
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0361TS239_3_2-D1
# Molecule2: number of CA atoms  158 ( 1268),  selected   23 , name T0361_D1.pdb
# PARAMETERS: T0361TS239_3_2-D1.T0361_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:    22       145 - 167         4.29     5.27
  LCS_AVERAGE:     13.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       145 - 161         1.20     6.79
  LONGEST_CONTINUOUS_SEGMENT:    17       146 - 162         1.98     6.38
  LCS_AVERAGE:      9.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       146 - 160         0.96     6.70
  LONGEST_CONTINUOUS_SEGMENT:    15       147 - 161         0.94     6.61
  LCS_AVERAGE:      7.93

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:  158
LCS_GDT     E     145     E     145     13   17   22     6    7   11   14   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     A     146     A     146     15   17   22     6    9   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     R     147     R     147     15   17   22     6   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     F     148     F     148     15   17   22     6   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     S     149     S     149     15   17   22     6    9   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     G     150     G     150     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     M     151     M     151     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     V     152     V     152     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     K     153     K     153     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     T     154     T     154     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     A     155     A     155     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     L     156     L     156     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     T     157     T     157     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     L     158     L     158     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     A     159     A     159     15   17   22     8   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     V     160     V     160     15   17   22     9   11   15   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     T     161     T     161     15   17   22     4    6   13   16   17   17   17   17   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     T     162     T     162      7   17   22     4    6    6    7    8    8    8   11   13   16   18   21   21   21   21   21   21   21   22   22 
LCS_GDT     T     163     T     163      7    8   22     4    6    6    7    8    8    8   11   14   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     L     164     L     164      7    8   22     4    6    6    7    8    8    8    9    9   16   18   21   21   21   21   21   21   21   22   22 
LCS_GDT     K     165     K     165      7    8   22     4    6    6    7    8   10   12   15   17   17   19   21   21   21   21   21   21   21   22   22 
LCS_GDT     L     167     L     167      7    8   22     0    4    5    7    8    8    8    9    9   10   12   12   13   15   16   17   19   20   22   22 
LCS_GDT     T     168     T     168      0    8   20     0    2    5    7    8    8    8    9    9   10   12   12   12   14   15   16   17   18   19   20 
LCS_AVERAGE  LCS_A:  10.44  (   7.93    9.52   13.87 )

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      9     11     15     16     17     17     17     17     17     17     19     21     21     21     21     21     21     21     22     22 
GDT PERCENT_CA   5.70   6.96   9.49  10.13  10.76  10.76  10.76  10.76  10.76  10.76  12.03  13.29  13.29  13.29  13.29  13.29  13.29  13.29  13.92  13.92
GDT RMS_LOCAL    0.24   0.33   0.96   1.04   1.20   1.20   1.20   1.20   1.20   1.20   2.86   3.37   3.37   3.37   3.37   3.37   3.37   3.37   4.29   4.29
GDT RMS_ALL_CA   6.53   6.41   6.70   6.70   6.79   6.79   6.79   6.79   6.79   6.79   5.76   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.27   5.27

#      Molecule1      Molecule2       DISTANCE
LGA    E     145      E     145          2.429
LGA    A     146      A     146          1.195
LGA    R     147      R     147          0.647
LGA    F     148      F     148          1.005
LGA    S     149      S     149          1.352
LGA    G     150      G     150          1.219
LGA    M     151      M     151          1.199
LGA    V     152      V     152          0.976
LGA    K     153      K     153          1.183
LGA    T     154      T     154          0.869
LGA    A     155      A     155          0.157
LGA    L     156      L     156          0.842
LGA    T     157      T     157          0.184
LGA    L     158      L     158          0.401
LGA    A     159      A     159          1.366
LGA    V     160      V     160          1.279
LGA    T     161      T     161          1.857
LGA    T     162      T     162          8.008
LGA    T     163      T     163          9.886
LGA    L     164      L     164          8.707
LGA    K     165      K     165          9.182
LGA    L     167      L     167         17.289
LGA    T     168      T     168         20.391

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  158    4.0     17    1.20    10.285    10.464     1.307

LGA_LOCAL      RMSD =  1.200  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.793  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  5.165  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.031866 * X  +   0.131741 * Y  +  -0.990772 * Z  +  13.204966
  Y_new =   0.216681 * X  +   0.968611 * Y  +   0.121825 * Z  + -76.542885
  Z_new =   0.975722 * X  +  -0.210799 * Y  +  -0.059412 * Z  +  12.763549 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.845512    1.296081  [ DEG:  -105.7401     74.2599 ]
  Theta =  -1.349995   -1.791598  [ DEG:   -77.3490   -102.6510 ]
  Phi   =   1.716816   -1.424777  [ DEG:    98.3663    -81.6337 ]
 
