
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0356TS383_5-D1
# Molecule2: number of CA atoms  124 (  963),  selected   34 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_5-D1.T0356_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:    25       321 - 345         4.83    14.61
  LONGEST_CONTINUOUS_SEGMENT:    25       322 - 346         4.91    15.38
  LCS_AVERAGE:     18.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       326 - 342         1.96    10.95
  LONGEST_CONTINUOUS_SEGMENT:    17       327 - 343         1.78    11.57
  LONGEST_CONTINUOUS_SEGMENT:    17       328 - 344         1.92    12.41
  LCS_AVERAGE:      9.58

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       327 - 340         0.97    10.73
  LCS_AVERAGE:      7.07

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:  124
LCS_GDT     D     314     D     314      5    6    9     4    5    5    6    6    6    6    7    7    8   17   19   19   22   23   23   23   25   26   27 
LCS_GDT     A     315     A     315      5    6    9     4    5    5    6    6    6    6   11   14   16   18   21   21   22   23   24   25   25   26   27 
LCS_GDT     I     316     I     316      5    6   10     4    5    5    6    6    8    8   11   14   15   18   21   21   22   23   24   25   25   26   27 
LCS_GDT     Y     317     Y     317      5    6   16     4    5    5    6    6    8    8   11   14   16   18   21   21   22   23   24   25   25   26   27 
LCS_GDT     H     318     H     318      5    6   18     3    5    5    6    6    6    8   11   14   16   18   21   21   22   23   24   25   25   26   27 
LCS_GDT     S     319     S     319      5    6   18     3    4    5    6    6    6    8    9   12   15   18   21   21   22   23   24   25   25   26   27 
LCS_GDT     T     320     T     320      3    5   19     0    3    4    5    7   10   12   14   14   18   18   21   21   22   23   24   25   25   26   27 
LCS_GDT     Y     321     Y     321      4    5   25     0    3    4    5    6    7    8    9   12   14   17   21   21   22   23   24   25   25   26   27 
LCS_GDT     T     322     T     322      4    5   25     2    3    4    5   10   13   14   18   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     G     323     G     323      4    5   25     3    3    4    5    6    7   10   12   15   18   19   21   22   23   24   24   25   25   26   27 
LCS_GDT     R     324     R     324      4    5   25     3    3    4    5    6    7    7    8   10   12   14   18   22   23   24   24   24   24   25   26 
LCS_GDT     P     325     P     325      4    5   25     3    3    4    5    6    7    7    8    9    9   11   13   21   23   24   24   24   25   26   27 
LCS_GDT     P     326     P     326      3   17   25     0    3    4    8   11   13   17   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     D     327     D     327     14   17   25     7   12   12   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     E     328     E     328     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     P     329     P     329     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     A     330     A     330     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     V     331     V     331     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     L     332     L     332     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     G     333     G     333     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     V     334     V     334     14   17   25     8   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     