
#######################################################
#                                                     #
#                        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 (  158),  selected   21 , name T0347TS389_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   21 , name T0347_D2.pdb
# PARAMETERS: T0347TS389_4-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       157 - 190         4.79     8.98
  LCS_AVERAGE:     23.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       174 - 190         1.96    11.25
  LCS_AVERAGE:     20.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       177 - 189         0.80    11.90
  LONGEST_CONTINUOUS_SEGMENT:    13       178 - 190         0.99    12.49
  LCS_AVERAGE:     13.88

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     I     154     I     154      3    3    4     3    3    3    3    3    4    4    4    4    6   13   13   14   14   16   17   19   19   19   19 
LCS_GDT     P     155     P     155      3    3    4     3    3    4    4    6    7    8    8    9   12   13   13   14   14   16   17   19   19   19   20 
LCS_GDT     F     156     F     156      3    3   13     3    3    4    4    6    7    8    8   10   12   13   13   14   14   16   17   19   19   19   20 
LCS_GDT     S     157     S     157      3    3   18     0    3    3    3    6    7    8    8    9   12   13   13   14   14   16   17   19   19   19   20 
LCS_GDT     L     174     L     174      4   17   18     3    4    4    4    5    6   14   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     S     175     S     175      4   17   18     3    4    4    4   13   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     D     176     D     176      5   17   18     3    4    5    6   13   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     S     177     S     177     13   17   18     8   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     F     178     F     178     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     D     179     D     179     13   17   18     4   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     D     180     D     180     13   17   18     4   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     A     181     A     181     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     L     182     L     182     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     A     183     A     183     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     E     184     E     184     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     A     185     A     185     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     M     186     M     186     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     K     187     K     187     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     L     188     L     188     13   17   18     9   12   13   14   14   15   16   16   17   17   17   17   17   17   17   17   19   19   19   20 
LCS_GDT     A     189     A     189     13   17   18     3    6   13   14   14   15   16   16   17   17   17   17   17   17   17   17   17   17   17   20 
LCS_GDT     K     190     K     190     13   17   18     3    3    7   14   14   14   16   16   17   17   17   17   17   17   17   17   17   17   17   20 
LCS_AVERAGE  LCS_A:  19.07  (  13.88   20.19   23.14 )

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     12     13     14     14     15     16     16     17     17     17     17     17     17     17     17     19     19     19     20 
GDT PERCENT_CA  12.68  16.90  18.31  19.72  19.72  21.13  22.54  22.54  23.94  23.94  23.94  23.94  23.94  23.94  23.94  23.94  26.76  26.76  26.76  28.17
GDT RMS_LOCAL    0.39   0.55   0.80   1.01   1.01   1.58   1.72   1.72   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   5.86   5.86   5.86   6.18
GDT RMS_ALL_CA  11.47  11.40  11.90  12.28  12.28  11.12  11.41  11.41  11.25  11.25  11.25  11.25  11.25  11.25  11.25  11.25   6.91   6.91   6.91   6.88

#      Molecule1      Molecule2       DISTANCE
LGA    I     154      I     154         31.614
LGA    P     155      P     155         26.115
LGA    F     156      F     156         22.965
