
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0289AL243_1-D2
# Molecule2: number of CA atoms   74 (  581),  selected   33 , name T0289_D2.pdb
# PARAMETERS: T0289AL243_1-D2.T0289_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:    12       267 - 283         4.28    11.68
  LCS_AVERAGE:     13.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       269 - 283         1.85    12.51
  LCS_AVERAGE:      8.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       276 - 283         0.97    12.12
  LCS_AVERAGE:      6.10

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:   74
LCS_GDT     I     224     I     224      6    6    9     5   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     M     225     M     225      6    6    9     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     E     226     E     226      6    6    9     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     K     227     K     227      6    6    9     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     V     228     V     228      6    6    9     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     D     229     D     229      6    6    9     3   10   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     R     232     R     232      3    3    9     3    3    3    3    4    4   13   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     N     233     N     233      3    3    9     3    3    3    3    3    4   10   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     E     234     E     234      3    3    9     3    3    3    3    4    6   10   12   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     W     251     W     251      0    4    7     1    2    3    4    4    4    5    5    6    6    7    8    8   11   11   12   13   15   16   16 
LCS_GDT     K     252     K     252      0    4    7     1    1    3    4    4    4    5    5    6    6    7    8    8   11   11   12   13   15   16   16 
LCS_GDT     L     254     L     254      0    4    7     0    0    3    4    4    4    5    5    6    6   13   13   14   14   15   16   17   18   19   21 
LCS_GDT     H     255     H     255      0    4    7     0    0    0    2    4    4    5    7    7   11   13   13   14   15   16   18   18   20   20   21 
LCS_GDT     P     256     P     256      0    0    9     0    0    0    2    2    4    8    9   11   11   11   12   12   14   15   16   16   18   19   19 
LCS_GDT     G     257     G     257      0    0    9     0    0    0    0    3    4    4    9   11   11   11   12   12   12   15   16   16   18   19   19 
LCS_GDT     F     261     F     261      4    5   10     3    4    4    5    5    5    6    7    7    7    8    9    9   11   11   12   12   14   16   18 
LCS_GDT     V     262     V     262      4    5   10     3    4    4    5    5    5    6    7    7    7    8    9    9   11   12   12   14   15   16   18 
LCS_GDT     S     263     S     263      4    5   10     3    4    4    5    5    5    6    7    7    8    9   10   10   11   12   12   13   15   16   18 
LCS_GDT     L     264     L     264      4    7   10     3    4    5    6    6    7    8    8    8    9    9   10   10   11   12   12   14   15   16   18 
LCS_GDT     D     265     D     265      4    7   10     1    4    5    6    6    7    8    8    8    9    9   10   10   11   12   12   14   15   16   18 
LCS_GDT     G     266     G     266      4    7   10     3    3    5    6    6    7    8    8    8    9    9   11   12   13   17   19   21   21   21   22 
LCS_GDT     K     267     K     267      4    7   12     3    4    5    6    6    7    8    8    9    9   11   13   14   20   20   20   21   21   21   22 
LCS_GDT     V     268     V     268      4    7   12     3    3    5    6    6    7    8    8   12   13   17   19   19   20   20   20   21   21   21   22 
LCS_GDT     I     269     I     269      4   10   12     3    4    5    6    9    9   11   15   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     P     270     P     270      4   10   12     3    4    5    7    7    9   13   14   16   16   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     T     276     T     276      8   10   12     3    5    7   11   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     V     277     V     277      8   10   12     3   10   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     Y     278     Y     278      8   10   12     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     P     279     P     279      8   10   12     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     V     280     V     280      8   10   12     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     F     281     F     281      8   10   12     5   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     V     282     V     282      8   10   12     7   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_GDT     N     283     N     283      8   10   12     5   11   13   13   14   14   14   16   17   17   18   19   19   20   20   20   21   21   21   22 
