
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0304AL381_4-D1
# Molecule2: number of CA atoms  101 (  799),  selected   22 , name T0304_D1.pdb
# PARAMETERS: T0304AL381_4-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:    22        96 - 117         4.37     4.37
  LCS_AVERAGE:     21.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       106 - 117         1.96     7.18
  LCS_AVERAGE:     10.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       110 - 117         0.75     6.80
  LCS_AVERAGE:      6.57

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     G      96     G      96      6    9   22     3    4    5    6   13   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     L      97     L      97      7    9   22     5    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     T      98     T      98      7    9   22     5    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     C      99     C      99      7    9   22     5    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     K     100     K     100      7    9   22     5    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     A     101     A     101      7    9   22     5    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     D     102     D     102      7    9   22     3    5    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     T     103     T     103      7    9   22     0    6    9   11   14   17   17   17   18   19   19   19   21   21   21   21   22   22   22   22 
LCS_GDT     L     104     L     104      0    9   22     0    3    4    6    8   11   12   16   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     S     105     S     105      3    3   22     3    3    3    3    4    4    5    7   10   13   17   20   21   21   21   21   22   22   22   22 
LCS_GDT     S     106     S     106      3   12   22     3    3    3    3    4    4    5    6   12   15   17   20   21   21   21   21   22   22   22   22 
LCS_GDT     C     107     C     107      7   12   22     3    6    8   11   11   11   12   14   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     D     108     D     108      7   12   22     4    6    8   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     Y     109     Y     109      7   12   22     3    6    8   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     V     110     V     110      8   12   22     3    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     Y     111     Y     111      8   12   22     5    6    8   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     L     112     L     112      8   12   22     5    6    9   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     A     113     A     113      8   12   22     5    6    8   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     V     114     V     114      8   12   22     4    6    8   11   11   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     Y     115     Y     115      8   12   22     5    6    8   11   14   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     P     116     P     116      8   12   22     5    6    8   11   13   17   17   17   18   19   19   20   21   21   21   21   22   22   22   22 
LCS_GDT     T     117     T     117      8   12   22     4    6    8   11   11   11   11   11   12   12   12   14   14   15   16   21   22   22   22   22 
LCS_AVERAGE  LCS_A:  12.87  (   6.57   10.26   21.78 )

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      9     11     14     17     17     17     18     19     19     20     21     21     21     21     22     22     22     22 
GDT PERCENT_CA   4.95   5.94   8.91  10.89  13.86  16.83  16.83  16.83  17.82  18.81  18.81  19.80  20.79  20.79  20.79  20.79  21.78  21.78  21.78  21.78
GDT RMS_LOCAL    0.26   0.39   1.13   1.36   1.83   2.10   2.10   2.10   2.46   2.88   2.88   3.77   3.84   3.84   3.84   3.84   4.37   4.37   4.37   4.37
GDT RMS_ALL_CA   6.92   6.94   6.08   7.25   5.27   5.11   5.11   5.11   4.87   4.65   4.65   4.52   4.48   4.48   4.48   4.48   4.37   4.37   4.37   4.37

#      Molecule1      Molecule2       DISTANCE
LGA    G      96      G      96          2.553
LGA    L      97      L      97          1.953
LGA    T      98      T      98          2.419
LGA    C      99      C      99          2.130
LGA    K     100      K     100          1.934
LGA    A     101      A     101          1.833
LGA    D     102      D     102          1.635
LGA    T     103      T     103          1.027
LGA    L     104      L     104          6.380
LGA    S     105      S     105         12.600
LGA    S     106      S     106         11.607
LGA    C     107      C     107          8.403
LGA    D     108      D     108          1.692
LGA    Y     109      Y     109          1.967
LGA    V     110      V     110          2.265
LGA    Y     111      Y     111          2.411
LGA    L     112      L     112          1.690
LGA    A     113      A     113          2.284
LGA    V     114      V     114          2.937
LGA    Y     115      Y     115          1.446
LGA    P     116      P     116          2.683
LGA    T     117      T     117          9.772

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  101    4.0     17    2.10    13.614    13.956     0.771

