
#######################################################
#                                                     #
#                        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 (  129),  selected   25 , name T0361TS239_3_2
# Molecule2: number of CA atoms  166 ( 1335),  selected   25 , name T0361.pdb
# PARAMETERS: T0361TS239_3_2.T0361.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:    24       143 - 167         4.66     5.60
  LCS_AVERAGE:     14.36

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       144 - 161         1.25     6.78
  LCS_AVERAGE:      9.59

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       146 - 160         0.96     6.69
  LONGEST_CONTINUOUS_SEGMENT:    15       147 - 161         0.94     6.62
  LCS_AVERAGE:      7.33

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:  166
LCS_GDT     W     143     W     143      3   17   24     3    3    3    3    3    6    9    9   13   17   19   19   20   21   22   23   23   23   23   23 
LCS_GDT     S     144     S     144     13   18   24     7   10   14   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     E     145     E     145     13   18   24     7   10   13   16   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     A     146     A     146     15   18   24     7   10   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     R     147     R     147     15   18   24     7   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     F     148     F     148     15   18   24     7   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     S     149     S     149     15   18   24     7   10   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     G     150     G     150     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     M     151     M     151     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     V     152     V     152     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     K     153     K     153     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     T     154     T     154     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     A     155     A     155     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     L     156     L     156     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     T     157     T     157     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     L     158     L     158     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     A     159     A     159     15   18   24     8   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     V     160     V     160     15   18   24    10   11   15   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     T     161     T     161     15   18   24     4    6   13   17   18   18   18   18   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     T     162     T     162      7   17   24     4    6    6    7    8    8    8   11   13   16   19   22   22   22   22   23   23   23   23   23 
LCS_GDT     T     163     T     163      7    8   24     4    6    6    7    8    8    8   11   14   18   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     L     164     L     164      7    8   24     4    6    6    7    8    8    8    9    9   16   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     K     165     K     165      7    8   24     4    6    6    7    8   10   12   16   18   19   20   22   22   22   22   23   23   23   23   23 
LCS_GDT     L     167     L     167      7    8   24     0    4    5    7    8    8    8    9    9   10   12   12   13   15   16   17   19   20   22   23 
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:  10.43  (   7.33    9.59   14.36 )

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     11     15     17     18     18     18     18     18     19     20     22     22     22     22     23     23     23     23     23 
GDT PERCENT_CA   6.02   6.63   9.04  10.24  10.84  10.84  10.84  10.84  10.84  11.45  12.05  13.25  13.25  13.25  13.25  13.86  13.86  13.86  13.86  13.86
GDT RMS_LOCAL    0.29   0.33   0.96   1.16   1.25   1.25   1.25   1.25   1.25   2.27   2.87   3.37   3.37   3.37   3.37   3.76   3.76   3.76   3.76   3.76
GDT RMS_ALL_CA   6.59   6.59   6.69   6.74   6.78   6.78   6.78   6.78   6.78   6.22   5.94   5.80   5.80   5.80   5.80   5.86   5.86   5.86   5.86   5.86

#      Molecule1      Molecule2       DISTANCE
LGA    W     143      W     143          8.030
LGA    S     144      S     144          1.672
LGA    E     145      E     145          2.132
LGA    A     146      A     146          0.946
LGA    R     147      R     147          0.588
LGA    F     148      F     148          1.155
LGA    S     149      S     149          1.403
LGA    G     150      G     150          1.354
LGA    M     151      M     151          1.423
LGA    V     152      V     152          1.150
LGA    K     153      K     153          1.215
LGA    T     154      T     154          0.911
LGA    A     155      A     155          0.276
LGA    L     156      L     156          0.857
LGA    T     157      T     157          0.173
LGA    L     158      L     158          0.421
LGA    A     159      A     159          1.408
LGA    V     160      V     160          1.473
LGA    T     161      T     161          1.873
LGA    T     162      T     162          7.964
LGA    T     163      T     163          9.983
LGA    L     164      L     164          8.875
LGA    K     165      K     165          9.326
LGA    L     167      L     167         17.476
LGA    T     168      T     168         20.582

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  166    4.0     18    1.25    10.392    10.501     1.335