LCS_AVERAGE  LCS_A:   9.43  (   6.10    8.64   13.55 )

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     11     13     13     14     14     14     16     17     17     18     19     19     20     20     20     21     21     21     22 
GDT PERCENT_CA   9.46  14.86  17.57  17.57  18.92  18.92  18.92  21.62  22.97  22.97  24.32  25.68  25.68  27.03  27.03  27.03  28.38  28.38  28.38  29.73
GDT RMS_LOCAL    0.22   0.53   0.79   0.79   1.14   1.14   1.14   2.19   2.53   2.53   2.79   3.46   3.14   3.64   3.64   3.64   4.29   4.29   4.29   5.12
GDT RMS_ALL_CA  12.47  12.42  12.29  12.29  12.02  12.02  12.02  12.06  11.97  11.97  12.14  11.72  11.99  11.84  11.84  11.84  11.64  11.64  11.64  11.56

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          3.366
LGA    M     225      M     225          2.579
LGA    E     226      E     226          2.460
LGA    K     227      K     227          2.403
LGA    V     228      V     228          2.348
LGA    D     229      D     229          2.792
LGA    R     232      R     232          3.391
LGA    N     233      N     233          3.772
LGA    E     234      E     234          4.393
LGA    W     251      W     251         23.627
LGA    K     252      K     252         20.290
LGA    L     254      L     254         13.106
LGA    H     255      H     255         11.111
LGA    P     256      P     256         15.983
LGA    G     257      G     257         17.037
LGA    F     261      F     261         14.846
LGA    V     262      V     262         15.905
LGA    S     263      S     263         21.030
LGA    L     264      L     264         22.520
LGA    D     265      D     265         24.780
LGA    G     266      G     266         20.801
LGA    K     267      K     267         14.512
LGA    V     268      V     268         12.027
LGA    I     269      I     269          7.898
LGA    P     270      P     270          9.520
LGA    T     276      T     276          3.857
LGA    V     277      V     277          1.945
LGA    Y     278      Y     278          2.255
LGA    P     279      P     279          2.293
LGA    V     280      V     280          2.504
LGA    F     281      F     281          2.840
LGA    V     282      V     282          3.260
LGA    N     283      N     283          3.593

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   74    4.0     16    2.19    20.270    17.790     0.698

LGA_LOCAL      RMSD =  2.193  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.240  Number of atoms =   33 
Std_ALL_ATOMS  RMSD = 11.060  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.449171 * X  +   0.715901 * Y  +  -0.534538 * Z  +  97.065918
  Y_new =  -0.137791 * X  +   0.535622 * Y  +   0.833140 * Z  + -55.760433
  Z_new =   0.882756 * X  +   0.447877 * Y  +  -0.141941 * Z  + -19.527523 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.877703   -1.263890  [ DEG:   107.5844    -72.4156 ]
  Theta =  -1.081697   -2.059896  [ DEG:   -61.9767   -118.0233 ]
  Phi   =  -2.843938    0.297654  [ DEG:  -162.9457     17.0543 ]
 
# 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: T0289AL243_1-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289AL243_1-D2.T0289_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   74   4.0   16   2.19  17.790    11.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL243_1-D2
REMARK Aligment from pdb entry: 1yw4A
ATOM    833  N   ILE   224      24.086  30.872  19.254  1.00  0.00              
ATOM    834  CA  ILE   224      23.528  31.404  20.486  1.00  0.00              
ATOM    835  C   ILE   224      23.189  30.240  21.410  1.00  0.00              
ATOM    836  O   ILE   224      22.686  29.210  20.963  1.00  0.00              
ATOM    837  N   MET   225      23.478  30.401  22.695  1.00  0.00              
ATOM    838  CA  MET   225      23.173  29.370  23.677  1.00  0.00              
ATOM    839  C   MET   225      21.895  29.797  24.396  1.00  0.00              
ATOM    840  O   MET   225      20.959  29.013  24.534  1.00  0.00              
ATOM    841  N   GLU   226      21.870  31.050  24.842  1.00  0.00              
ATOM    842  CA  GLU   226      20.715  31.620  25.533  1.00  0.00              
ATOM    843  C   GLU   226      20.878  33.137  25.654  1.00  0.00              
ATOM    844  O   GLU   226      21.997  33.652  25.619  1.00  0.00              
ATOM    845  N   LYS   227      19.763  33.848  25.798  1.00  0.00              
ATOM    846  CA  LYS   227      19.809  35.300  25.925  1.00  0.00              
