
#######################################################
#                                                     #
#                        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   26 (  128),  selected   26 , name T0372TS261_1_3-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   26 , name T0372_D2.pdb
# PARAMETERS: T0372TS261_1_3-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:    22       268 - 289         4.56    10.39
  LCS_AVERAGE:     12.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       273 - 281         1.81    22.49
  LONGEST_CONTINUOUS_SEGMENT:     9       274 - 282         1.21    21.77
  LONGEST_CONTINUOUS_SEGMENT:     9       281 - 289         1.56    10.52
  LCS_AVERAGE:      4.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       274 - 281         0.27    22.40
  LCS_AVERAGE:      3.09

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     T     151     T     151      3    4    8     3    3    3    3    5    5    5    5    6    8    8    9   14   15   16   23   24   25   25   26 
LCS_GDT     Y     152     Y     152      3    4   17     3    3    3    3    5    5    5    8    9   13   14   18   19   21   22   23   24   25   25   26 
LCS_GDT     P     153     P     153      3    4   17     3    3    3    3    5    5    5    9   10   13   14   18   19   21   22   23   24   25   25   26 
LCS_GDT     D     154     D     154      3    4   19     3    3    4    6    7    9   11   13   13   13   15   19   19   21   22   23   24   25   25   26 
LCS_GDT     E     268     E     268      4    5   22     0    3    4    5    5    6    8   10   11   16   18   20   21   22   22   22   23   24   25   26 
LCS_GDT     D     269     D     269      4    5   22     2    3    4    5    5    5    8   11   11   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     L     270     L     270      4    5   22     3    3    4    5    5    6    8   10   11   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     G     271     G     271      4    5   22     3    3    4    5    5    6   10   12   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     I     272     I     272      4    5   22     3    4    4    5    5    6    8   10   11   13   16   20   21   22   22   23   24   25   25   26 
LCS_GDT     E     273     E     273      4    9   22     3    4    4    4    5    9   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     G     274     G     274      8    9   22     8    8    8    8    8    9   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     L     275     L     275      8    9   22     8    8    8    8    8    9    9   11   12   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     R     276     R     276      8    9   22     8    8    8    8    8    9    9   11   12   13   16   20   21   22   22   23   24   25   25   26 
LCS_GDT     K     277     K     277      8    9   22     8    8    8    9   10   10   11   13   14   15   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     A     278     A     278      8    9   22     8    8    8    8    8    9   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     K     279     K     279      8    9   22     8    8    8    8    8    9    9   10   11   14   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     L     280     L     280      8    9   22     8    8    8    8    8    9    9    9   10   13   14   19   21   22   22   23   24   25   25   26 
LCS_GDT     S     281     S     281      8    9   22     8    8    8    9   10   10   11   13   14   15   17   20   21   22   22   23   24   25   25   26 