LGA    S     157      S     157         21.368
LGA    L     174      L     174          4.389
LGA    S     175      S     175          3.264
LGA    D     176      D     176          3.139
LGA    S     177      S     177          0.533
LGA    F     178      F     178          1.649
LGA    D     179      D     179          1.685
LGA    D     180      D     180          1.064
LGA    A     181      A     181          1.371
LGA    L     182      L     182          0.378
LGA    A     183      A     183          0.662
LGA    E     184      E     184          1.438
LGA    A     185      A     185          1.162
LGA    M     186      M     186          0.530
LGA    K     187      K     187          1.306
LGA    L     188      L     188          1.318
LGA    A     189      A     189          1.539
LGA    K     190      K     190          2.850

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   71    4.0     16    1.72    20.775    21.201     0.877

LGA_LOCAL      RMSD =  1.724  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.407  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  6.680  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.232543 * X  +  -0.847998 * Y  +   0.476259 * Z  +  -4.988284
  Y_new =   0.540618 * X  +  -0.519766 * Y  +  -0.661495 * Z  +  59.506920
  Z_new =   0.808490 * X  +   0.103648 * Y  +   0.579311 * Z  +  -9.387615 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.177043   -2.964550  [ DEG:    10.1438   -169.8562 ]
  Theta =  -0.941581   -2.200011  [ DEG:   -53.9486   -126.0514 ]
  Phi   =   1.977015   -1.164577  [ DEG:   113.2746    -66.7254 ]
 
# 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_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS389_4-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   16   1.72  21.201     6.68
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS389_4-D2
PFRMAT TS
TARGET T0347
MODEL  4
PARENT N/A
ATOM    512  N   ILE   154      -1.355  54.687 -13.770  1.00  0.00
ATOM    513  CA  ILE   154      -2.537  54.589 -12.954  1.00  0.00
ATOM    514  CB  ILE   154      -2.905  53.121 -12.665  1.00  0.00
ATOM    515  CG1 ILE   154      -3.185  52.374 -13.972  1.00  0.00
ATOM    516  CG2 ILE   154      -4.147  53.043 -11.791  1.00  0.00
ATOM    517  CD1 ILE   154      -3.380  50.885 -13.795  1.00  0.00
ATOM    518  O   ILE   154      -3.104  56.047 -11.184  1.00  0.00
ATOM    519  C   ILE   154      -2.266  55.292 -11.660  1.00  0.00
ATOM    520  N   PRO   155      -1.121  55.052 -11.053  1.00  0.00
ATOM    521  CA  PRO   155      -0.854  55.819  -9.856  1.00  0.00
ATOM    522  CB  PRO   155      -0.297  54.788  -8.872  1.00  0.00
ATOM    523  CG  PRO   155       0.541  53.883  -9.711  1.00  0.00
ATOM    524  CD  PRO   155      -0.200  53.716 -11.009  1.00  0.00
ATOM    525  O   PRO   155       0.645  56.884 -11.415  1.00  0.00
ATOM    526  C   PRO   155       0.174  56.896 -10.276  1.00  0.00
ATOM    527  N   PHE   156       0.453  57.863  -9.410  1.00  0.00
ATOM    528  CA  PHE   156       1.438  58.894  -9.709  1.00  0.00
ATOM    529  CB  PHE   156       0.747  60.178 -10.173  1.00  0.00
ATOM    530  CG  PHE   156      -0.062  60.012 -11.426  1.00  0.00
ATOM    531  CD1 PHE   156      -1.412  59.712 -11.364  1.00  0.00
ATOM    532  CD2 PHE   156       0.526  60.156 -12.671  1.00  0.00
ATOM    533  CE1 PHE   156      -2.156  59.558 -12.518  1.00  0.00
ATOM    534  CE2 PHE   156      -0.218  60.005 -13.827  1.00  0.00
ATOM    535  CZ  PHE   156      -1.554  59.706 -13.753  1.00  0.00
ATOM    536  O   PHE   156       1.777  59.244  -7.314  1.00  0.00
ATOM    537  C   PHE   156       2.272  59.204  -8.447  1.00  0.00
ATOM    538  N   SER   157       3.549  59.459  -8.657  1.00  0.00
ATOM    539  CA  SER   157       4.454  59.782  -7.573  1.00  0.00
ATOM    540  CB  SER   157       5.865  59.285  -7.887  1.00  0.00
ATOM    541  OG  SER   157       5.894  57.875  -8.018  1.00  0.00
ATOM    542  O   SER   157       4.198  61.927  -8.560  1.00  0.00
ATOM    543  C   SER   157       4.362  61.290  -7.529  1.00  0.00
ATOM    547  N   LEU   174       6.065  65.043  -6.389  1.00  0.00
