
#######################################################
#                                                     #
#                        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   21 (  155),  selected   21 , name T0347TS389_3-D2
# Molecule2: number of CA atoms   71 (  561),  selected   21 , name T0347_D2.pdb
# PARAMETERS: T0347TS389_3-D2.T0347_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:    18       174 - 191         1.78    12.33
  LCS_AVERAGE:     24.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       174 - 191         1.78    12.33
  LCS_AVERAGE:     22.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       177 - 191         0.66    13.20
  LCS_AVERAGE:     16.50

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:   71
LCS_GDT     V     152     V     152      3    3   13     3    3    3    3    3    5    5    7    9    9   10   11   12   14   14   15   15   17   17   18 
LCS_GDT     I     153     I     153      3    3   13     3    3    3    3    3    3    3    6    7    8    8   10   12   14   14   15   15   17   17   18 
LCS_GDT     I     154     I     154      3    3   13     3    3    3    3    3    5    5    6    7    8   10   11   12   14   14   15   15   17   17   18 
LCS_GDT     L     174     L     174      4   18   18     3    4    4    4    6    8    8   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     S     175     S     175      4   18   18     3    4    4    4   11   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     D     176     D     176      4   18   18     3    4    4    7   13   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     S     177     S     177     15   18   18    10   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     F     178     F     178     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     D     179     D     179     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     D     180     D     180     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     181     A     181     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     182     L     182     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     183     A     183     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     E     184     E     184     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     185     A     185     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     M     186     M     186     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     187     K     187     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     188     L     188     15   18   18    11   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     A     189     A     189     15   18   18     8   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     190     K     190     15   18   18     8   14   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_GDT     S     191     S     191     15   18   18     3    6   15   15   15   17   17   18   18   18   18   18   18   18   18   18   18   18   18   18 
LCS_AVERAGE  LCS_A:  21.06  (  16.50   22.33   24.35 )

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     11     14     15     15     15     17     17     18     18     18     18     18     18     18     18     18     18     18     18     18 
GDT PERCENT_CA  15.49  19.72  21.13  21.13  21.13  23.94  23.94  25.35  25.35  25.35  25.35  25.35  25.35  25.35  25.35  25.35  25.35  25.35  25.35  25.35
GDT RMS_LOCAL    0.28   0.52   0.66   0.66   0.66   1.46   1.46   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78
GDT RMS_ALL_CA  12.78  13.12  13.20  13.20  13.20  12.46  12.46  12.33  12.33  12.33  12.33  12.33  12.33  12.33  12.33  12.33  12.33  12.33  12.33  12.33

#      Molecule1      Molecule2       DISTANCE
LGA    V     152      V     152         31.829
LGA    I     153      I     153         30.661
LGA    I     154      I     154         28.989
LGA    L     174      L     174          3.937
LGA    S     175      S     175          3.181
LGA    D     176      D     176          3.726