LGA_LOCAL      RMSD =  2.104  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.115  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  4.369  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.445793 * X  +  -0.874432 * Y  +  -0.191410 * Z  + 142.382797
  Y_new =  -0.862519 * X  +  -0.476811 * Y  +   0.169448 * Z  + -26.674484
  Z_new =  -0.239437 * X  +   0.089556 * Y  +  -0.966773 * Z  + 238.613754 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.049222   -0.092370  [ DEG:   174.7076     -5.2924 ]
  Theta =   0.241786    2.899807  [ DEG:    13.8533    166.1467 ]
  Phi   =  -1.093760    2.047833  [ DEG:   -62.6678    117.3322 ]
 
# 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_4-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_4-D1.T0304_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  101   4.0   17   2.10  13.956     4.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_4-D1
REMARK Aligment from pdb entry: 2alaA
ATOM      1  N   GLY    96      47.106  25.291  27.836  1.00  0.00              
ATOM      2  CA  GLY    96      47.034  26.613  28.473  1.00  0.00              
ATOM      3  C   GLY    96      46.964  26.495  30.003  1.00  0.00              
ATOM      4  O   GLY    96      46.135  27.137  30.652  1.00  0.00              
ATOM      5  N   LEU    97      47.844  25.674  30.571  1.00  0.00              
ATOM      6  CA  LEU    97      47.884  25.471  32.018  1.00  0.00              
ATOM      7  C   LEU    97      48.548  26.657  32.718  1.00  0.00              
ATOM      8  O   LEU    97      49.719  26.957  32.476  1.00  0.00              
ATOM      9  N   THR    98      47.789  27.325  33.582  1.00  0.00              
ATOM     10  CA  THR    98      48.297  28.438  34.382  1.00  0.00              
ATOM     11  C   THR    98      47.837  28.293  35.831  1.00  0.00              
ATOM     12  O   THR    98      46.831  27.638  36.105  1.00  0.00              
ATOM     13  N   CYS    99      48.573  28.920  36.747  1.00  0.00              
ATOM     14  CA  CYS    99      48.407  28.686  38.181  1.00  0.00              
ATOM     15  C   CYS    99      48.341  29.980  38.991  1.00  0.00              
ATOM     16  O   CYS    99      49.359  30.644  39.193  1.00  0.00              
ATOM     17  N   LYS   100      47.141  30.321  39.461  1.00  0.00              
ATOM     18  CA  LYS   100      46.937  31.473  40.344  1.00  0.00              
ATOM     19  C   LYS   100      46.815  31.007  41.798  1.00  0.00              
ATOM     20  O   LYS   100      46.290  29.925  42.067  1.00  0.00              
ATOM     21  N   ALA   101      47.308  31.830  42.724  1.00  0.00              
ATOM     22  CA  ALA   101      47.219  31.553  44.157  1.00  0.00              
ATOM     23  C   ALA   101      46.293  32.578  44.808  1.00  0.00              
ATOM     24  O   ALA   101      46.578  33.776  44.790  1.00  0.00              
ATOM     25  N   ASP   102      45.189  32.101  45.378  1.00  0.00              
ATOM     26  CA  ASP   102      44.180  32.978  45.978  1.00  0.00              
ATOM     27  C   ASP   102      44.643  33.519  47.328  1.00  0.00              
ATOM     28  O   ASP   102      44.745  34.733  47.515  1.00  0.00              
ATOM     29  N   THR   103      44.910  32.611  48.264  1.00  0.00              
ATOM     30  CA  THR   103      45.412  32.971  49.591  1.00  0.00              
ATOM     31  C   THR   103      46.424  31.934  50.064  1.00  0.00              
ATOM     32  O   THR   103      46.483  30.823  49.533  1.00  0.00              
ATOM     33  N   LEU   104      47.214  32.305  51.068  1.00  0.00              
ATOM     34  CA  LEU   104      48.306  31.457  51.540  1.00  0.00              
ATOM     35  C   LEU   104      48.835  31.895  52.911  1.00  0.00              
ATOM     36  O   LEU   104      48.853  33.086  53.226  1.00  0.00              
ATOM     37  N   SER   105      51.727  26.837  58.001  1.00  0.00              
ATOM     38  CA  SER   105      50.560  26.137  58.537  1.00  0.00              