ATOM    548  CA  LEU   174       7.243  65.690  -5.832  1.00  0.00
ATOM    549  CB  LEU   174       8.232  66.050  -6.943  1.00  0.00
ATOM    550  CG  LEU   174       8.848  64.878  -7.708  1.00  0.00
ATOM    551  CD1 LEU   174       9.684  65.380  -8.875  1.00  0.00
ATOM    552  CD2 LEU   174       9.745  64.054  -6.799  1.00  0.00
ATOM    553  O   LEU   174       6.805  68.022  -5.669  1.00  0.00
ATOM    554  C   LEU   174       7.074  66.987  -5.056  1.00  0.00
ATOM    555  N   SER   175       7.228  66.969  -3.731  1.00  0.00
ATOM    556  CA  SER   175       7.167  68.254  -3.047  1.00  0.00
ATOM    557  CB  SER   175       7.208  68.059  -1.530  1.00  0.00
ATOM    558  OG  SER   175       7.105  69.299  -0.852  1.00  0.00
ATOM    559  O   SER   175       8.393  69.754  -4.475  1.00  0.00
ATOM    560  C   SER   175       8.439  68.818  -3.674  1.00  0.00
ATOM    561  N   ASP   176       9.572  68.203  -3.294  1.00  0.00
ATOM    562  CA  ASP   176      10.917  68.564  -3.779  1.00  0.00
ATOM    563  CB  ASP   176      11.983  68.145  -2.766  1.00  0.00
ATOM    564  CG  ASP   176      11.976  69.009  -1.520  1.00  0.00
ATOM    565  OD1 ASP   176      11.327  70.077  -1.543  1.00  0.00
ATOM    566  OD2 ASP   176      12.619  68.622  -0.524  1.00  0.00
ATOM    567  O   ASP   176      10.582  66.881  -5.467  1.00  0.00
ATOM    568  C   ASP   176      11.218  67.871  -5.104  1.00  0.00
ATOM    569  N   SER   177      12.206  68.387  -5.817  1.00  0.00
ATOM    570  CA  SER   177      12.562  67.796  -7.093  1.00  0.00
ATOM    571  CB  SER   177      13.581  68.672  -7.824  1.00  0.00
ATOM    572  OG  SER   177      13.044  69.954  -8.106  1.00  0.00
ATOM    573  O   SER   177      13.109  65.841  -5.793  1.00  0.00
ATOM    574  C   SER   177      13.175  66.411  -6.889  1.00  0.00
ATOM    575  N   PHE   178      13.751  65.866  -7.958  1.00  0.00
ATOM    576  CA  PHE   178      14.407  64.565  -7.916  1.00  0.00
ATOM    577  CB  PHE   178      14.231  63.833  -9.247  1.00  0.00
ATOM    578  CG  PHE   178      14.844  62.460  -9.270  1.00  0.00
ATOM    579  CD1 PHE   178      14.208  61.395  -8.659  1.00  0.00
ATOM    580  CD2 PHE   178      16.054  62.237  -9.902  1.00  0.00
ATOM    581  CE1 PHE   178      14.771  60.132  -8.680  1.00  0.00
ATOM    582  CE2 PHE   178      16.617  60.976  -9.922  1.00  0.00
ATOM    583  CZ  PHE   178      15.980  59.926  -9.315  1.00  0.00
ATOM    584  O   PHE   178      16.358  64.634  -6.528  1.00  0.00
ATOM    585  C   PHE   178      15.884  64.856  -7.646  1.00  0.00
ATOM    586  N   ASP   179      16.581  65.394  -8.659  1.00  0.00
ATOM    587  CA  ASP   179      18.011  65.750  -8.583  1.00  0.00
ATOM    588  CB  ASP   179      18.417  66.600  -9.790  1.00  0.00
ATOM    589  CG  ASP   179      18.478  65.794 -11.075  1.00  0.00
ATOM    590  OD1 ASP   179      18.430  64.550 -10.997  1.00  0.00
ATOM    591  OD2 ASP   179      18.576  66.411 -12.157  1.00  0.00
ATOM    592  O   ASP   179      19.411  66.964  -7.057  1.00  0.00
ATOM    593  C   ASP   179      18.285  66.538  -7.327  1.00  0.00
ATOM    594  N   ASP   180      17.213  66.763  -6.592  1.00  0.00
ATOM    595  CA  ASP   180      17.256  67.473  -5.349  1.00  0.00
ATOM    596  CB  ASP   180      16.234  68.611  -5.345  1.00  0.00
ATOM    597  CG  ASP   180      16.617  69.741  -6.280  1.00  0.00
ATOM    598  OD1 ASP   180      17.786  69.778  -6.719  1.00  0.00
ATOM    599  OD2 ASP   180      15.749  70.589  -6.576  1.00  0.00
ATOM    600  O   ASP   180      17.730  66.233  -3.358  1.00  0.00
ATOM    601  C   ASP   180      16.929  66.456  -4.267  1.00  0.00
ATOM    602  N   ALA   181      15.777  65.797  -4.400  1.00  0.00
ATOM    603  CA  ALA   181      15.355  64.870  -3.366  1.00  0.00
ATOM    604  CB  ALA   181      14.149  64.069  -3.832  1.00  0.00
ATOM    605  O   ALA   181      16.226  63.193  -1.900  1.00  0.00
ATOM    606  C   ALA   181      16.382  63.845  -2.936  1.00  0.00
ATOM    607  N   LEU   182      17.448  63.703  -3.707  1.00  0.00
ATOM    608  CA  LEU   182      18.487  62.768  -3.310  1.00  0.00
ATOM    609  CB  LEU   182      19.278  62.296  -4.532  1.00  0.00
ATOM    610  CG  LEU   182      18.510  61.450  -5.551  1.00  0.00