LGA    S     177      S     177          1.047
LGA    F     178      F     178          1.184
LGA    D     179      D     179          0.512
LGA    D     180      D     180          0.725
LGA    A     181      A     181          1.085
LGA    L     182      L     182          0.960
LGA    A     183      A     183          0.590
LGA    E     184      E     184          0.547
LGA    A     185      A     185          0.586
LGA    M     186      M     186          0.681
LGA    K     187      K     187          0.580
LGA    L     188      L     188          0.593
LGA    A     189      A     189          2.392
LGA    K     190      K     190          2.934
LGA    S     191      S     191          2.877

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   71    4.0     18    1.78    22.887    23.096     0.956

LGA_LOCAL      RMSD =  1.783  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.677  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  7.815  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.157155 * X  +  -0.813306 * Y  +   0.560210 * Z  +  -3.997695
  Y_new =   0.497719 * X  +  -0.555176 * Y  +  -0.666374 * Z  +  58.356052
  Z_new =   0.852982 * X  +   0.174103 * Y  +   0.492047 * Z  +  -6.760455 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.340086   -2.801507  [ DEG:    19.4855   -160.5145 ]
  Theta =  -1.021672   -2.119921  [ DEG:   -58.5375   -121.4625 ]
  Phi   =   1.876640   -1.264953  [ DEG:   107.5236    -72.4764 ]
 
# 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: T0347TS389_3-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS389_3-D2.T0347_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   71   4.0   18   1.78  23.096     7.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS389_3-D2
PFRMAT TS
TARGET T0347
MODEL  3
PARENT N/A
ATOM    535  N   VAL   152       0.039  51.283 -17.245  1.00  0.00
ATOM    536  CA  VAL   152      -0.930  51.136 -16.172  1.00  0.00
ATOM    537  CB  VAL   152      -1.257  49.655 -15.908  1.00  0.00
ATOM    538  CG1 VAL   152      -2.245  49.524 -14.759  1.00  0.00
ATOM    539  CG2 VAL   152      -1.869  49.014 -17.144  1.00  0.00
ATOM    540  O   VAL   152       0.280  51.070 -14.105  1.00  0.00
ATOM    541  C   VAL   152      -0.276  51.769 -14.951  1.00  0.00
ATOM    542  N   ILE   153      -0.287  53.097 -14.895  1.00  0.00
ATOM    543  CA  ILE   153       0.263  53.796 -13.745  1.00  0.00
ATOM    544  CB  ILE   153       0.673  55.237 -14.103  1.00  0.00
ATOM    545  CG1 ILE   153       1.771  55.230 -15.167  1.00  0.00
ATOM    546  CG2 ILE   153       1.195  55.963 -12.874  1.00  0.00
ATOM    547  CD1 ILE   153       2.070  56.596 -15.744  1.00  0.00
ATOM    548  O   ILE   153      -1.995  54.205 -13.091  1.00  0.00
ATOM    549  C   ILE   153      -0.901  53.746 -12.776  1.00  0.00
ATOM    550  N   ILE   154      -0.656  53.150 -11.615  1.00  0.00
ATOM    551  CA  ILE   154      -1.677  52.968 -10.595  1.00  0.00
ATOM    552  CB  ILE   154      -1.488  51.640  -9.836  1.00  0.00
ATOM    553  CG1 ILE   154      -1.615  50.455 -10.798  1.00  0.00
ATOM    554  CG2 ILE   154      -2.540  51.492  -8.749  1.00  0.00
ATOM    555  CD1 ILE   154      -1.141  49.143 -10.216  1.00  0.00
ATOM    556  O   ILE   154      -2.771  54.418  -8.979  1.00  0.00
ATOM    557  C   ILE   154      -1.703  54.071  -9.509  1.00  0.00
ATOM    561  N   LEU   174       6.114  64.615  -5.555  1.00  0.00
ATOM    562  CA  LEU   174       7.424  65.229  -5.411  1.00  0.00
ATOM    563  CB  LEU   174       8.177  65.203  -6.741  1.00  0.00
ATOM    564  CG  LEU   174       8.536  63.822  -7.291  1.00  0.00
ATOM    565  CD1 LEU   174       9.199  63.940  -8.656  1.00  0.00
ATOM    566  CD2 LEU   174       9.499  63.105  -6.357  1.00  0.00
ATOM    567  O   LEU   174       7.521  67.582  -5.788  1.00  0.00
ATOM    568  C   LEU   174       7.387  66.674  -4.969  1.00  0.00
ATOM    569  N   SER   175       7.213  66.891  -3.670  1.00  0.00
ATOM    570  CA  SER   175       7.194  68.248  -3.159  1.00  0.00
ATOM    571  CB  SER   175       6.569  68.287  -1.763  1.00  0.00