ATOM    847  C   LYS   227      19.769  35.722  27.387  1.00  0.00              
ATOM    848  O   LYS   227      19.186  35.039  28.232  1.00  0.00              
ATOM    849  N   VAL   228      20.399  36.855  27.680  1.00  0.00              
ATOM    850  CA  VAL   228      20.426  37.389  29.036  1.00  0.00              
ATOM    851  C   VAL   228      19.202  38.268  29.232  1.00  0.00              
ATOM    852  O   VAL   228      19.269  39.480  29.043  1.00  0.00              
ATOM    853  N   ASP   229      18.083  37.650  29.601  1.00  0.00              
ATOM    854  CA  ASP   229      16.838  38.378  29.818  1.00  0.00              
ATOM    855  C   ASP   229      16.989  39.348  30.988  1.00  0.00              
ATOM    856  O   ASP   229      17.366  38.951  32.090  1.00  0.00              
ATOM    857  N   ARG   232      16.702  40.621  30.748  1.00  0.00              
ATOM    858  CA  ARG   232      16.814  41.620  31.802  1.00  0.00              
ATOM    859  C   ARG   232      15.472  42.063  32.380  1.00  0.00              
ATOM    860  O   ARG   232      14.503  42.291  31.654  1.00  0.00              
ATOM    861  N   ASN   233      15.437  42.173  33.704  1.00  0.00              
ATOM    862  CA  ASN   233      14.254  42.602  34.434  1.00  0.00              
ATOM    863  C   ASN   233      14.684  43.301  35.724  1.00  0.00              
ATOM    864  O   ASN   233      15.661  42.900  36.362  1.00  0.00              
ATOM    865  N   GLU   234      13.954  44.352  36.087  1.00  0.00              
ATOM    866  CA  GLU   234      14.231  45.146  37.284  1.00  0.00              
ATOM    867  C   GLU   234      15.600  45.812  37.187  1.00  0.00              
ATOM    868  O   GLU   234      15.803  46.727  36.388  1.00  0.00              
ATOM    869  N   TRP   251      19.527  44.001  38.833  1.00  0.00              
ATOM    870  CA  TRP   251      20.149  43.957  37.516  1.00  0.00              
ATOM    871  C   TRP   251      21.535  44.588  37.516  1.00  0.00              
ATOM    872  O   TRP   251      21.697  45.757  37.869  1.00  0.00              
ATOM    873  N   LYS   252      22.528  43.800  37.110  1.00  0.00              
ATOM    874  CA  LYS   252      23.919  44.249  37.054  1.00  0.00              
ATOM    875  C   LYS   252      24.713  43.418  36.052  1.00  0.00              
ATOM    876  O   LYS   252      24.725  42.188  36.122  1.00  0.00              
ATOM    877  N   LEU   254      25.378  44.104  35.126  1.00  0.00              
ATOM    878  CA  LEU   254      26.189  43.452  34.100  1.00  0.00              
ATOM    879  C   LEU   254      27.642  43.410  34.579  1.00  0.00              
ATOM    880  O   LEU   254      28.318  44.436  34.623  1.00  0.00              
ATOM    881  N   HIS   255      28.114  42.217  34.928  1.00  0.00              
ATOM    882  CA  HIS   255      29.469  42.041  35.442  1.00  0.00              
ATOM    883  C   HIS   255      30.602  42.125  34.418  1.00  0.00              
ATOM    884  O   HIS   255      31.585  41.390  34.505  1.00  0.00              
ATOM    885  N   PRO   256      34.554  43.717  24.789  1.00  0.00              
ATOM    886  CA  PRO   256      34.553  43.332  23.377  1.00  0.00              
ATOM    887  C   PRO   256      33.635  42.150  23.092  1.00  0.00              
ATOM    888  O   PRO   256      33.384  41.319  23.966  1.00  0.00              
ATOM    889  N   GLY   257      33.135  42.078  21.860  1.00  0.00              
ATOM    890  CA  GLY   257      32.273  40.973  21.473  1.00  0.00              
ATOM    891  C   GLY   257      33.105  39.697  21.438  1.00  0.00              
ATOM    892  O   GLY   257      34.303  39.731  21.135  1.00  0.00              
ATOM    893  N   PHE   261      32.450  38.581  21.741  1.00  0.00              
ATOM    894  CA  PHE   261      33.068  37.258  21.764  1.00  0.00              
ATOM    895  C   PHE   261      34.036  37.091  22.924  1.00  0.00              
ATOM    896  O   PHE   261      34.896  36.211  22.902  1.00  0.00              
ATOM    897  N   VAL   262      33.900  37.939  23.940  1.00  0.00              
ATOM    898  CA  VAL   262      34.764  37.829  25.110  1.00  0.00              
ATOM    899  C   VAL   262      34.448  36.509  25.808  1.00  0.00              
ATOM    900  O   VAL   262      33.291  36.234  26.124  1.00  0.00              
ATOM    901  N   SER   263      35.482  35.703  26.043  1.00  0.00              
ATOM    902  CA  SER   263      35.347  34.402  26.694  1.00  0.00              
ATOM    903  C   SER   263      34.915  34.515  28.158  1.00  0.00              
ATOM    904  O   SER   263      35.472  35.308  28.920  1.00  0.00              
ATOM    905  N   LEU   264      33.922  33.717  28.545  1.00  0.00              