LGA_LOCAL      RMSD =  1.248  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.784  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  5.511  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.033000 * X  +   0.150224 * Y  +  -0.988101 * Z  +  12.002274
  Y_new =   0.181536 * X  +   0.973095 * Y  +   0.141880 * Z  + -75.754364
  Z_new =   0.982830 * X  +  -0.174694 * Y  +  -0.059383 * Z  +  10.102358 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.898470    1.243123  [ DEG:  -108.7743     71.2257 ]
  Theta =  -1.385222   -1.756371  [ DEG:   -79.3674   -100.6326 ]
  Phi   =   1.750615   -1.390978  [ DEG:   100.3028    -79.6972 ]
 
# 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                                
REMARK     2: T0361.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0361TS239_3_2.T0361.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  166   4.0   18   1.25  10.501     5.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0361TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0361
PARENT 1f5q_B
ATOM    702  N   TRP   143      -0.082  -6.245  48.943  1.00  9.99
ATOM    703  CA  TRP   143       1.327  -6.273  48.572  1.00  9.99
ATOM    704  C   TRP   143       1.777  -7.402  47.654  1.00  9.99
ATOM    705  O   TRP   143       2.351  -7.152  46.604  1.00  9.99
ATOM    706  CB  TRP   143       2.208  -6.285  49.815  1.00  9.99
ATOM    707  N   SER   144       1.524  -8.642  48.042  1.00  9.99
ATOM    708  CA  SER   144       1.967  -9.766  47.233  1.00  9.99
ATOM    709  C   SER   144       1.551  -9.709  45.785  1.00  9.99
ATOM    710  O   SER   144       2.398  -9.676  44.899  1.00  9.99
ATOM    711  CB  SER   144       1.480 -11.089  47.818  1.00  9.99
ATOM    712  N   GLU   145       0.247  -9.728  45.537  1.00  9.99
ATOM    713  CA  GLU   145      -0.248  -9.707  44.164  1.00  9.99
ATOM    714  C   GLU   145       0.365  -8.554  43.399  1.00  9.99
ATOM    715  O   GLU   145       0.756  -8.708  42.246  1.00  9.99
ATOM    716  CB  GLU   145      -1.772  -9.566  44.128  1.00  9.99
ATOM    717  N   ALA   146       0.448  -7.401  44.056  1.00  9.99
ATOM    718  CA  ALA   146       0.985  -6.190  43.450  1.00  9.99
ATOM    719  C   ALA   146       2.464  -6.298  43.147  1.00  9.99
ATOM    720  O   ALA   146       2.907  -6.005  42.040  1.00  9.99
ATOM    721  CB  ALA   146       0.700  -4.977  44.347  1.00  9.99
ATOM    722  N   ARG   147       3.238  -6.727  44.123  1.00  9.99
ATOM    723  CA  ARG   147       4.657  -6.883  43.888  1.00  9.99
ATOM    724  C   ARG   147       4.878  -7.764  42.664  1.00  9.99
ATOM    725  O   ARG   147       5.649  -7.421  41.766  1.00  9.99
ATOM    726  CB  ARG   147       5.320  -7.536  45.082  1.00  9.99
ATOM    727  N   PHE   148       4.189  -8.897  42.628  1.00  9.99
ATOM    728  CA  PHE   148       4.344  -9.827  41.534  1.00  9.99
ATOM    729  C   PHE   148       3.908  -9.342  40.174  1.00  9.99
ATOM    730  O   PHE   148       4.321  -9.901  39.159  1.00  9.99
ATOM    731  CB  PHE   148       3.646 -11.139  41.856  1.00  9.99
ATOM    732  N   SER   149       3.065  -8.324  40.125  1.00  9.99
ATOM    733  CA  SER   149       2.653  -7.834  38.827  1.00  9.99
ATOM    734  C   SER   149       3.648  -6.792  38.357  1.00  9.99