A     335     A     335     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     L     336     L     336     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     N     337     N     337     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     E     338     E     338     14   17   25    10   12   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     V     339     V     339     14   17   25     4    8   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     F     340     F     340     14   17   25     4    8   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     V     341     V     341     13   17   25     4    6   13   14   15   17   18   19   20   20   20   21   22   23   24   24   25   25   26   27 
LCS_GDT     P     342     P     342      8   17   25     4    6    9   14   15   17   18   19   20   20   20   21   22   23   24   24   24   25   26   27 
LCS_GDT     I     343     I     343      8   17   25     4    6    8   12   14   17   18   19   20   20   20   21   22   23   24   24   24   24   25   26 
LCS_GDT     L     344     L     344      5   17   25     4    4    5    8   13   17   18   19   20   20   20   21   22   23   24   24   24   24   25   26 
LCS_GDT     Q     345     Q     345      4    5   25     4    4    4    4    5    5    8   10   13   19   19   20   21   23   24   24   24   24   25   26 
LCS_GDT     K     346     K     346      4    5   25     4    4    4    4    5    5    5    8    9   11   11   13   16   16   19   20   22   22   25   26 
LCS_GDT     Q     347     Q     347      4    5   24     4    4    4    4    5    5    6   10   10   11   14   15   16   17   19   21   22   24   25   26 
LCS_AVERAGE  LCS_A:  11.66  (   7.07    9.58   18.33 )

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     10     12     13     14     15     17     18     19     20     20     20     21     22     23     24     24     25     25     26     27 
GDT PERCENT_CA   8.06   9.68  10.48  11.29  12.10  13.71  14.52  15.32  16.13  16.13  16.13  16.94  17.74  18.55  19.35  19.35  20.16  20.16  20.97  21.77
GDT RMS_LOCAL    0.39   0.50   0.88   0.97   1.14   1.78   2.03   2.34   2.64   2.64   2.64   3.30   3.86   4.13   4.37   4.37   5.37   5.16   5.42   5.77
GDT RMS_ALL_CA  10.38  10.36  10.83  10.73  10.86  11.57  12.30  12.42  12.75  12.75  12.75  13.50  14.59  14.86  15.26  15.26   9.88  10.08   9.83   9.76

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         31.944
LGA    A     315      A     315         29.439
LGA    I     316      I     316         28.113
LGA    Y     317      Y     317         24.701
LGA    H     318      H     318         23.009
LGA    S     319      S     319         18.695
LGA    T     320      T     320         13.184
LGA    Y     321      Y     321          9.916
LGA    T     322      T     322          5.273
LGA    G     323      G     323         11.020
LGA    R     324      R     324         15.011
LGA    P     325      P     325         13.631
LGA    P     326      P     326          3.849
LGA    D     327      D     327          2.750
LGA    E     328      E     328          1.500
LGA    P     329      P     329          2.972
LGA    A     330      A     330          2.844
LGA    V     331      V     331          1.413
LGA    L     332      L     332          2.040
LGA    G     333      G     333          2.740
LGA    V     334      V     334          1.465
LGA    A     335      A     335          1.081
LGA    L     336      L     336          2.929
LGA    N     337      N     337          2.838