ATOM    906  CA  LEU   264      33.423  33.716  29.917  1.00  0.00              
ATOM    907  C   LEU   264      33.963  32.491  30.661  1.00  0.00              
ATOM    908  O   LEU   264      33.561  31.367  30.394  1.00  0.00              
ATOM    909  N   ASP   265      34.878  32.699  31.617  1.00  0.00              
ATOM    910  CA  ASP   265      35.450  31.575  32.369  1.00  0.00              
ATOM    911  C   ASP   265      34.443  30.785  33.191  1.00  0.00              
ATOM    912  O   ASP   265      33.383  31.293  33.555  1.00  0.00              
ATOM    913  N   GLY   266      32.588  29.632  36.065  1.00  0.00              
ATOM    914  CA  GLY   266      32.365  30.220  37.374  1.00  0.00              
ATOM    915  C   GLY   266      31.322  31.323  37.314  1.00  0.00              
ATOM    916  O   GLY   266      30.193  31.150  37.785  1.00  0.00              
ATOM    917  N   LYS   267      31.692  32.462  36.732  1.00  0.00              
ATOM    918  CA  LYS   267      30.765  33.588  36.609  1.00  0.00              
ATOM    919  C   LYS   267      29.646  33.233  35.640  1.00  0.00              
ATOM    920  O   LYS   267      29.899  32.788  34.521  1.00  0.00              
ATOM    921  N   VAL   268      28.404  33.416  36.068  1.00  0.00              
ATOM    922  CA  VAL   268      27.267  33.123  35.201  1.00  0.00              
ATOM    923  C   VAL   268      26.103  34.040  35.565  1.00  0.00              
ATOM    924  O   VAL   268      26.276  35.003  36.316  1.00  0.00              
ATOM    925  N   ILE   269      24.920  33.762  35.037  1.00  0.00              
ATOM    926  CA  ILE   269      23.776  34.608  35.342  1.00  0.00              
ATOM    927  C   ILE   269      22.893  33.989  36.422  1.00  0.00              
ATOM    928  O   ILE   269      22.673  32.775  36.440  1.00  0.00              
ATOM    929  N   PRO   270      22.405  34.828  37.333  1.00  0.00              
ATOM    930  CA  PRO   270      21.539  34.381  38.420  1.00  0.00              
ATOM    931  C   PRO   270      20.731  35.560  38.962  1.00  0.00              
ATOM    932  O   PRO   270      19.549  35.415  39.287  1.00  0.00              
ATOM    933  N   THR   276      33.763  27.854  27.835  1.00  0.00              
ATOM    934  CA  THR   276      33.629  27.820  26.383  1.00  0.00              
ATOM    935  C   THR   276      32.715  28.926  25.856  1.00  0.00              
ATOM    936  O   THR   276      32.811  29.320  24.694  1.00  0.00              
ATOM    937  N   VAL   277      31.831  29.426  26.715  1.00  0.00              
ATOM    938  CA  VAL   277      30.902  30.466  26.306  1.00  0.00              
ATOM    939  C   VAL   277      31.560  31.841  26.149  1.00  0.00              
ATOM    940  O   VAL   277      32.612  32.110  26.721  1.00  0.00              
ATOM    941  N   TYR   278      30.934  32.698  25.349  1.00  0.00              
ATOM    942  CA  TYR   278      31.436  34.044  25.114  1.00  0.00              
ATOM    943  C   TYR   278      30.235  34.982  25.060  1.00  0.00              
ATOM    944  O   TYR   278      29.130  34.569  24.711  1.00  0.00              
ATOM    945  N   PRO   279      30.453  36.240  25.410  1.00  0.00              
ATOM    946  CA  PRO   279      29.381  37.224  25.399  1.00  0.00              
ATOM    947  C   PRO   279      29.366  37.887  24.021  1.00  0.00              
ATOM    948  O   PRO   279      30.417  38.111  23.415  1.00  0.00              
ATOM    949  N   VAL   280      28.179  38.187  23.517  1.00  0.00              
ATOM    950  CA  VAL   280      28.074  38.819  22.211  1.00  0.00              
ATOM    951  C   VAL   280      26.984  39.885  22.231  1.00  0.00              
ATOM    952  O   VAL   280      25.906  39.666  22.776  1.00  0.00              
ATOM    953  N   PHE   281      27.291  41.043  21.655  1.00  0.00              
ATOM    954  CA  PHE   281      26.356  42.166  21.583  1.00  0.00              
ATOM    955  C   PHE   281      25.738  42.569  22.925  1.00  0.00              
ATOM    956  O   PHE   281      24.523  42.707  23.041  1.00  0.00              
ATOM    957  N   VAL   282      26.569  42.773  23.958  1.00  0.00              
ATOM    958  CA  VAL   282      26.044  43.165  25.271  1.00  0.00              
ATOM    959  C   VAL   282      25.411  44.562  25.245  1.00  0.00              
ATOM    960  O   VAL   282      25.966  45.487  24.654  1.00  0.00              
ATOM    961  N   ASN   283      24.257  44.712  25.888  1.00  0.00              
ATOM    962  CA  ASN   283      23.573  46.001  25.931  1.00  0.00              
ATOM    963  C   ASN   283      22.703  46.080  27.182  1.00  0.00              
ATOM    964  O   ASN   283      21.484  45.909  27.116  1.00  0.00              
END