ATOM     39  C   SER   105      50.539  24.689  58.048  1.00  0.00              
ATOM     40  O   SER   105      51.438  24.260  57.317  1.00  0.00              
ATOM     41  N   SER   106      49.519  23.937  58.460  1.00  0.00              
ATOM     42  CA  SER   106      49.348  22.560  58.001  1.00  0.00              
ATOM     43  C   SER   106      49.045  22.557  56.501  1.00  0.00              
ATOM     44  O   SER   106      49.723  21.875  55.736  1.00  0.00              
ATOM     45  N   CYS   107      48.030  23.324  56.096  1.00  0.00              
ATOM     46  CA  CYS   107      47.688  23.517  54.677  1.00  0.00              
ATOM     47  C   CYS   107      47.098  24.912  54.447  1.00  0.00              
ATOM     48  O   CYS   107      45.903  25.057  54.173  1.00  0.00              
ATOM     49  N   ASP   108      47.941  25.935  54.561  1.00  0.00              
ATOM     50  CA  ASP   108      47.500  27.322  54.419  1.00  0.00              
ATOM     51  C   ASP   108      47.212  27.748  52.988  1.00  0.00              
ATOM     52  O   ASP   108      46.403  28.647  52.756  1.00  0.00              
ATOM     53  N   TYR   109      47.869  27.099  52.030  1.00  0.00              
ATOM     54  CA  TYR   109      47.797  27.501  50.627  1.00  0.00              
ATOM     55  C   TYR   109      46.469  27.217  49.942  1.00  0.00              
ATOM     56  O   TYR   109      45.829  26.197  50.208  1.00  0.00              
ATOM     57  N   VAL   110      46.064  28.131  49.060  1.00  0.00              
ATOM     58  CA  VAL   110      44.858  27.970  48.241  1.00  0.00              
ATOM     59  C   VAL   110      45.123  28.475  46.816  1.00  0.00              
ATOM     60  O   VAL   110      45.031  29.677  46.550  1.00  0.00              
ATOM     61  N   TYR   111      45.452  27.552  45.911  1.00  0.00              
ATOM     62  CA  TYR   111      45.724  27.887  44.509  1.00  0.00              
ATOM     63  C   TYR   111      44.674  27.284  43.580  1.00  0.00              
ATOM     64  O   TYR   111      44.019  26.301  43.927  1.00  0.00              
ATOM     65  N   LEU   112      44.532  27.882  42.396  1.00  0.00              
ATOM     66  CA  LEU   112      43.616  27.393  41.361  1.00  0.00              
ATOM     67  C   LEU   112      44.324  27.349  40.004  1.00  0.00              
ATOM     68  O   LEU   112      45.184  28.187  39.717  1.00  0.00              
ATOM     69  N   ALA   113      43.955  26.371  39.179  1.00  0.00              
ATOM     70  CA  ALA   113      44.562  26.190  37.863  1.00  0.00              
ATOM     71  C   ALA   113      43.540  26.373  36.746  1.00  0.00              
ATOM     72  O   ALA   113      42.529  25.671  36.705  1.00  0.00              
ATOM     73  N   VAL   114      43.808  27.320  35.849  1.00  0.00              
ATOM     74  CA  VAL   114      43.016  27.478  34.630  1.00  0.00              
ATOM     75  C   VAL   114      43.686  26.707  33.496  1.00  0.00              
ATOM     76  O   VAL   114      44.914  26.601  33.444  1.00  0.00              
ATOM     77  N   TYR   115      42.867  26.171  32.594  1.00  0.00              
ATOM     78  CA  TYR   115      43.339  25.278  31.536  1.00  0.00              
ATOM     79  C   TYR   115      42.241  25.028  30.497  1.00  0.00              
ATOM     80  O   TYR   115      41.136  25.567  30.600  1.00  0.00              
ATOM     81  N   PRO   116      42.566  24.216  29.495  1.00  0.00              
ATOM     82  CA  PRO   116      41.582  23.674  28.560  1.00  0.00              
ATOM     83  C   PRO   116      41.862  22.187  28.368  1.00  0.00              
ATOM     84  O   PRO   116      43.018  21.784  28.268  1.00  0.00              
ATOM     85  N   THR   117      40.808  21.379  28.319  1.00  0.00              
ATOM     86  CA  THR   117      40.949  19.942  28.087  1.00  0.00              
ATOM     87  C   THR   117      39.877  19.428  27.126  1.00  0.00              
ATOM     88  O   THR   117      38.753  19.933  27.108  1.00  0.00              
END