LGA    E     338      E     338          0.806
LGA    V     339      V     339          1.223
LGA    F     340      F     340          1.562
LGA    V     341      V     341          1.431
LGA    P     342      P     342          2.805
LGA    I     343      I     343          3.078
LGA    L     344      L     344          3.531
LGA    Q     345      Q     345          9.234
LGA    K     346      K     346         13.048
LGA    Q     347      Q     347         12.771

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  124    4.0     19    2.34    13.911    13.053     0.777

LGA_LOCAL      RMSD =  2.345  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.752  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  8.918  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.058890 * X  +  -0.777300 * Y  +   0.626368 * Z  + 120.333626
  Y_new =  -0.964744 * X  +  -0.205549 * Y  +  -0.164376 * Z  + 120.152451
  Z_new =   0.256519 * X  +  -0.594604 * Y  +  -0.762000 * Z  + 106.470146 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.478967    0.662625  [ DEG:  -142.0344     37.9656 ]
  Theta =  -0.259419   -2.882174  [ DEG:   -14.8636   -165.1364 ]
  Phi   =  -1.509830    1.631763  [ DEG:   -86.5069     93.4931 ]
 
# 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: T0356TS383_5-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_5-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  124   4.0   19   2.34  13.053     8.92
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_5-D1
PFRMAT TS
TARGET t0356
MODEL 5
PARENT 2bmoA
ATOM    745  N   ASP   314      78.069  57.743  69.547  1.00  0.00
ATOM    746  CA  ASP   314      76.909  57.750  70.427  1.00  0.00
ATOM    747  C   ASP   314      75.830  56.823  69.911  1.00  0.00
ATOM    748  O   ASP   314      75.783  56.494  68.711  1.00  0.00
ATOM    749  N   ALA   315      74.960  56.419  70.829  1.00  0.00
ATOM    750  CA  ALA   315      73.716  55.752  70.494  1.00  0.00
ATOM    751  C   ALA   315      72.528  56.687  70.604  1.00  0.00
ATOM    752  O   ALA   315      72.585  57.730  71.273  1.00  0.00
ATOM    753  N   ILE   316      71.449  56.298  69.929  1.00  0.00
ATOM    754  CA  ILE   316      70.177  57.011  69.935  1.00  0.00
ATOM    755  C   ILE   316      69.061  56.020  70.264  1.00  0.00
ATOM    756  O   ILE   316      68.841  55.063  69.516  1.00  0.00
ATOM    757  N   TYR   317      68.377  56.246  71.383  1.00  0.00
ATOM    758  CA  TYR   317      67.128  55.549  71.723  1.00  0.00
ATOM    759  C   TYR   317      65.972  56.505  71.423  1.00  0.00
ATOM    760  O   TYR   317      65.782  57.516  72.105  1.00  0.00
ATOM    761  N   HIS   318      65.205  56.192  70.382  1.00  0.00
ATOM    762  CA  HIS   318      64.161  57.100  69.910  1.00  0.00
ATOM    763  C   HIS   318      63.134  57.478  70.978  1.00  0.00
ATOM    764  O   HIS   318      62.585  56.608  71.657  1.00  0.00
ATOM    765  N   SER   319      62.871  58.775  71.111  1.00  0.00
ATOM    766  CA  SER   319      61.763  59.268  71.914  1.00  0.00
ATOM    767  C   SER   319      61.983  59.381  73.413  1.00  0.00
ATOM    768  O   SER   319      61.149  59.967  74.108  1.00  0.00
ATOM    769  N   THR   320      63.095  58.837  73.916  1.00  0.00
ATOM    770  CA  THR   320      63.282  58.646  75.369  1.00  0.00
ATOM    771  C   THR   320      63.838  59.885  76.084  1.00  0.00
ATOM    772  O   THR   320      64.867  59.836  76.755  1.00  0.00
ATOM    773  N   TYR   321      63.123  60.994  75.950  1.00  0.00
ATOM    774  CA  TYR   321      63.574  62.303  76.427  1.00  0.00
