_ALL_CA   6.05   6.62   6.56   6.89   5.39   5.27   5.27   5.27   5.01   4.76   4.76   4.64   4.60   4.60   4.60   4.60   4.60   4.47   4.47   4.47

#      Molecule1      Molecule2       DISTANCE
LGA    L      97      L      97          2.045
LGA    T      98      T      98          2.224
LGA    C      99      C      99          2.216
LGA    K     100      K     100          2.072
LGA    A     101      A     101          2.045
LGA    D     102      D     102          1.522
LGA    T     103      T     103          1.345
LGA    L     104      L     104          6.263
LGA    S     105      S     105         12.960
LGA    S     106      S     106         11.486
LGA    C     107      C     107          8.776
LGA    D     108      D     108          1.839
LGA    Y     109      Y     109          1.894
LGA    V     110      V     110          2.172
LGA    Y     111      Y     111          2.748
LGA    L     112      L     112          1.709
LGA    A     113      A     113          1.999
LGA    V     114      V     114          3.000
LGA    Y     115      Y     115          1.131
LGA    P     116      P     116          2.741
LGA    T     117      T     117          9.797

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  101    4.0     16    2.10    13.119    13.290     0.727

LGA_LOCAL      RMSD =  2.100  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.268  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  4.470  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.230777 * X  +   0.255314 * Y  +   0.938913 * Z  +  11.363824
  Y_new =  -0.151931 * X  +   0.943668 * Y  +  -0.293950 * Z  +  68.291992
  Z_new =  -0.961072 * X  +  -0.210487 * Y  +  -0.178987 * Z  + 139.284836 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.275492    0.866100  [ DEG:  -130.3761     49.6239 ]
  Theta =   1.290856    1.850737  [ DEG:    73.9606    106.0394 ]
  Phi   =  -2.559374    0.582219  [ DEG:  -146.6413     33.3587 ]
 