# 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: T0361TS239_3_2-D1                             
REMARK     2: T0361_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0361TS239_3_2-D1.T0361_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  158   4.0   17   1.20  10.464     5.17
REMARK  ---------------------------------------------------------- 
MOLECULE T0361TS239_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0361
PARENT 1f5q_B
ATOM    712  N   GLU   145       0.412  -9.489  45.829  1.00  9.99
ATOM    713  CA  GLU   145      -0.090  -9.526  44.459  1.00  9.99
ATOM    714  C   GLU   145       0.499  -8.392  43.650  1.00  9.99
ATOM    715  O   GLU   145       0.888  -8.580  42.501  1.00  9.99
ATOM    716  CB  GLU   145      -1.616  -9.415  44.427  1.00  9.99
ATOM    717  N   ALA   146       0.565  -7.214  44.264  1.00  9.99
ATOM    718  CA  ALA   146       1.076  -6.017  43.611  1.00  9.99
ATOM    719  C   ALA   146       2.556  -6.109  43.305  1.00  9.99
ATOM    720  O   ALA   146       2.988  -5.849  42.185  1.00  9.99
ATOM    721  CB  ALA   146       0.774  -4.777  44.465  1.00  9.99
ATOM    722  N   ARG   147       3.342  -6.488  44.292  1.00  9.99
ATOM    723  CA  ARG   147       4.762  -6.627  44.056  1.00  9.99
ATOM    724  C   ARG   147       4.994  -7.548  42.863  1.00  9.99
ATOM    725  O   ARG   147       5.754  -7.224  41.950  1.00  9.99
ATOM    726  CB  ARG   147       5.443  -7.224  45.269  1.00  9.99
ATOM    727  N   PHE   148       4.325  -8.694  42.872  1.00  9.99
ATOM    728  CA  PHE   148       4.493  -9.660  41.812  1.00  9.99
ATOM    729  C   PHE   148       4.041  -9.233  40.438  1.00  9.99
ATOM    730  O   PHE   148       4.460  -9.821  39.441  1.00  9.99
ATOM    731  CB  PHE   148       3.820 -10.972  42.185  1.00  9.99
ATOM    732  N   SER   149       3.180  -8.233  40.355  1.00  9.99
ATOM    733  CA  SER   149       2.753  -7.798  39.043  1.00  9.99
ATOM    734  C   SER   149       3.727  -6.756  38.530  1.00  9.99
ATOM    735  O   SER   149       4.035  -6.707  37.337  1.00  9.99
ATOM    736  CB  SER   149       1.337  -7.233  39.094  1.00  9.99
ATOM    737  N   GLY   150       4.238  -5.945  39.446  1.00  9.99
ATOM    738  CA  GLY   150       5.167  -4.886  39.095  1.00  9.99
ATOM    739  C   GLY   150       6.565  -5.362  38.746  1.00  9.99
ATOM    740  O   GLY   150       7.200  -4.807  37.864  1.00  9.99
ATOM    741  N   MET   151       7.044  -6.384  39.444  1.00  9.99
ATOM    742  CA  MET   151       8.385  -6.905  39.214  1.00  9.99
ATOM    743  C   MET   151       8.702  -7.111  37.730  1.00  9.99
ATOM    744  O   MET   151       9.623  -6.493  37.194  1.00  9.99
ATOM    745  CB  MET   151       8.578  -8.231  39.968  1.00  9.99
ATOM    746  N   VAL   152       7.928  -7.964  37.038  1.00  9.99
ATOM    747  CA  VAL   152       8.206  -8.197  35.619  1.00  9.99
ATOM    748  C   VAL   152       8.274  -6.954  34.742  1.00  9.99
ATOM    749  O   VAL   152       9.081  -6.886  33.818  1.00  9.99
ATOM    750  CB  VAL   152       7.096  -9.167  35.206  1.00  9.99
ATOM    751  N   LYS   153       7.431  -5.971  35.021  1.00  9.99
ATOM    752  CA  LYS   153       7.427  -4.743  34.236  1.00  9.99
ATOM    753  C   LYS   153       8.696  -3.933  34.469  1.00  9.99
ATOM    754  O   LYS   153       9.251  -3.361  33.532  1.00  9.99
ATOM    755  CB  LYS   153       6.219  -3.884  34.593  1.00  9.99
ATOM    756  N   THR   154       9.140  -3.894  35.725  1.00  9.99
ATOM    757  CA  THR   154      10.332  -3.154  36.121  1.00  9.99
ATOM    758  C   THR   154      11.600  -3.720  35.490  1.00  9.99
ATOM    759  O   THR   154      12.483  -2.977  35.081  1.00  9.99
ATOM    760  CB  THR   154      10.501  -3.174  37.643  1.00  9.99
ATOM    761  N   ALA   155      11.678  -5.046  35.428  1.00  9.99
ATOM    762  CA  ALA   155      12.828  -5.730  34.856  1.00  9.99
ATOM    763  C   ALA   155      12.941  -5.418  33.381  1.00  9.99
ATOM    764  O   ALA   155      14.035  -5.256  32.866  1.00  9.99
ATOM    765  CB  ALA   155      12.696  -7.242  35.066  1.00  9.99