ATOM    775  C   TYR   321      63.784  62.359  77.938  1.00  0.00
ATOM    776  O   TYR   321      64.551  63.172  78.418  1.00  0.00
ATOM    777  N   THR   322      63.116  61.495  78.690  1.00  0.00
ATOM    778  CA  THR   322      63.306  61.493  80.140  1.00  0.00
ATOM    779  C   THR   322      64.443  60.568  80.591  1.00  0.00
ATOM    780  O   THR   322      64.786  60.549  81.768  1.00  0.00
ATOM    781  N   GLY   323      65.017  59.806  79.665  1.00  0.00
ATOM    782  CA  GLY   323      66.218  59.011  79.926  1.00  0.00
ATOM    783  C   GLY   323      66.164  58.193  81.202  1.00  0.00
ATOM    784  O   GLY   323      65.208  57.452  81.440  1.00  0.00
ATOM    785  N   ARG   324      67.197  58.333  82.032  1.00  0.00
ATOM    786  CA  ARG   324      67.302  57.565  83.274  1.00  0.00
ATOM    787  C   ARG   324      66.559  58.185  84.459  1.00  0.00
ATOM    788  O   ARG   324      66.750  57.754  85.602  1.00  0.00
ATOM    789  N   PRO   325      65.707  59.179  84.217  1.00  0.00
ATOM    790  CA  PRO   325      64.920  59.770  85.300  1.00  0.00
ATOM    791  C   PRO   325      63.727  58.881  85.678  1.00  0.00
ATOM    792  O   PRO   325      63.194  58.130  84.855  1.00  0.00
ATOM    793  N   PRO   326      56.211  63.044  83.088  1.00  0.00
ATOM    794  CA  PRO   326      55.170  63.859  82.442  1.00  0.00
ATOM    795  C   PRO   326      55.611  65.285  82.074  1.00  0.00
ATOM    796  O   PRO   326      55.400  65.721  80.931  1.00  0.00
ATOM    797  N   ASP   327      56.239  66.001  83.000  1.00  0.00
ATOM    798  CA  ASP   327      56.609  67.388  82.728  1.00  0.00
ATOM    799  C   ASP   327      57.726  67.500  81.694  1.00  0.00
ATOM    800  O   ASP   327      57.693  68.383  80.834  1.00  0.00
ATOM    801  N   GLU   328      58.717  66.614  81.757  1.00  0.00
ATOM    802  CA  GLU   328      59.794  66.664  80.782  1.00  0.00
ATOM    803  C   GLU   328      59.313  66.299  79.398  1.00  0.00
ATOM    804  O   GLU   328      59.648  66.975  78.427  1.00  0.00
ATOM    805  N   PRO   329      58.518  65.234  79.306  1.00  0.00
ATOM    806  CA  PRO   329      57.998  64.784  78.017  1.00  0.00
ATOM    807  C   PRO   329      57.149  65.857  77.361  1.00  0.00
ATOM    808  O   PRO   329      57.259  66.068  76.153  1.00  0.00
ATOM    809  N   ALA   330      56.324  66.548  78.148  1.00  0.00
ATOM    810  CA  ALA   330      55.501  67.644  77.621  1.00  0.00
ATOM    811  C   ALA   330      56.355  68.790  77.076  1.00  0.00
ATOM    812  O   ALA   330      56.057  69.346  76.018  1.00  0.00
ATOM    813  N   VAL   331      57.430  69.128  77.783  1.00  0.00
ATOM    814  CA  VAL   331      58.321  70.190  77.335  1.00  0.00
ATOM    815  C   VAL   331      59.010  69.820  76.018  1.00  0.00
ATOM    816  O   VAL   331      59.042  70.616  75.073  1.00  0.00
ATOM    817  N   LEU   332      59.559  68.613  75.957  1.00  0.00
ATOM    818  CA  LEU   332      60.233  68.134  74.753  1.00  0.00
ATOM    819  C   LEU   332      59.298  67.972  73.567  1.00  0.00
ATOM    820  O   LEU   332      59.660  68.313  72.441  1.00  0.00
ATOM    821  N   GLY   333      58.088  67.467  73.811  1.00  0.00
ATOM    822  CA  GLY   333      57.110  67.290  72.734  1.00  0.00
ATOM    823  C   GLY   333      56.703  68.621  72.123  1.00  0.00
ATOM    824  O   GLY   333      56.555  68.731  70.902  1.00  0.00
ATOM    825  N   VAL   334      56.539  69.635  72.963  1.00  0.00
ATOM    826  CA  VAL   334      56.150  70.954  72.488  1.00  0.00
ATOM    827  C   VAL   334      57.234  71.584  71.621  1.00  0.00