# 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: T0304AL381_3-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_3-D1.T0304_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  101   4.0   16   2.10  13.290     4.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_3-D1
REMARK Aligment from pdb entry: 1rerA
ATOM      1  N   LEU    97      47.815  25.719  30.764  1.00  0.00              
ATOM      2  CA  LEU    97      47.718  25.654  32.206  1.00  0.00              
ATOM      3  C   LEU    97      48.047  26.992  32.833  1.00  0.00              
ATOM      4  O   LEU    97      48.903  27.725  32.332  1.00  0.00              
ATOM      5  N   THR    98      47.358  27.319  33.921  1.00  0.00              
ATOM      6  CA  THR    98      47.620  28.580  34.596  1.00  0.00              
ATOM      7  C   THR    98      47.348  28.543  36.097  1.00  0.00              
ATOM      8  O   THR    98      46.219  28.256  36.545  1.00  0.00              
ATOM      9  N   CYS    99      48.394  28.854  36.869  1.00  0.00              
ATOM     10  CA  CYS    99      48.310  28.845  38.325  1.00  0.00              
ATOM     11  C   CYS    99      47.995  30.210  38.902  1.00  0.00              
ATOM     12  O   CYS    99      48.481  31.234  38.411  1.00  0.00              
ATOM     13  N   LYS   100      47.204  30.223  39.965  1.00  0.00              
ATOM     14  CA  LYS   100      46.832  31.489  40.587  1.00  0.00              
ATOM     15  C   LYS   100      46.580  31.282  42.072  1.00  0.00              
ATOM     16  O   LYS   100      45.567  30.688  42.471  1.00  0.00              
ATOM     17  N   ALA   101      47.483  31.783  42.903  1.00  0.00              
ATOM     18  CA  ALA   101      47.318  31.612  44.340  1.00  0.00              
ATOM     19  C   ALA   101      46.484  32.709  44.991  1.00  0.00              
ATOM     20  O   ALA   101      46.900  33.868  45.011  1.00  0.00              
ATOM     21  N   ASP   102      45.320  32.345  45.534  1.00  0.00              
ATOM     22  CA  ASP   102      44.439  33.329  46.180  1.00  0.00              
ATOM     23  C   ASP   102      45.033  33.758  47.506  1.00  0.00              
ATOM     24  O   ASP   102      45.714  34.792  47.610  1.00  0.00              
ATOM     25  N   THR   103      44.752  32.953  48.527  1.00  0.00              
ATOM     26  CA  THR   103      45.274  33.204  49.861  1.00  0.00              
ATOM     27  C   THR   103      46.280  32.137  50.201  1.00  0.00              
ATOM     28  O   THR   103      46.233  31.021  49.659  1.00  0.00              
ATOM     29  N   LEU   104      47.190  32.511  51.095  1.00  0.00              
ATOM     30  CA  LEU   104      48.246  31.634  51.558  1.00  0.00              
ATOM     31  C   LEU   104      48.819  32.009  52.926  1.00  0.00              
ATOM     32  O   LEU   104      49.180  33.162  53.187  1.00  0.00              
ATOM     33  N   SER   105      51.937  26.481  58.113  1.00  0.00              
ATOM     34  CA  SER   105      50.740  25.842  58.651  1.00  0.00              
ATOM     35  C   SER   105      50.193  24.819  57.653  1.00  0.00              
ATOM     36  O   SER   105      50.025  25.115  56.471  1.00  0.00              
ATOM     37  N   SER   106      49.926  23.615  58.148  1.00  0.00              
ATOM     38  CA  SER   106      49.413  22.520  57.338  1.00  0.00              
ATOM     39  C   SER   106      48.415  22.968  56.283  1.00  0.00              
ATOM     40  O   SER   106      47.253  23.266  56.582  1.00  0.00              
ATOM     41  N   CYS   107      48.915  23.018  55.047  1.00  0.00              
ATOM     42  CA  CYS   107      48.158  23.412  53.858  1.00  0.00              
ATOM     43  C   CYS   107      47.413  24.724  54.021  1.00  0.00              
ATOM     44  O   CYS   107      46.180  24.771  53.959  1.00  0.00              
ATOM     45  N   ASP   108      48.174  25.791  54.208  1.00  0.00              
ATOM     46  CA  ASP   108      47.567  27.091  54.393  1.00  0.00              
ATOM     47  C   ASP   108      47.370  27.862  53.105  1.00  0.00              
ATOM     48  O   ASP   108      46.829  28.968  53.114  1.00  0.00              
ATOM     49  N   TYR   109      47.798  27.274  51.998  1.00  0.00              
ATOM     50  CA  TYR   109      47.667  27.943  50.724  1.00  0.00              
ATOM     51  C   TYR   109      46.581  27.343  49.866  1.00  0.00              
ATOM     52  O   TYR   109      46.176  26.198  50.062  1.00  0.00              
ATOM     53  N   VAL   110      46.121  28.127  48.898  1.00  0.00              
ATOM     54  CA  VAL   110      45.063  27.698  48.001  1.00  0.00              
ATOM     55  C   VAL   110      45.352  28.091  46.552  1.00  0.00              
ATOM     56  O   VAL   110      45.297  29.267  46.190  1.00  0.00              
ATOM     57  N   TYR   111      45.661  27.089  45.733  1.00  0.00              
ATOM     58  CA  TYR   111      45.974  27.295  44.328  1.00  0.00              
ATOM     59  C   TYR   111      44.742  27.073  43.486  1.00  0.00              
ATOM     60  O   TYR   111      43.846  26.329  43.866  1.00  0.00              
ATOM     61  N   LEU   112      44.695  27.723  42.335  1.00  0.00              
ATOM     62  CA  LEU   112      43.567  27.564  41.437  1.00  0.00              
ATOM     63  C   LEU   112      44.097  27.460  40.020  1.00  0.00              
ATOM     64  O   LEU   112      44.766  28.376  39.513  1.00  0.00              
ATOM     65  N   ALA   113      43.798  26.345  39.371  1.00  0.00              
ATOM     66  CA  ALA   113      44.306  26.164  38.032  1.00  0.00              
ATOM     67  C   ALA   113      43.257  26.354  36.964  1.00  0.00              
ATOM     68  O   ALA   113      42.178  25.767  37.036  1.00  0.00              
ATOM     69  N   VAL   114      43.571  27.192  35.977  1.00  0.00              
ATOM     70  CA  VAL   114      42.655  27.425  34.867  1.00  0.00              
ATOM     71  C   VAL   114      43.252  26.627  33.717  1.00  0.00              
ATOM     72  O   VAL   114      44.486  26.454  33.637  1.00  0.00              
ATOM     73  N   TYR   115      42.401  26.152  32.814  1.00  0.00              
ATOM     74  CA  TYR   115      42.920  25.343  31.718  1.00  0.00              
ATOM     75  C   TYR   115      41.881  25.029  30.649  1.00  0.00              
ATOM     76  O   TYR   115      40.746  25.539  30.662  1.00  0.00              
ATOM     77  N   PRO   116      42.303  24.168  29.725  1.00  0.00              
ATOM     78  CA  PRO   116      41.455  23.700  28.635  1.00  0.00              
ATOM     79  C   PRO   116      41.673  22.206  28.462  1.00  0.00              
ATOM     80  O   PRO   116      42.811  21.728  28.337  1.00  0.00              
ATOM     81  N   THR   117      40.577  21.468  28.456  1.00  0.00              
ATOM     82  CA  THR   117      40.653  20.033  28.287  1.00  0.00              
ATOM     83  C   THR   117      39.999  19.610  26.972  1.00  0.00              
ATOM     84  O   THR   117      39.259  20.385  26.348  1.00  0.00              
END