ATOM    735  O   SER   149       3.963  -6.705  37.168  1.00  9.99
ATOM    736  CB  SER   149       1.247  -7.246  38.892  1.00  9.99
ATOM    737  N   GLY   150       4.168  -6.024  39.305  1.00  9.99
ATOM    738  CA  GLY   150       5.118  -4.970  38.996  1.00  9.99
ATOM    739  C   GLY   150       6.509  -5.458  38.637  1.00  9.99
ATOM    740  O   GLY   150       7.158  -4.883  37.778  1.00  9.99
ATOM    741  N   MET   151       6.966  -6.514  39.299  1.00  9.99
ATOM    742  CA  MET   151       8.299  -7.051  39.056  1.00  9.99
ATOM    743  C   MET   151       8.619  -7.208  37.567  1.00  9.99
ATOM    744  O   MET   151       9.555  -6.588  37.058  1.00  9.99
ATOM    745  CB  MET   151       8.464  -8.406  39.762  1.00  9.99
ATOM    746  N   VAL   152       7.834  -8.021  36.841  1.00  9.99
ATOM    747  CA  VAL   152       8.115  -8.207  35.415  1.00  9.99
ATOM    748  C   VAL   152       8.211  -6.934  34.585  1.00  9.99
ATOM    749  O   VAL   152       9.023  -6.847  33.668  1.00  9.99
ATOM    750  CB  VAL   152       6.991  -9.140  34.962  1.00  9.99
ATOM    751  N   LYS   153       7.383  -5.947  34.896  1.00  9.99
ATOM    752  CA  LYS   153       7.406  -4.691  34.156  1.00  9.99
ATOM    753  C   LYS   153       8.688  -3.914  34.424  1.00  9.99
ATOM    754  O   LYS   153       9.258  -3.318  33.511  1.00  9.99
ATOM    755  CB  LYS   153       6.212  -3.824  34.539  1.00  9.99
ATOM    756  N   THR   154       9.126  -3.928  35.683  1.00  9.99
ATOM    757  CA  THR   154      10.329  -3.225  36.111  1.00  9.99
ATOM    758  C   THR   154      11.589  -3.790  35.465  1.00  9.99
ATOM    759  O   THR   154      12.488  -3.049  35.088  1.00  9.99
ATOM    760  CB  THR   154      10.490  -3.304  37.632  1.00  9.99
ATOM    761  N   ALA   155      11.645  -5.115  35.355  1.00  9.99
ATOM    762  CA  ALA   155      12.784  -5.798  34.764  1.00  9.99
ATOM    763  C   ALA   155      12.911  -5.435  33.302  1.00  9.99
ATOM    764  O   ALA   155      14.010  -5.274  32.798  1.00  9.99
ATOM    765  CB  ALA   155      12.624  -7.314  34.918  1.00  9.99
ATOM    766  N   LEU   156      11.778  -5.319  32.624  1.00  9.99
ATOM    767  CA  LEU   156      11.769  -4.960  31.219  1.00  9.99
ATOM    768  C   LEU   156      12.198  -3.516  31.068  1.00  9.99
ATOM    769  O   LEU   156      12.892  -3.160  30.117  1.00  9.99
ATOM    770  CB  LEU   156      10.372  -5.125  30.627  1.00  9.99
ATOM    771  N   THR   157      11.779  -2.688  32.017  1.00  9.99
ATOM    772  CA  THR   157      12.116  -1.280  31.998  1.00  9.99
ATOM    773  C   THR   157      13.615  -1.110  32.128  1.00  9.99
ATOM    774  O   THR   157      14.207  -0.239  31.494  1.00  9.99
ATOM    775  CB  THR   157      11.419  -0.571  33.122  1.00  9.99
ATOM    776  N   LEU   158      14.223  -1.960  32.947  1.00  9.99
ATOM    777  CA  LEU   158      15.654  -1.914  33.186  1.00  9.99
ATOM    778  C   LEU   158      16.467  -2.242  31.952  1.00  9.99
ATOM    779  O   LEU   158      17.542  -1.701  31.753  1.00  9.99
ATOM    780  CB  LEU   158      16.013  -2.847  34.348  1.00  9.99
ATOM    781  N   ALA   159      15.943  -3.114  31.105  1.00  9.99
ATOM    782  CA  ALA   159      16.648  -3.489  29.891  1.00  9.99