ATOM    828  O   VAL   334      56.938  72.139  70.561  1.00  0.00
ATOM    829  N   ALA   335      58.492  71.484  72.043  1.00  0.00
ATOM    830  CA  ALA   335      59.574  72.055  71.249  1.00  0.00
ATOM    831  C   ALA   335      59.840  71.258  69.974  1.00  0.00
ATOM    832  O   ALA   335      60.170  71.839  68.936  1.00  0.00
ATOM    833  N   LEU   336      59.670  69.940  70.045  1.00  0.00
ATOM    834  CA  LEU   336      59.801  69.074  68.871  1.00  0.00
ATOM    835  C   LEU   336      58.898  69.536  67.725  1.00  0.00
ATOM    836  O   LEU   336      59.324  69.578  66.563  1.00  0.00
ATOM    837  N   ASN   337      57.654  69.870  68.063  1.00  0.00
ATOM    838  CA  ASN   337      56.684  70.355  67.068  1.00  0.00
ATOM    839  C   ASN   337      57.187  71.617  66.356  1.00  0.00
ATOM    840  O   ASN   337      57.034  71.745  65.130  1.00  0.00
ATOM    841  N   GLU   338      57.771  72.539  67.118  1.00  0.00
ATOM    842  CA  GLU   338      58.348  73.758  66.554  1.00  0.00
ATOM    843  C   GLU   338      59.575  73.444  65.701  1.00  0.00
ATOM    844  O   GLU   338      59.692  73.921  64.569  1.00  0.00
ATOM    845  N   VAL   339      60.473  72.622  66.244  1.00  0.00
ATOM    846  CA  VAL   339      61.731  72.269  65.573  1.00  0.00
ATOM    847  C   VAL   339      61.575  71.535  64.249  1.00  0.00
ATOM    848  O   VAL   339      62.388  71.702  63.343  1.00  0.00
ATOM    849  N   PHE   340      60.536  70.717  64.141  1.00  0.00
ATOM    850  CA  PHE   340      60.286  69.966  62.915  1.00  0.00
ATOM    851  C   PHE   340      60.179  70.896  61.699  1.00  0.00
ATOM    852  O   PHE   340      60.625  70.547  60.608  1.00  0.00
ATOM    853  N   VAL   341      59.634  72.092  61.914  1.00  0.00
ATOM    854  CA  VAL   341      59.486  73.082  60.840  1.00  0.00
ATOM    855  C   VAL   341      60.814  73.703  60.408  1.00  0.00
ATOM    856  O   VAL   341      60.932  74.195  59.283  1.00  0.00
ATOM    857  N   PRO   342      61.799  73.680  61.304  1.00  0.00
ATOM    858  CA  PRO   342      63.098  74.312  61.077  1.00  0.00
ATOM    859  C   PRO   342      64.152  73.330  60.577  1.00  0.00
ATOM    860  O   PRO   342      64.926  73.644  59.669  1.00  0.00
ATOM    861  N   ILE   343      64.194  72.145  61.183  1.00  0.00
ATOM    862  CA  ILE   343      65.238  71.157  60.882  1.00  0.00
ATOM    863  C   ILE   343      64.724  69.809  60.369  1.00  0.00
ATOM    864  O   ILE   343      65.518  68.924  60.055  1.00  0.00
ATOM    865  N   LEU   344      63.404  69.666  60.257  1.00  0.00
ATOM    866  CA  LEU   344      62.802  68.442  59.722  1.00  0.00
ATOM    867  C   LEU   344      62.384  67.437  60.784  1.00  0.00
ATOM    868  O   LEU   344      62.812  67.524  61.935  1.00  0.00
ATOM    869  N   GLN   345      61.554  66.471  60.395  1.00  0.00
ATOM    870  CA  GLN   345      60.985  65.492  61.336  1.00  0.00
ATOM    871  C   GLN   345      62.027  64.626  62.053  1.00  0.00
ATOM    872  O   GLN   345      61.973  64.473  63.276  1.00  0.00
ATOM    873  N   LYS   346      62.951  64.043  61.299  1.00  0.00
ATOM    874  CA  LYS   346      63.941  63.135  61.884  1.00  0.00
ATOM    875  C   LYS   346      64.793  63.840  62.946  1.00  0.00
ATOM    876  O   LYS   346      64.952  63.349  64.078  1.00  0.00
ATOM    877  N   GLN   347      65.326  65.002  62.594  1.00  0.00
ATOM    878  CA  GLN   347      66.201  65.713  63.512  1.00  0.00
ATOM    879  C   GLN   347      65.441  66.288  64.709  1.00  0.00
ATOM    880  O   GLN   347      65.982  66.342  65.814  1.00  0.00
TER
END
