
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0372AL044_2-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   24 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_2-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:    18       118 - 135         4.84    10.96
  LCS_AVERAGE:      8.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       124 - 129         1.91    12.62
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       125 - 129         0.87    13.36
  LCS_AVERAGE:      1.96

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   18     4    4    4    4    5    5    6    8    9   13   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     A     119     A     119      4    5   18     4    4    4    4    5    5    6    8    9    9   10   12   15   17   18   20   20   21   21   22 
LCS_GDT     Y     120     Y     120      4    5   18     4    4    4    4    5    5    6    8    9    9   10   10   13   15   18   20   20   21   21   22 
LCS_GDT     A     121     A     121      4    5   18     4    4    4    4    5    5    6    8    9   13   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     D     122     D     122      3    5   18     2    4    4    5    7    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     Y     123     Y     123      3    3   18     2    3    3    5    7    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     I     124     I     124      3    6   18     1    4    4    5    7    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     Y     125     Y     125      5    6   18     3    4    5    5    5    6    9   10   11   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     L     126     L     126      5    6   18     3    4    5    5    6    6    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     R     127     R     127      5    6   18     3    4    5    5    6    6    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     S     128     S     128      5    6   18     3    4    5    5    6    6    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     D     129     D     129      5    6   18     3    4    5    5    6    6    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     L     130     L     130      4    5   18     3    4    4    5    5    6    8   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     A     131     A     131      4    5   18     3    4    4    5    5    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     T     132     T     132      4    5   18     3    4    4    5    7    8    9    9   11   14   14   16   16   17   17   18   19   19   21   22 
LCS_GDT     L     133     L     133      4    5   18     3    4    4    5    7    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     K     134     K     134      3    5   18     3    3    4    5    7    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     G     135     G     135      3    5   18     3    3    4    5    7    8    9   11   12   14   15   16   16   17   18   20   20   21   21   22 
LCS_GDT     K     136     K     136      0    4   15     0    1    2    3    4    5    5    5    7    8   10   13   13   15   18   20   20   21   21   22 
LCS_GDT     K     137     K     137      3    4   10     3    3    3    3    4    5    5    5    7    8    9   10   12   15   15   17   20   21   21   22 
LCS_GDT     F     138     F     138      3    4   10     3    3    3    3    4    5    5    5    7    8   10   10   13   15   17   20   20   21   21   22 
LCS_GDT     Q     139     Q     139      3    4   10     3    3    3    3    4    5    5    5    5    6   10   11   13   15   17   20   20   21   21   22 
LCS_GDT     A     140     A     140      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     N     143     N     143      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    1    1 
LCS_AVERAGE  LCS_A:   4.52  (   1.96    2.66    8.94 )

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      4      4      5      5      7      8      9     11     12     14     15     16     16     17     18     20     20     21     21     22 
GDT PERCENT_CA   2.33   2.33   2.91   2.91   4.07   4.65   5.23   6.40   6.98   8.14   8.72   9.30   9.30   9.88  10.47  11.63  11.63  12.21  12.21  12.79
GDT RMS_LOCAL    0.20   0.20   0.87   0.87   1.93   2.45   2.60   3.35   3.45   3.75   3.94   4.10   4.10   4.47   5.33   5.89   5.89   6.09   6.09   6.35
GDT RMS_ALL_CA  26.28  26.28  13.36  13.36  12.21  11.56  11.52  10.76  10.81  10.88  10.85  10.80  10.80  10.85  10.68  11.12  11.12  11.37  11.37  11.16

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          6.212
LGA    A     119      A     119          8.767
LGA    Y     120      Y     120         10.317
LGA    A     121      A     121          6.751
LGA    D     122      D     122          3.972
LGA    Y     123      Y     123          3.745
LGA    I     124      I     124          3.730
LGA    Y     125      Y     125          4.864
LGA    L     126      L     126          3.254
LGA    R     127      R     127          3.725
LGA    S     128      S     128          3.968
LGA    D     129      D     129          2.262
LGA    L     130      L     130          3.455
LGA    A     131      A     131          3.938
LGA    T     132      T     132          5.886
LGA    L     133      L     133          2.431
LGA    K     134      K     134          2.238
LGA    G     135      G     135          4.210
LGA    K     136      K     136         14.452
LGA    K     137      K     137         17.442
LGA    F     138      F     138         15.568
LGA    Q     139      Q     139         17.341
LGA    A     140      A     140         24.770
LGA    N     143      N     143         26.066

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  172    4.0     11    3.30     5.814     5.116     0.324