ATOM    611  CD1 LEU   182      19.367  61.178  -6.778  1.00  0.00
ATOM    612  CD2 LEU   182      18.111  60.112  -4.944  1.00  0.00
ATOM    613  O   LEU   182      19.655  63.118  -1.230  1.00  0.00
ATOM    614  C   LEU   182      19.369  63.552  -2.352  1.00  0.00
ATOM    615  N   ALA   183      19.761  64.737  -2.800  1.00  0.00
ATOM    616  CA  ALA   183      20.621  65.585  -2.012  1.00  0.00
ATOM    617  CB  ALA   183      20.623  67.000  -2.568  1.00  0.00
ATOM    618  O   ALA   183      20.908  66.303   0.244  1.00  0.00
ATOM    619  C   ALA   183      20.205  65.684  -0.548  1.00  0.00
ATOM    620  N   GLU   184      19.068  65.084  -0.188  1.00  0.00
ATOM    621  CA  GLU   184      18.588  65.091   1.200  1.00  0.00
ATOM    622  CB  GLU   184      17.097  65.429   1.251  1.00  0.00
ATOM    623  CG  GLU   184      16.764  66.836   0.781  1.00  0.00
ATOM    624  CD  GLU   184      15.273  67.108   0.776  1.00  0.00
ATOM    625  OE1 GLU   184      14.499  66.194   1.129  1.00  0.00
ATOM    626  OE2 GLU   184      14.877  68.240   0.420  1.00  0.00
ATOM    627  O   GLU   184      19.226  63.465   2.884  1.00  0.00
ATOM    628  C   GLU   184      18.850  63.678   1.724  1.00  0.00
ATOM    629  N   ALA   185      18.630  62.705   0.856  1.00  0.00
ATOM    630  CA  ALA   185      18.914  61.350   1.224  1.00  0.00
ATOM    631  CB  ALA   185      18.560  60.406   0.085  1.00  0.00
ATOM    632  O   ALA   185      20.835  61.359   2.624  1.00  0.00
ATOM    633  C   ALA   185      20.405  61.427   1.490  1.00  0.00
ATOM    634  N   MET   186      21.177  61.608   0.424  1.00  0.00
ATOM    635  CA  MET   186      22.633  61.729   0.498  1.00  0.00
ATOM    636  CB  MET   186      23.173  62.466  -0.728  1.00  0.00
ATOM    637  CG  MET   186      24.691  62.503  -0.811  1.00  0.00
ATOM    638  SD  MET   186      25.415  60.865  -1.014  1.00  0.00
ATOM    639  CE  MET   186      25.051  60.544  -2.739  1.00  0.00
ATOM    640  O   MET   186      23.980  62.048   2.466  1.00  0.00
ATOM    641  C   MET   186      23.097  62.501   1.737  1.00  0.00
ATOM    642  N   LYS   187      22.504  63.672   1.951  1.00  0.00
ATOM    643  CA  LYS   187      22.822  64.526   3.090  1.00  0.00
ATOM    644  CB  LYS   187      22.172  65.902   2.925  1.00  0.00
ATOM    645  CG  LYS   187      22.617  66.926   3.955  1.00  0.00
ATOM    646  CD  LYS   187      22.002  68.288   3.684  1.00  0.00
ATOM    647  CE  LYS   187      22.490  69.325   4.681  1.00  0.00
ATOM    648  NZ  LYS   187      21.913  70.671   4.411  1.00  0.00
ATOM    649  O   LYS   187      22.265  64.455   5.411  1.00  0.00
ATOM    650  C   LYS   187      22.287  63.851   4.346  1.00  0.00
ATOM    651  N   LEU   188      21.828  62.605   4.211  1.00  0.00
ATOM    652  CA  LEU   188      21.357  61.830   5.362  1.00  0.00
ATOM    653  CB  LEU   188      20.443  60.691   4.903  1.00  0.00
ATOM    654  CG  LEU   188      19.867  59.799   6.003  1.00  0.00
ATOM    655  CD1 LEU   188      18.990  60.606   6.948  1.00  0.00
ATOM    656  CD2 LEU   188      19.022  58.684   5.405  1.00  0.00
ATOM    657  O   LEU   188      23.107  61.648   7.010  1.00  0.00
ATOM    658  C   LEU   188      22.688  61.383   5.881  1.00  0.00
ATOM    659  N   ALA   189      23.342  60.687   4.976  1.00  0.00
ATOM    660  CA  ALA   189      24.637  60.101   5.165  1.00  0.00
ATOM    661  CB  ALA   189      25.042  59.298   3.938  1.00  0.00
ATOM    662  O   ALA   189      26.394  61.175   6.389  1.00  0.00
ATOM    663  C   ALA   189      25.672  61.200   5.400  1.00  0.00
ATOM    664  N   LYS   190      25.722  62.183   4.512  1.00  0.00
ATOM    665  CA  LYS   190      26.650  63.288   4.688  1.00  0.00
ATOM    666  CB  LYS   190      26.272  64.457   3.778  1.00  0.00
ATOM    667  CG  LYS   190      27.231  65.634   3.847  1.00  0.00
ATOM    668  CD  LYS   190      26.835  66.729   2.869  1.00  0.00
ATOM    669  CE  LYS   190      27.787  67.911   2.944  1.00  0.00
ATOM    670  NZ  LYS   190      27.411  68.988   1.988  1.00  0.00
ATOM    671  O   LYS   190      27.532  63.528   6.919  1.00  0.00
ATOM    672  C   LYS   190      26.580  63.730   6.165  1.00  0.00
TER
END