LCS_GDT     Y     282     Y     282      4    9   22     3    4    5    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     Q     283     Q     283      4    9   22     3    4    4    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     P     284     P     284      5    9   22     3    4    6    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     V     285     V     285      5    9   22     4    5    6    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     T     286     T     286      5    9   22     4    5    6    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     I     287     I     287      5    9   22     4    5    6    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     L     288     L     288      5    9   22     4    5    6    9   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_GDT     E     289     E     289      5    9   22     3    5    5    8   10   10   11   13   14   16   18   20   21   22   22   23   24   25   25   26 
LCS_AVERAGE  LCS_A:   6.54  (   3.09    4.34   12.19 )

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      8      8      8      9     10     10     11     13     14     16     18     20     21     22     22     23     24     25     25     26 
GDT PERCENT_CA   4.65   4.65   4.65   5.23   5.81   5.81   6.40   7.56   8.14   9.30  10.47  11.63  12.21  12.79  12.79  13.37  13.95  14.53  14.53  15.12
GDT RMS_LOCAL    0.27   0.27   0.27   1.52   1.57   1.57   2.14   2.70   2.87   3.69   3.96   4.18   4.34   4.56   4.56   5.22   5.39   5.68   5.68   5.91
GDT RMS_ALL_CA  22.40  22.40  22.40   9.34   9.88   9.88   9.42   8.76   8.98  12.17  11.94  11.07  10.85  10.39  10.39   5.99   6.00   5.93   5.93   5.91

#      Molecule1      Molecule2       DISTANCE
LGA    T     151      T     151         22.254
LGA    Y     152      Y     152         19.793
LGA    P     153      P     153         21.136
LGA    D     154      D     154         15.360
LGA    E     268      E     268          8.207
LGA    D     269      D     269          5.726
LGA    L     270      L     270          7.306
LGA    G     271      G     271          4.314
LGA    I     272      I     272          7.065
LGA    E     273      E     273          3.963
LGA    G     274      G     274          3.688
LGA    L     275      L     275          6.691
LGA    R     276      R     276          6.697
LGA    K     277      K     277          3.418
LGA    A     278      A     278          2.802
LGA    K     279      K     279          7.380
LGA    L     280      L     280          7.931
LGA    S     281      S     281          3.389
LGA    Y     282      Y     282          2.493
LGA    Q     283      Q     283          2.150
LGA    P     284      P     284          2.395
LGA    V     285      V     285          2.102
LGA    T     286      T     286          1.941
LGA    I     287      I     287          2.049
LGA    L     288      L     288          1.664
LGA    E     289      E     289          2.232

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  172    4.0     13    2.70     7.703     6.891     0.464

LGA_LOCAL      RMSD =  2.701  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.978  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  5.911  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.035263 * X  +   0.035368 * Y  +   0.998752 * Z  +  12.602811
  Y_new =  -0.729399 * X  +   0.684087 * Y  +   0.001529 * Z  +  34.118301
  Z_new =  -0.683179 * X  +  -0.728543 * Y  +   0.049920 * Z  +  73.390236 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.502383    1.639210  [ DEG:   -86.0802     93.9198 ]
  Theta =   0.752107    2.389486  [ DEG:    43.0926    136.9075 ]
  Phi   =  -1.522488    1.619105  [ DEG:   -87.2321     92.7679 ]
 
# 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: T0372TS261_1_3-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS261_1_3-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  172   4.0   13   2.70   6.891     5.91
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS261_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0372
PARENT 2fck_A
ATOM    891  N   THR   151      49.822  42.975  34.024  1.00  6.37
ATOM    892  CA  THR   151      49.821  41.937  32.963  1.00  6.37
ATOM    893  C   THR   151      51.224  41.367  32.747  1.00  6.37
ATOM    894  O   THR   151      52.212  42.081  32.541  1.00  6.37
ATOM    895  CB  THR   151      49.265  42.497  31.658  1.00  6.37
ATOM    896  N   TYR   152      51.282  40.055  32.812  1.00  5.43
ATOM    897  CA  TYR   152      52.400  39.294  32.359  1.00  5.43