LGA_LOCAL      RMSD =  3.298  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.840  Number of atoms =   24 
Std_ALL_ATOMS  RMSD = 10.076  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.190449 * X  +   0.965370 * Y  +   0.178296 * Z  +  15.610354
  Y_new =   0.943125 * X  +  -0.129513 * Y  +  -0.306171 * Z  +  34.685436
  Z_new =  -0.272477 * X  +   0.226465 * Y  +  -0.935131 * Z  +  45.712730 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.903992   -0.237600  [ DEG:   166.3865    -13.6135 ]
  Theta =   0.275966    2.865626  [ DEG:    15.8117    164.1883 ]
  Phi   =   1.371542   -1.770051  [ DEG:    78.5836   -101.4164 ]
 
# 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_2-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_2-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  172   4.0   11   3.30   5.116    10.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_2-D2
REMARK Aligment from pdb entry: 1tz0_A
ATOM    149  N   ARG   118      26.300  39.918  14.689  1.00  0.00              
ATOM    150  CA  ARG   118      25.996  41.336  14.380  1.00  0.00              
ATOM    151  C   ARG   118      25.284  41.970  15.558  1.00  0.00              
ATOM    152  O   ARG   118      25.608  43.067  15.960  1.00  0.00              
ATOM    153  N   ALA   119      24.336  41.260  16.148  1.00  0.00              
ATOM    154  CA  ALA   119      23.610  41.798  17.304  1.00  0.00              
ATOM    155  C   ALA   119      24.525  42.003  18.495  1.00  0.00              
ATOM    156  O   ALA   119      24.445  43.006  19.170  1.00  0.00              
ATOM    157  N   TYR   120      25.393  41.033  18.776  1.00  0.00              
ATOM    158  CA  TYR   120      26.366  41.181  19.832  1.00  0.00              
ATOM    159  C   TYR   120      27.302  42.365  19.536  1.00  0.00              
ATOM    160  O   TYR   120      27.620  43.127  20.432  1.00  0.00              
ATOM    161  N   ALA   121      27.725  42.525  18.285  1.00  0.00              
ATOM    162  CA  ALA   121      28.657  43.608  17.965  1.00  0.00              
ATOM    163  C   ALA   121      27.914  44.951  18.031  1.00  0.00              
ATOM    164  O   ALA   121      28.503  45.953  18.388  1.00  0.00              
ATOM    165  N   ASP   122      26.625  44.944  17.722  1.00  0.00              
ATOM    166  CA  ASP   122      25.806  46.161  17.859  1.00  0.00              
ATOM    167  C   ASP   122      25.778  46.576  19.327  1.00  0.00              
ATOM    168  O   ASP   122      26.072  47.718  19.674  1.00  0.00              
ATOM    169  N   TYR   123      25.493  45.620  20.207  1.00  0.00              
ATOM    170  CA  TYR   123      25.587  45.816  21.652  1.00  0.00              
ATOM    171  C   TYR   123      26.958  46.281  22.120  1.00  0.00              
ATOM    172  O   TYR   123      27.068  47.053  23.082  1.00  0.00              
ATOM    173  N   ILE   124      28.016  45.810  21.472  1.00  0.00              
ATOM    174  CA  ILE   124      29.365  46.274  21.817  1.00  0.00              
ATOM    175  C   ILE   124      29.604  47.737  21.409  1.00  0.00              
ATOM    176  O   ILE   124      30.544  48.336  21.887  1.00  0.00              
ATOM    177  N   TYR   125      28.791  48.315  20.511  1.00  0.00              
ATOM    178  CA  TYR   125      28.871  49.768  20.237  1.00  0.00              
ATOM    179  C   TYR   125      28.182  50.632  21.300  1.00  0.00              
ATOM    180  O   TYR   125      28.279  51.881  21.283  1.00  0.00              
ATOM    181  N   LEU   126      27.499  49.990  22.232  1.00  0.00              
ATOM    182  CA  LEU   126      26.632  50.701  23.142  1.00  0.00              
ATOM    183  C   LEU   126      27.399  51.447  24.223  1.00  0.00              
ATOM    184  O   LEU   126      28.451  51.034  24.661  1.00  0.00              
ATOM    185  N   ARG   127      26.806  52.547  24.661  1.00  0.00              
ATOM    186  CA  ARG   127      27.248  53.301  25.827  1.00  0.00              
ATOM    187  C   ARG   127      26.556  52.796  27.078  1.00  0.00              
ATOM    188  O   ARG   127      26.788  53.330  28.162  1.00  0.00              
ATOM    189  N   SER   128      25.724  51.766  26.945  1.00  0.00              
ATOM    190  CA  SER   128      24.750  51.423  27.977  1.00  0.00              