ATOM    766  N   LEU   156      11.803  -5.348  32.705  1.00  9.99
ATOM    767  CA  LEU   156      11.781  -5.040  31.289  1.00  9.99
ATOM    768  C   LEU   156      12.183  -3.595  31.082  1.00  9.99
ATOM    769  O   LEU   156      12.866  -3.262  30.116  1.00  9.99
ATOM    770  CB  LEU   156      10.385  -5.252  30.710  1.00  9.99
ATOM    771  N   THR   157      11.754  -2.740  32.003  1.00  9.99
ATOM    772  CA  THR   157      12.065  -1.328  31.931  1.00  9.99
ATOM    773  C   THR   157      13.561  -1.127  32.047  1.00  9.99
ATOM    774  O   THR   157      14.135  -0.269  31.378  1.00  9.99
ATOM    775  CB  THR   157      11.361  -0.591  33.032  1.00  9.99
ATOM    776  N   LEU   158      14.188  -1.935  32.893  1.00  9.99
ATOM    777  CA  LEU   158      15.620  -1.855  33.122  1.00  9.99
ATOM    778  C   LEU   158      16.432  -2.214  31.897  1.00  9.99
ATOM    779  O   LEU   158      17.497  -1.661  31.673  1.00  9.99
ATOM    780  CB  LEU   158      16.001  -2.738  34.316  1.00  9.99
ATOM    781  N   ALA   159      15.921  -3.125  31.086  1.00  9.99
ATOM    782  CA  ALA   159      16.627  -3.531  29.882  1.00  9.99
ATOM    783  C   ALA   159      16.407  -2.571  28.731  1.00  9.99
ATOM    784  O   ALA   159      17.061  -2.678  27.697  1.00  9.99
ATOM    785  CB  ALA   159      16.188  -4.925  29.459  1.00  9.99
ATOM    786  N   VAL   160      15.466  -1.646  28.890  1.00  9.99
ATOM    787  CA  VAL   160      15.207  -0.672  27.841  1.00  9.99
ATOM    788  C   VAL   160      15.848   0.636  28.302  1.00  9.99
ATOM    789  O   VAL   160      15.486   1.178  29.336  1.00  9.99
ATOM    790  CB  VAL   160      13.700  -0.485  27.633  1.00  9.99
ATOM    791  N   THR   161      16.819   1.123  27.542  1.00  9.99
ATOM    792  CA  THR   161      17.497   2.354  27.899  1.00  9.99
ATOM    793  C   THR   161      16.590   3.567  27.933  1.00  9.99
ATOM    794  O   THR   161      16.807   4.473  28.726  1.00  9.99
ATOM    795  CB  THR   161      18.656   2.574  26.913  1.00  9.99
ATOM    796  N   THR   162      15.578   3.591  27.074  1.00  9.99
ATOM    797  CA  THR   162      14.660   4.716  27.045  1.00  9.99
ATOM    798  C   THR   162      13.759   4.765  28.266  1.00  9.99
ATOM    799  O   THR   162      13.114   5.775  28.507  1.00  9.99
ATOM    800  CB  THR   162      13.814   4.693  25.771  1.00  9.99
ATOM    801  N   THR   163      13.718   3.685  29.038  1.00  9.99
ATOM    802  CA  THR   163      12.894   3.650  30.243  1.00  9.99
ATOM    803  C   THR   163      13.725   3.413  31.493  1.00  9.99
ATOM    804  O   THR   163      13.280   3.691  32.595  1.00  9.99
ATOM    805  CB  THR   163      11.812   2.568  30.137  1.00  9.99
ATOM    806  N   LEU   164      14.933   2.912  31.313  1.00  9.99
ATOM    807  CA  LEU   164      15.807   2.637  32.430  1.00  9.99
ATOM    808  C   LEU   164      16.540   3.879  32.932  1.00  9.99
ATOM    809  O   LEU   164      17.092   3.869  34.033  1.00  9.99
ATOM    810  CB  LEU   164      16.805   1.560  32.049  1.00  9.99
ATOM    811  N   LYS   165      16.556   4.945  32.140  1.00  9.99
ATOM    812  CA  LYS   165      17.234   6.165  32.564  1.00  9.99
ATOM    813  C   LYS   165      16.273   7.084  33.339  1.00  9.99
ATOM    814  O   LYS   165      16.648   8.153  33.829  1.00  9.99
ATOM    815  CB  LYS   165      17.851   6.888  31.358  1.00  9.99
ATOM    816  N   LEU   167      15.029   6.639  33.472  1.00  9.99
ATOM    817  CA  LEU   167      14.029   7.400  34.203  1.00  9.99
ATOM    818  C   LEU   167      14.231   7.200  35.702  1.00  9.99
ATOM    819  O   LEU   167      14.745   6.172  36.129  1.00  9.99
ATOM    820  CB  LEU   167      12.628   6.943  33.790  1.00  9.99
ATOM    821  N   THR   168      13.831   8.190  36.492  1.00  9.99
ATOM    822  CA  THR   168      13.955   8.118  37.946  1.00  9.99
ATOM    823  C   THR   168      13.291   6.837  38.438  1.00  9.99
ATOM    824  O   THR   168      12.326   6.370  37.842  1.00  9.99
ATOM    825  CB  THR   168      13.271   9.324  38.607  1.00  9.99
TER
END
