
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0372AL044_5-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   19 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_5-D2.T0372_D2.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       120 - 136         4.63     5.26
  LCS_AVERAGE:      9.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       125 - 133         0.93    10.26
  LCS_AVERAGE:      3.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       125 - 133         0.93    10.26
  LCS_AVERAGE:      3.43

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:  172
LCS_GDT     R     118     R     118      4    5   16     4    4    4    4    5    5    6    8    8   10   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     A     119     A     119      4    5   16     4    4    4    4    5    5    6    8    8    9   12   12   12   14   16   16   19   19   19   19 
LCS_GDT     Y     120     Y     120      4    5   17     4    4    4    4    5    5    6    8    8    9   12   12   12   14   16   18   19   19   19   19 
LCS_GDT     A     121     A     121      4    5   17     4    4    4    4    5    5    6    8    8   10   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     D     122     D     122      3    5   17     3    3    3    3    5    5    6   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     Y     123     Y     123      3    3   17     3    3    3    3    3    5    6   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     I     124     I     124      3    4   17     3    3    3    3    4    6    8   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     Y     125     Y     125      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     L     126     L     126      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     R     127     R     127      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     S     128     S     128      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     D     129     D     129      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     L     130     L     130      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     A     131     A     131      9    9   17     7    8    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     T     132     T     132      9    9   17     3    8    9    9    9    9    9   10   11   12   13   15   17   17   17   18   19   19   19   19 
LCS_GDT     L     133     L     133      9    9   17     3    5    9    9    9    9    9   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     K     134     K     134      3    4   17     3    3    4    5    6    6    8   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     G     135     G     135      3    4   17     3    3    4    5    6    6    8   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_GDT     K     136     K     136      0    4   17     0    0    0    3    5    6    8   10   12   14   15   16   17   17   17   18   19   19   19   19 
LCS_AVERAGE  LCS_A:   5.69  (   3.43    3.82    9.82 )

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      7      8      9      9      9      9      9     10     12     14     15     16     17     17     17     18     19     19     19     19 
GDT PERCENT_CA   4.07   4.65   5.23   5.23   5.23   5.23   5.23   5.81   6.98   8.14   8.72   9.30   9.88   9.88   9.88  10.47  11.05  11.05  11.05  11.05
GDT RMS_LOCAL    0.34   0.53   0.93   0.93   0.93   0.93   0.93   2.43   3.31   3.74   3.90   4.13   4.33   4.33   4.33   4.77   5.08   5.08   5.08   5.08
GDT RMS_ALL_CA  10.34  10.38  10.26  10.26  10.26  10.26  10.26   9.48   6.88   5.48   5.46   5.27   5.32   5.32   5.32   5.15   5.08   5.08   5.08   5.08

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118         15.409
LGA    A     119      A     119         20.358
LGA    Y     120      Y     120         19.291
LGA    A     121      A     121         12.179
LGA    D     122      D     122          9.244
LGA    Y     123      Y     123         10.635
LGA    I     124      I     124          6.269
LGA    Y     125      Y     125          0.166
LGA    L     126      L     126          2.704
LGA    R     127      R     127          2.263
LGA    S     128      S     128          1.798
LGA    D     129      D     129          2.838
LGA    L     130      L     130          2.850
LGA    A     131      A     131          3.080
LGA    T     132      T     132          3.986
LGA    L     133      L     133          3.623
LGA    K     134      K     134          3.308
LGA    G     135      G     135          5.763
LGA    K     136      K     136          7.390

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  172    4.0     10    2.43     6.541     5.970     0.396

LGA_LOCAL      RMSD =  2.427  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.117  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  5.077  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.687725 * X  +  -0.096095 * Y  +   0.719583 * Z  + -13.616880
  Y_new =  -0.689410 * X  +  -0.397038 * Y  +   0.605867 * Z  +  44.537247
  Z_new =   0.227481 * X  +  -0.912758 * Y  +  -0.339302 * Z  +  40.807793 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.926700    1.214893  [ DEG:  -110.3918     69.6082 ]
  Theta =  -0.229490   -2.912103  [ DEG:   -13.1488   -166.8512 ]
  Phi   =  -0.786622    2.354971  [ DEG:   -45.0701    134.9299 ]
 