ATOM    898  C   TYR   152      51.768  38.038  31.813  1.00  5.43
ATOM    899  O   TYR   152      50.567  37.778  32.052  1.00  5.43
ATOM    900  CB  TYR   152      53.281  38.924  33.521  1.00  5.43
ATOM    901  N   PRO   153      52.525  37.253  31.058  1.00  3.03
ATOM    902  CA  PRO   153      51.922  35.999  30.600  1.00  3.03
ATOM    903  C   PRO   153      51.435  35.086  31.742  1.00  3.03
ATOM    904  O   PRO   153      50.717  34.113  31.478  1.00  3.03
ATOM    905  CB  PRO   153      53.066  35.315  29.830  1.00  3.03
ATOM    906  N   ASP   154      51.814  35.407  32.974  1.00  5.30
ATOM    907  CA  ASP   154      51.442  34.569  34.115  1.00  5.30
ATOM    908  C   ASP   154      50.135  35.014  34.772  1.00  5.30
ATOM    909  O   ASP   154      49.647  34.372  35.745  1.00  5.30
ATOM    910  CB  ASP   154      52.570  34.573  35.149  1.00  5.30
ATOM    911  N   GLU   268      29.592  43.357  23.362  1.00  3.01
ATOM    912  CA  GLU   268      29.610  41.984  22.853  1.00  3.01
ATOM    913  C   GLU   268      28.923  41.956  21.502  1.00  3.01
ATOM    914  O   GLU   268      27.877  42.594  21.396  1.00  3.01
ATOM    915  CB  GLU   268      28.880  41.098  23.823  1.00  3.01
ATOM    916  N   ASP   269      29.515  41.312  20.471  1.00  3.69
ATOM    917  CA  ASP   269      28.873  41.183  19.154  1.00  3.69
ATOM    918  C   ASP   269      28.568  39.705  18.951  1.00  3.69
ATOM    919  O   ASP   269      29.486  38.896  18.989  1.00  3.69
ATOM    920  CB  ASP   269      29.787  41.650  17.974  1.00  3.69
ATOM    921  N   LEU   270      27.304  39.360  18.763  1.00  6.60
ATOM    922  CA  LEU   270      26.960  37.959  18.537  1.00  6.60
ATOM    923  C   LEU   270      26.523  37.744  17.112  1.00  6.60
ATOM    924  O   LEU   270      25.869  38.605  16.524  1.00  6.60
ATOM    925  CB  LEU   270      25.804  37.525  19.451  1.00  6.60
ATOM    926  N   GLY   271      26.841  36.574  16.563  1.00  5.45
ATOM    927  CA  GLY   271      26.290  36.184  15.276  1.00  5.45
ATOM    928  C   GLY   271      24.783  36.067  15.488  1.00  5.45
ATOM    929  O   GLY   271      24.362  35.377  16.427  1.00  5.45
ATOM    930  N   ILE   272      23.951  36.702  14.622  1.00  4.52
ATOM    931  CA  ILE   272      22.482  36.585  14.844  1.00  4.52
ATOM    932  C   ILE   272      21.973  35.135  14.874  1.00  4.52
ATOM    933  O   ILE   272      20.899  34.862  15.430  1.00  4.52
ATOM    934  CB  ILE   272      21.877  37.308  13.626  1.00  4.52
ATOM    935  N   GLU   273      22.732  34.208  14.299  1.00  4.56
ATOM    936  CA  GLU   273      22.269  32.807  14.223  1.00  4.56
ATOM    937  C   GLU   273      22.736  31.960  15.386  1.00  4.56
ATOM    938  O   GLU   273      22.400  30.785  15.460  1.00  4.56
ATOM    939  CB  GLU   273      22.754  32.154  12.948  1.00  4.56
ATOM    940  N   GLY   274      23.533  32.546  16.271  1.00  5.71
ATOM    941  CA  GLY   274      24.067  31.850  17.431  1.00  5.71
ATOM    942  C   GLY   274      23.277  32.259  18.681  1.00  5.71
ATOM    943  O   GLY   274      23.677  33.110  19.472  1.00  5.71
ATOM    944  N   LEU   275      22.127  31.640  18.852  1.00  6.59
ATOM    945  CA  LEU   275      21.256  32.010  19.964  1.00  6.59
ATOM    946  C   LEU   275      21.850  31.737  21.363  1.00  6.59
ATOM    947  O   LEU   275      21.733  32.572  22.253  1.00  6.59
ATOM    948  CB  LEU   275      19.845  31.400  19.777  1.00  6.59
ATOM    949  N   ARG   276      22.498  30.573  21.574  1.00  5.99
ATOM    950  CA  ARG   276      23.112  30.343  22.898  1.00  5.99
ATOM    951  C   ARG   276      24.101  31.464  23.299  1.00  5.99
ATOM    952  O   ARG   276      24.145  31.837  24.465  1.00  5.99
ATOM    953  CB  ARG   276      23.797  28.978  22.735  1.00  5.99
ATOM    954  N   LYS   277      24.809  32.059  22.338  1.00  6.38
ATOM    955  CA  LYS   277      25.806  33.106  22.668  1.00  6.38
ATOM    956  C   LYS   277      25.068  34.387  23.100  1.00  6.38
ATOM    957  O   LYS   277      25.503  35.153  23.978  1.00  6.38