ATOM    572  OG  SER   175       7.387  67.615  -0.819  1.00  0.00
ATOM    573  O   SER   175       8.867  69.899  -2.921  1.00  0.00
ATOM    574  C   SER   175       8.611  68.730  -3.098  1.00  0.00
ATOM    575  N   ASP   176       9.525  67.787  -3.255  1.00  0.00
ATOM    576  CA  ASP   176      10.956  68.031  -3.244  1.00  0.00
ATOM    577  CB  ASP   176      11.576  67.519  -1.943  1.00  0.00
ATOM    578  CG  ASP   176      11.106  68.295  -0.729  1.00  0.00
ATOM    579  OD1 ASP   176      11.370  69.515  -0.665  1.00  0.00
ATOM    580  OD2 ASP   176      10.475  67.686   0.159  1.00  0.00
ATOM    581  O   ASP   176      11.142  66.079  -4.625  1.00  0.00
ATOM    582  C   ASP   176      11.459  67.257  -4.459  1.00  0.00
ATOM    583  N   SER   177      12.206  67.912  -5.331  1.00  0.00
ATOM    584  CA  SER   177      12.741  67.254  -6.516  1.00  0.00
ATOM    585  CB  SER   177      13.764  68.153  -7.213  1.00  0.00
ATOM    586  OG  SER   177      13.174  69.372  -7.629  1.00  0.00
ATOM    587  O   SER   177      13.809  65.738  -5.024  1.00  0.00
ATOM    588  C   SER   177      13.425  65.954  -6.168  1.00  0.00
ATOM    589  N   PHE   178      13.572  65.079  -7.152  1.00  0.00
ATOM    590  CA  PHE   178      14.266  63.830  -6.900  1.00  0.00
ATOM    591  CB  PHE   178      14.143  62.896  -8.106  1.00  0.00
ATOM    592  CG  PHE   178      14.860  61.589  -7.933  1.00  0.00
ATOM    593  CD1 PHE   178      14.304  60.572  -7.175  1.00  0.00
ATOM    594  CD2 PHE   178      16.090  61.372  -8.531  1.00  0.00
ATOM    595  CE1 PHE   178      14.963  59.369  -7.017  1.00  0.00
ATOM    596  CE2 PHE   178      16.749  60.167  -8.371  1.00  0.00
ATOM    597  CZ  PHE   178      16.191  59.169  -7.618  1.00  0.00
ATOM    598  O   PHE   178      16.316  63.775  -5.692  1.00  0.00
ATOM    599  C   PHE   178      15.707  64.223  -6.657  1.00  0.00
ATOM    600  N   ASP   179      16.256  65.067  -7.527  1.00  0.00
ATOM    601  CA  ASP   179      17.626  65.512  -7.336  1.00  0.00
ATOM    602  CB  ASP   179      18.010  66.536  -8.405  1.00  0.00
ATOM    603  CG  ASP   179      18.208  65.908  -9.770  1.00  0.00
ATOM    604  OD1 ASP   179      18.281  64.664  -9.847  1.00  0.00
ATOM    605  OD2 ASP   179      18.290  66.661 -10.765  1.00  0.00
ATOM    606  O   ASP   179      18.656  65.906  -5.204  1.00  0.00
ATOM    607  C   ASP   179      17.707  66.146  -5.950  1.00  0.00
ATOM    608  N   ASP   180      16.694  66.934  -5.595  1.00  0.00
ATOM    609  CA  ASP   180      16.651  67.585  -4.291  1.00  0.00
ATOM    610  CB  ASP   180      15.362  68.396  -4.137  1.00  0.00
ATOM    611  CG  ASP   180      15.365  69.656  -4.981  1.00  0.00
ATOM    612  OD1 ASP   180      16.442  70.026  -5.493  1.00  0.00
ATOM    613  OD2 ASP   180      14.289  70.273  -5.130  1.00  0.00
ATOM    614  O   ASP   180      17.457  66.685  -2.206  1.00  0.00
ATOM    615  C   ASP   180      16.700  66.549  -3.165  1.00  0.00
ATOM    616  N   ALA   181      15.882  65.514  -3.267  1.00  0.00
ATOM    617  CA  ALA   181      15.904  64.469  -2.258  1.00  0.00
ATOM    618  CB  ALA   181      14.869  63.401  -2.576  1.00  0.00
ATOM    619  O   ALA   181      17.889  63.637  -1.215  1.00  0.00
ATOM    620  C   ALA   181      17.289  63.861  -2.259  1.00  0.00
ATOM    621  N   LEU   182      17.792  63.596  -3.458  1.00  0.00
ATOM    622  CA  LEU   182      19.108  63.014  -3.627  1.00  0.00
ATOM    623  CB  LEU   182      19.567  63.141  -5.081  1.00  0.00
ATOM    624  CG  LEU   182      20.951  62.574  -5.407  1.00  0.00
ATOM    625  CD1 LEU   182      20.987  61.072  -5.167  1.00  0.00
ATOM    626  CD2 LEU   182      21.307  62.830  -6.863  1.00  0.00
ATOM    627  O   LEU   182      20.786  63.121  -1.930  1.00  0.00
ATOM    628  C   LEU   182      20.089  63.738  -2.733  1.00  0.00
ATOM    629  N   ALA   183      20.131  65.057  -2.859  1.00  0.00
ATOM    630  CA  ALA   183      21.048  65.853  -2.064  1.00  0.00
ATOM    631  CB  ALA   183      20.867  67.332  -2.366  1.00  0.00