# 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: T0372AL044_5-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_5-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  172   4.0   10   2.43   5.970     5.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_5-D2
REMARK Aligment from pdb entry: 1x7v_A
ATOM    141  N   ARG   118      20.800  54.605  15.104  1.00  0.00              
ATOM    142  CA  ARG   118      22.059  53.862  15.168  1.00  0.00              
ATOM    143  C   ARG   118      22.906  54.355  16.333  1.00  0.00              
ATOM    144  O   ARG   118      23.544  53.550  17.014  1.00  0.00              
ATOM    145  N   ALA   119      22.879  55.662  16.574  1.00  0.00              
ATOM    146  CA  ALA   119      23.605  56.221  17.725  1.00  0.00              
ATOM    147  C   ALA   119      23.024  55.726  19.037  1.00  0.00              
ATOM    148  O   ALA   119      23.766  55.285  19.924  1.00  0.00              
ATOM    149  N   TYR   120      21.698  55.725  19.153  1.00  0.00              
ATOM    150  CA  TYR   120      21.038  55.159  20.339  1.00  0.00              
ATOM    151  C   TYR   120      21.344  53.671  20.520  1.00  0.00              
ATOM    152  O   TYR   120      21.575  53.199  21.640  1.00  0.00              
ATOM    153  N   ALA   121      21.323  52.929  19.432  1.00  0.00              
ATOM    154  CA  ALA   121      21.622  51.485  19.462  1.00  0.00              
ATOM    155  C   ALA   121      23.050  51.217  19.950  1.00  0.00              
ATOM    156  O   ALA   121      23.282  50.408  20.828  1.00  0.00              
ATOM    157  N   ASP   122      24.002  51.979  19.446  1.00  0.00              
ATOM    158  CA  ASP   122      25.375  51.916  19.963  1.00  0.00              
ATOM    159  C   ASP   122      25.476  52.245  21.486  1.00  0.00              
ATOM    160  O   ASP   122      26.176  51.589  22.249  1.00  0.00              
ATOM    161  N   TYR   123      24.790  53.278  21.935  1.00  0.00              
ATOM    162  CA  TYR   123      24.733  53.594  23.361  1.00  0.00              
ATOM    163  C   TYR   123      24.414  52.384  24.254  1.00  0.00              
ATOM    164  O   TYR   123      25.048  52.174  25.296  1.00  0.00              
ATOM    165  N   ILE   124      23.508  51.531  23.810  1.00  0.00              
ATOM    166  CA  ILE   124      23.111  50.377  24.641  1.00  0.00              
ATOM    167  C   ILE   124      24.070  49.200  24.647  1.00  0.00              
ATOM    168  O   ILE   124      23.928  48.232  25.453  1.00  0.00              
ATOM    169  N   TYR   125      25.054  49.263  23.760  1.00  0.00              
ATOM    170  CA  TYR   125      26.083  48.265  23.753  1.00  0.00              
ATOM    171  C   TYR   125      27.319  48.703  24.495  1.00  0.00              
ATOM    172  O   TYR   125      28.263  47.959  24.566  1.00  0.00              
ATOM    173  N   LEU   126      27.285  49.905  25.080  1.00  0.00              
ATOM    174  CA  LEU   126      28.454  50.425  25.762  1.00  0.00              
ATOM    175  C   LEU   126      28.577  49.749  27.092  1.00  0.00              
ATOM    176  O   LEU   126      27.592  49.268  27.644  1.00  0.00              
ATOM    177  N   ARG   127      29.806  49.797  27.599  1.00  0.00              
ATOM    178  CA  ARG   127      30.217  49.322  28.911  1.00  0.00              
ATOM    179  C   ARG   127      29.461  50.022  30.034  1.00  0.00              
ATOM    180  O   ARG   127      28.903  49.369  30.879  1.00  0.00              
ATOM    181  N   SER   128      29.431  51.350  30.001  1.00  0.00              
ATOM    182  CA  SER   128      28.712  52.136  31.011  1.00  0.00              
ATOM    183  C   SER   128      27.228  51.817  31.055  1.00  0.00              
ATOM    184  O   SER   128      26.655  51.619  32.141  1.00  0.00              
ATOM    185  N   ASP   129      26.602  51.711  29.895  1.00  0.00              
ATOM    186  CA  ASP   129      25.208  51.426  29.861  1.00  0.00              
ATOM    187  C   ASP   129      24.910  50.023  30.411  1.00  0.00              
ATOM    188  O   ASP   129      23.939  49.815  31.168  1.00  0.00              
ATOM    189  N   LEU   130      25.715  49.048  30.013  1.00  0.00              
ATOM    190  CA  LEU   130      25.491  47.682  30.507  1.00  0.00              
ATOM    191  C   LEU   130      25.831  47.531  31.988  1.00  0.00              
ATOM    192  O   LEU   130      25.181  46.755  32.673  1.00  0.00              
ATOM    193  N   ALA   131      26.799  48.297  32.494  1.00  0.00              
ATOM    194  CA  ALA   131      27.060  48.321  33.942  1.00  0.00              
ATOM    195  C   ALA   131      25.871  48.816  34.786  1.00  0.00              
ATOM    196  O   ALA   131      25.667  48.351  35.932  1.00  0.00              
ATOM    197  N   THR   132      25.085  49.728  34.223  1.00  0.00              
ATOM    198  CA  THR   132      23.895  50.195  34.902  1.00  0.00              
ATOM    199  C   THR   132      22.877  49.035  35.012  1.00  0.00              
ATOM    200  O   THR   132      22.268  48.797  36.087  1.00  0.00              
ATOM    201  N   LEU   133      22.771  48.278  33.918  1.00  0.00              
ATOM    202  CA  LEU   133      21.904  47.108  33.843  1.00  0.00              
ATOM    203  C   LEU   133      22.298  46.013  34.818  1.00  0.00              
ATOM    204  O   LEU   133      21.427  45.254  35.262  1.00  0.00              
ATOM    205  N   LYS   134      23.580  45.923  35.149  1.00  0.00              
ATOM    206  CA  LYS   134      24.119  44.802  35.923  1.00  0.00              
ATOM    207  C   LYS   134      24.000  44.974  37.427  1.00  0.00              
ATOM    208  O   LYS   134      24.902  45.472  38.104  1.00  0.00              
ATOM    209  N   GLY   135      22.879  44.509  37.942  1.00  0.00              
ATOM    210  CA  GLY   135      22.718  44.350  39.360  1.00  0.00              
ATOM    211  C   GLY   135      21.748  45.345  39.951  1.00  0.00              
ATOM    212  O   GLY   135      21.419  45.228  41.117  1.00  0.00              
ATOM    213  N   LYS   136      16.751  45.485  41.499  1.00  0.00              
ATOM    214  CA  LYS   136      16.036  45.625  42.775  1.00  0.00              
ATOM    215  C   LYS   136      15.907  47.074  43.251  1.00  0.00              
ATOM    216  O   LYS   136      15.057  47.369  44.097  1.00  0.00              
END