ATOM    958  CB  LYS   277      26.750  33.406  21.473  1.00  6.38
ATOM    959  N   ALA   278      23.934  34.626  22.453  1.00  8.22
ATOM    960  CA  ALA   278      23.099  35.761  22.836  1.00  8.22
ATOM    961  C   ALA   278      22.527  35.556  24.242  1.00  8.22
ATOM    962  O   ALA   278      22.553  36.483  25.065  1.00  8.22
ATOM    963  CB  ALA   278      21.952  35.922  21.822  1.00  8.22
ATOM    964  N   LYS   279      22.012  34.345  24.488  1.00  4.87
ATOM    965  CA  LYS   279      21.373  33.987  25.767  1.00  4.87
ATOM    966  C   LYS   279      22.413  34.182  26.905  1.00  4.87
ATOM    967  O   LYS   279      22.071  34.686  27.968  1.00  4.87
ATOM    968  CB  LYS   279      20.840  32.524  25.733  1.00  4.87
ATOM    969  N   LEU   280      23.678  33.823  26.643  1.00  5.56
ATOM    970  CA  LEU   280      24.748  33.968  27.652  1.00  5.56
ATOM    971  C   LEU   280      25.010  35.474  27.917  1.00  5.56
ATOM    972  O   LEU   280      25.081  35.898  29.070  1.00  5.56
ATOM    973  CB  LEU   280      26.028  33.257  27.194  1.00  5.56
ATOM    974  N   SER   281      25.041  36.276  26.855  1.00  5.62
ATOM    975  CA  SER   281      25.250  37.711  27.022  1.00  5.62
ATOM    976  C   SER   281      24.149  38.257  27.954  1.00  5.62
ATOM    977  O   SER   281      24.430  38.997  28.930  1.00  5.62
ATOM    978  CB  SER   281      25.221  38.453  25.662  1.00  5.62
ATOM    979  N   TYR   282      23.823  41.749  30.042  1.00  3.69
ATOM    980  CA  TYR   282      24.028  42.645  28.895  1.00  3.69
ATOM    981  C   TYR   282      22.698  43.112  28.380  1.00  3.69
ATOM    982  O   TYR   282      21.660  42.477  28.626  1.00  3.69
ATOM    983  CB  TYR   282      24.869  41.988  27.773  1.00  3.69
ATOM    984  N   GLN   283      22.726  44.263  27.713  1.00  3.96
ATOM    985  CA  GLN   283      21.517  44.792  27.110  1.00  3.96
ATOM    986  C   GLN   283      21.640  44.757  25.601  1.00  3.96
ATOM    987  O   GLN   283      22.621  45.238  25.046  1.00  3.96
ATOM    988  CB  GLN   283      21.290  46.224  27.582  1.00  3.96
ATOM    989  N   PRO   284      20.643  44.205  24.934  1.00  6.99
ATOM    990  CA  PRO   284      20.712  44.184  23.476  1.00  6.99
ATOM    991  C   PRO   284      20.492  45.564  22.915  1.00  6.99
ATOM    992  O   PRO   284      19.580  46.298  23.355  1.00  6.99
ATOM    993  CB  PRO   284      19.663  43.202  22.938  1.00  6.99
ATOM    994  N   VAL   285      21.328  45.916  21.940  1.00  3.12
ATOM    995  CA  VAL   285      21.124  47.112  21.167  1.00  3.12
ATOM    996  C   VAL   285      20.864  46.651  19.744  1.00  3.12
ATOM    997  O   VAL   285      19.915  45.929  19.460  1.00  3.12
ATOM    998  CB  VAL   285      22.326  48.075  21.276  1.00  3.12
ATOM    999  N   THR   286      21.751  47.016  18.853  1.00  5.11
ATOM   1000  CA  THR   286      21.450  46.975  17.466  1.00  5.11
ATOM   1001  C   THR   286      21.757  45.657  16.758  1.00  5.11
ATOM   1002  O   THR   286      22.601  44.876  17.209  1.00  5.11
ATOM   1003  CB  THR   286      22.216  48.113  16.804  1.00  5.11
ATOM   1004  N   ILE   287      21.054  45.419  15.651  1.00  3.17
ATOM   1005  CA  ILE   287      21.531  44.508  14.660  1.00  3.17
ATOM   1006  C   ILE   287      22.317  45.423  13.694  1.00  3.17
ATOM   1007  O   ILE   287      21.715  46.279  13.022  1.00  3.17
ATOM   1008  CB  ILE   287      20.340  43.920  13.890  1.00  3.17
ATOM   1009  N   LEU   288      23.616  45.240  13.648  1.00  1.40
ATOM   1010  CA  LEU   288      24.514  46.166  12.944  1.00  1.40
ATOM   1011  C   LEU   288      25.154  45.500  11.722  1.00  1.40
ATOM   1012  O   LEU   288      25.887  44.519  11.865  1.00  1.40
ATOM   1013  CB  LEU   288      25.549  46.607  13.902  1.00  1.40
ATOM   1014  N   GLU   289      24.936  46.066  10.519  1.00  2.06
ATOM   1015  CA  GLU   289      25.595  45.478   9.339  1.00  2.06
ATOM   1016  C   GLU   289      27.126  45.608   9.381  1.00  2.06
ATOM   1017  O   GLU   289      27.672  46.550  10.001  1.00  2.06
ATOM   1018  CB  GLU   289      25.011  46.267   8.156  1.00  2.06
TER
END