ATOM    191  C   SER   128      25.124  50.207  28.838  1.00  0.00              
ATOM    192  O   SER   128      24.270  49.661  29.553  1.00  0.00              
ATOM    193  N   ASP   129      26.387  49.800  28.795  1.00  0.00              
ATOM    194  CA  ASP   129      26.810  48.588  29.513  1.00  0.00              
ATOM    195  C   ASP   129      26.833  48.827  31.025  1.00  0.00              
ATOM    196  O   ASP   129      27.279  49.886  31.486  1.00  0.00              
ATOM    197  N   LEU   130      26.405  47.816  31.785  1.00  0.00              
ATOM    198  CA  LEU   130      26.395  47.849  33.254  1.00  0.00              
ATOM    199  C   LEU   130      27.088  46.621  33.843  1.00  0.00              
ATOM    200  O   LEU   130      27.031  45.533  33.270  1.00  0.00              
ATOM    201  N   ALA   131      27.730  46.797  34.993  1.00  0.00              
ATOM    202  CA  ALA   131      28.419  45.695  35.666  1.00  0.00              
ATOM    203  C   ALA   131      27.329  44.748  36.086  1.00  0.00              
ATOM    204  O   ALA   131      26.287  45.204  36.593  1.00  0.00              
ATOM    205  N   THR   132      27.513  43.448  35.818  1.00  0.00              
ATOM    206  CA  THR   132      26.475  42.465  36.070  1.00  0.00              
ATOM    207  C   THR   132      25.225  42.551  35.205  1.00  0.00              
ATOM    208  O   THR   132      24.245  41.827  35.438  1.00  0.00              
ATOM    209  N   LEU   133      25.226  43.443  34.212  1.00  0.00              
ATOM    210  CA  LEU   133      24.031  43.681  33.391  1.00  0.00              
ATOM    211  C   LEU   133      22.786  43.955  34.221  1.00  0.00              
ATOM    212  O   LEU   133      21.692  43.517  33.883  1.00  0.00              
ATOM    213  N   LYS   134      22.981  44.703  35.311  1.00  0.00              
ATOM    214  CA  LYS   134      21.885  45.189  36.141  1.00  0.00              
ATOM    215  C   LYS   134      22.284  46.489  36.856  1.00  0.00              
ATOM    216  O   LYS   134      23.437  46.924  36.788  1.00  0.00              
ATOM    217  N   GLY   135      21.313  47.095  37.536  1.00  0.00              
ATOM    218  CA  GLY   135      21.565  48.171  38.492  1.00  0.00              
ATOM    219  C   GLY   135      21.503  47.625  39.933  1.00  0.00              
ATOM    220  O   GLY   135      20.802  46.642  40.213  1.00  0.00              
ATOM    221  N   LYS   136      25.301  43.838  45.043  1.00  0.00              
ATOM    222  CA  LYS   136      25.956  44.423  46.197  1.00  0.00              
ATOM    223  C   LYS   136      27.087  43.593  46.804  1.00  0.00              
ATOM    224  O   LYS   136      26.804  42.769  47.674  1.00  0.00              
ATOM    225  N   LYS   137      28.351  43.766  46.388  1.00  0.00              
ATOM    226  CA  LYS   137      28.776  44.645  45.275  1.00  0.00              
ATOM    227  C   LYS   137      30.225  44.335  44.769  1.00  0.00              
ATOM    228  O   LYS   137      30.480  43.163  44.479  1.00  0.00              
ATOM    229  N   PHE   138      31.176  45.289  44.658  1.00  0.00              
ATOM    230  CA  PHE   138      32.330  45.061  43.776  1.00  0.00              
ATOM    231  C   PHE   138      33.532  44.513  44.542  1.00  0.00              
ATOM    232  O   PHE   138      34.315  45.291  45.097  1.00  0.00              
ATOM    233  N   GLN   139      33.660  43.186  44.575  1.00  0.00              
ATOM    234  CA  GLN   139      34.698  42.517  45.359  1.00  0.00              
ATOM    235  C   GLN   139      35.519  41.527  44.515  1.00  0.00              
ATOM    236  O   GLN   139      35.110  40.386  44.297  1.00  0.00              
ATOM    237  N   ALA   140      24.916  23.755  14.852  1.00  0.00              
ATOM    238  CA  ALA   140      23.869  22.726  14.790  1.00  0.00              
ATOM    239  C   ALA   140      23.101  22.727  16.116  1.00  0.00              
ATOM    240  O   ALA   140      23.672  23.057  17.158  1.00  0.00              
ATOM    241  N   ASN   143      21.813  22.382  16.078  1.00  0.00              
ATOM    242  CA  ASN   143      21.010  22.204  17.288  1.00  0.00              
ATOM    243  C   ASN   143      19.748  21.413  17.011  1.00  0.00              
ATOM    244  O   ASN   143      19.356  21.279  15.865  1.00  0.00              
END