ATOM    783  C   ALA   159      16.451  -2.483  28.774  1.00  9.99
ATOM    784  O   ALA   159      17.109  -2.565  27.740  1.00  9.99
ATOM    785  CB  ALA   159      16.186  -4.858  29.415  1.00  9.99
ATOM    786  N   VAL   160      15.527  -1.548  28.963  1.00  9.99
ATOM    787  CA  VAL   160      15.290  -0.532  27.949  1.00  9.99
ATOM    788  C   VAL   160      15.952   0.747  28.460  1.00  9.99
ATOM    789  O   VAL   160      15.595   1.257  29.512  1.00  9.99
ATOM    790  CB  VAL   160      13.788  -0.310  27.741  1.00  9.99
ATOM    791  N   THR   161      16.936   1.243  27.723  1.00  9.99
ATOM    792  CA  THR   161      17.634   2.448  28.128  1.00  9.99
ATOM    793  C   THR   161      16.749   3.675  28.202  1.00  9.99
ATOM    794  O   THR   161      16.978   4.547  29.029  1.00  9.99
ATOM    795  CB  THR   161      18.802   2.683  27.155  1.00  9.99
ATOM    796  N   THR   162      15.742   3.749  27.340  1.00  9.99
ATOM    797  CA  THR   162      14.845   4.890  27.348  1.00  9.99
ATOM    798  C   THR   162      13.939   4.911  28.566  1.00  9.99
ATOM    799  O   THR   162      13.311   5.923  28.841  1.00  9.99
ATOM    800  CB  THR   162      14.005   4.929  26.070  1.00  9.99
ATOM    801  N   THR   163      13.873   3.804  29.298  1.00  9.99
ATOM    802  CA  THR   163      13.043   3.741  30.497  1.00  9.99
ATOM    803  C   THR   163      13.863   3.444  31.741  1.00  9.99
ATOM    804  O   THR   163      13.418   3.689  32.851  1.00  9.99
ATOM    805  CB  THR   163      11.942   2.684  30.347  1.00  9.99
ATOM    806  N   LEU   164      15.064   2.927  31.548  1.00  9.99
ATOM    807  CA  LEU   164      15.926   2.597  32.659  1.00  9.99
ATOM    808  C   LEU   164      16.679   3.805  33.209  1.00  9.99
ATOM    809  O   LEU   164      17.225   3.745  34.311  1.00  9.99
ATOM    810  CB  LEU   164      16.907   1.516  32.243  1.00  9.99
ATOM    811  N   LYS   165      16.718   4.899  32.456  1.00  9.99
ATOM    812  CA  LYS   165      17.415   6.091  32.928  1.00  9.99
ATOM    813  C   LYS   165      16.467   6.998  33.732  1.00  9.99
ATOM    814  O   LYS   165      16.859   8.041  34.262  1.00  9.99
ATOM    815  CB  LYS   165      18.052   6.845  31.752  1.00  9.99
ATOM    816  N   LEU   167      15.215   6.571  33.843  1.00  9.99
ATOM    817  CA  LEU   167      14.225   7.323  34.596  1.00  9.99
ATOM    818  C   LEU   167      14.415   7.065  36.087  1.00  9.99
ATOM    819  O   LEU   167      14.909   6.013  36.479  1.00  9.99
ATOM    820  CB  LEU   167      12.818   6.907  34.160  1.00  9.99
ATOM    821  N   THR   168      14.029   8.033  36.912  1.00  9.99
ATOM    822  CA  THR   168      14.144   7.906  38.363  1.00  9.99
ATOM    823  C   THR   168      13.455   6.620  38.804  1.00  9.99
ATOM    824  O   THR   168      12.485   6.192  38.187  1.00  9.99
ATOM    825  CB  THR   168      13.479   9.098  39.065  1.00  9.99
ATOM    826  N   PRO   169      13.960   5.981  39.871  1.00  9.99
ATOM    827  CA  PRO   169      13.418   4.740  40.430  1.00  9.99
ATOM    828  C   PRO   169      11.938   4.795  40.833  1.00  9.99
ATOM    829  O   PRO   169      11.171   3.916  40.469  1.00  9.99
ATOM    830  CB  PRO   169      14.325   4.484  41.622  1.00  9.99
TER
END