ATOM    632  O   ALA   183      21.723  65.220   0.127  1.00  0.00
ATOM    633  C   ALA   183      20.820  65.652  -0.586  1.00  0.00
ATOM    634  N   GLU   184      19.609  65.935  -0.124  1.00  0.00
ATOM    635  CA  GLU   184      19.316  65.787   1.290  1.00  0.00
ATOM    636  CB  GLU   184      17.814  65.925   1.542  1.00  0.00
ATOM    637  CG  GLU   184      17.420  65.840   3.008  1.00  0.00
ATOM    638  CD  GLU   184      15.933  66.042   3.223  1.00  0.00
ATOM    639  OE1 GLU   184      15.214  66.273   2.230  1.00  0.00
ATOM    640  OE2 GLU   184      15.487  65.971   4.389  1.00  0.00
ATOM    641  O   GLU   184      20.204  64.334   2.960  1.00  0.00
ATOM    642  C   GLU   184      19.744  64.439   1.832  1.00  0.00
ATOM    643  N   ALA   185      19.582  63.388   1.049  1.00  0.00
ATOM    644  CA  ALA   185      19.993  62.095   1.552  1.00  0.00
ATOM    645  CB  ALA   185      19.467  60.986   0.654  1.00  0.00
ATOM    646  O   ALA   185      22.129  61.900   2.590  1.00  0.00
ATOM    647  C   ALA   185      21.508  62.118   1.552  1.00  0.00
ATOM    648  N   MET   186      22.103  62.410   0.397  1.00  0.00
ATOM    649  CA  MET   186      23.557  62.464   0.304  1.00  0.00
ATOM    650  CB  MET   186      23.985  63.165  -0.988  1.00  0.00
ATOM    651  CG  MET   186      23.685  62.374  -2.251  1.00  0.00
ATOM    652  SD  MET   186      24.045  63.303  -3.755  1.00  0.00
ATOM    653  CE  MET   186      25.821  63.492  -3.619  1.00  0.00
ATOM    654  O   MET   186      25.027  62.818   2.162  1.00  0.00
ATOM    655  C   MET   186      24.080  63.236   1.500  1.00  0.00
ATOM    656  N   LYS   187      23.442  64.372   1.755  1.00  0.00
ATOM    657  CA  LYS   187      23.787  65.241   2.863  1.00  0.00
ATOM    658  CB  LYS   187      22.700  66.295   3.078  1.00  0.00
ATOM    659  CG  LYS   187      23.054  67.349   4.117  1.00  0.00
ATOM    660  CD  LYS   187      22.008  68.452   4.160  1.00  0.00
ATOM    661  CE  LYS   187      22.270  69.413   5.307  1.00  0.00
ATOM    662  NZ  LYS   187      21.347  70.583   5.273  1.00  0.00
ATOM    663  O   LYS   187      24.997  64.235   4.656  1.00  0.00
ATOM    664  C   LYS   187      23.920  64.377   4.103  1.00  0.00
ATOM    665  N   LEU   188      22.811  63.786   4.522  1.00  0.00
ATOM    666  CA  LEU   188      22.783  62.928   5.695  1.00  0.00
ATOM    667  CB  LEU   188      21.590  61.971   5.629  1.00  0.00
ATOM    668  CG  LEU   188      21.397  61.045   6.833  1.00  0.00
ATOM    669  CD1 LEU   188      21.135  61.854   8.096  1.00  0.00
ATOM    670  CD2 LEU   188      20.215  60.115   6.611  1.00  0.00
ATOM    671  O   LEU   188      24.704  62.099   6.847  1.00  0.00
ATOM    672  C   LEU   188      24.038  62.089   5.818  1.00  0.00
ATOM    673  N   ALA   189      24.334  61.348   4.758  1.00  0.00
ATOM    674  CA  ALA   189      25.509  60.495   4.696  1.00  0.00
ATOM    675  CB  ALA   189      25.744  60.022   3.269  1.00  0.00
ATOM    676  O   ALA   189      27.536  60.645   5.940  1.00  0.00
ATOM    677  C   ALA   189      26.776  61.197   5.150  1.00  0.00
ATOM    678  N   LYS   190      27.011  62.403   4.638  1.00  0.00
ATOM    679  CA  LYS   190      28.187  63.191   5.010  1.00  0.00
ATOM    680  CB  LYS   190      28.379  64.359   4.041  1.00  0.00
ATOM    681  CG  LYS   190      29.608  65.206   4.324  1.00  0.00
ATOM    682  CD  LYS   190      29.784  66.293   3.278  1.00  0.00
ATOM    683  CE  LYS   190      30.995  67.160   3.580  1.00  0.00
ATOM    684  NZ  LYS   190      31.147  68.265   2.593  1.00  0.00
ATOM    685  O   LYS   190      28.919  63.638   7.258  1.00  0.00
ATOM    686  C   LYS   190      28.023  63.751   6.427  1.00  0.00
ATOM    687  N   SER   191      26.872  64.350   6.698  1.00  0.00
ATOM    688  CA  SER   191      26.582  64.905   8.016  1.00  0.00
ATOM    689  CB  SER   191      25.253  65.663   8.000  1.00  0.00
ATOM    690  OG  SER   191      25.299  66.754   7.096  1.00  0.00
ATOM    691  O   SER   191      26.010  64.030  10.175  1.00  0.00
ATOM    692  C   SER   191      26.487  63.795   9.065  1.00  0.00
TER
END
