
#######################################################
#                                                     #
#                        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   16 (  145),  selected   16 , name T0386TS009_1_2
# Molecule2: number of CA atoms  291 ( 2337),  selected   16 , name T0386.pdb
# PARAMETERS: T0386TS009_1_2.T0386.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:    16        73 - 88          4.15     4.15
  LCS_AVERAGE:      5.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        73 - 80          1.94     6.32
  LCS_AVERAGE:      2.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        74 - 77          0.93     8.44
  LONGEST_CONTINUOUS_SEGMENT:     4        76 - 79          0.64    11.26
  LCS_AVERAGE:      1.16

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:  291
LCS_GDT     Q      73     Q      73      3    8   16     3    3    5    8    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     Q      74     Q      74      4    8   16     3    4    5    8    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     L      75     L      75      4    8   16     3    4    5    8    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     F      76     F      76      4    8   16     3    4    5    7    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     K      77     K      77      4    8   16     3    4    5    8    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     N      78     N      78      4    8   16     3    4    4    7    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     T      79     T      79      4    8   16     3    4    5    8    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     F      80     F      80      3    8   16     3    3    5    8    8    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     E      81     E      81      3    7   16     3    3    5    7    7    9   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     W      82     W      82      3    7   16     3    3    5    7    7    8   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     A      83     A      83      3    4   16     3    3    3    3    4    7   11   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     G      84     G      84      3    4   16     3    3    4    4    7    8    9   10   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     Y      85     Y      85      3    4   16     3    3    4    8    8    8    9   11   13   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     L      86     L      86      3    4   16     3    3    4    8    8    8    9   11   12   14   14   14   15   16   16   16   16   16   16   16 
LCS_GDT     R      87     R      87      3    4   16     3    3    3    4    5    6    8   10   11   12   13   14   15   16   16   16   16   16   16   16 
LCS_GDT     H      88     H      88      3    4   16     3    3    3    3    4    6    6    8    9   10   10   12   15   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   2.95  (   1.16    2.19    5.50 )

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      3      4      5      8      8      9     11     11     13     14     14     14     15     16     16     16     16     16     16     16 
GDT PERCENT_CA   1.03   1.37   1.72   2.75   2.75   3.09   3.78   3.78   4.47   4.81   4.81   4.81   5.15   5.50   5.50   5.50   5.50   5.50   5.50   5.50
GDT RMS_LOCAL    0.02   0.64   1.05   1.52   1.52   2.08   2.44   2.44   3.04   3.24   3.24   3.24   3.72   4.15   4.15   4.15   4.15   4.15   4.15   4.15
GDT RMS_ALL_CA   9.78  11.26   7.07   4.26   4.26   6.58   7.09   7.09   5.68   4.90   4.90   4.90   4.29   4.15   4.15   4.15   4.15   4.15   4.15   4.15

#      Molecule1      Molecule2       DISTANCE
LGA    Q      73      Q      73          2.676
LGA    Q      74      Q      74          1.633
LGA    L      75      L      75          2.867
LGA    F      76      F      76          2.534
LGA    K      77      K      77          2.429
LGA    N      78      N      78          1.827
LGA    T      79      T      79          0.916
LGA    F      80      F      80          0.856
LGA    E      81      E      81          2.362
LGA    W      82      W      82          3.668
LGA    A      83      A      83          3.361
LGA    G      84      G      84          5.834
LGA    Y      85      Y      85          7.022
LGA    L      86      L      86         10.028
LGA    R      87      R      87         15.407
LGA    H      88      H      88         17.790

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  291    4.0     11    2.44     3.351     3.212     0.433

LGA_LOCAL      RMSD =  2.442  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.086  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  4.155  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.806666 * X  +   0.181836 * Y  +   0.562339 * Z  +  -2.349375
  Y_new =   0.580478 * X  +   0.064957 * Y  +   0.811681 * Z  +   9.761351
  Z_new =   0.111065 * X  +   0.981181 * Y  +  -0.157951 * Z  +  38.029816 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.730407   -1.411186  [ DEG:    99.1450    -80.8550 ]
  Theta =  -0.111295   -3.030298  [ DEG:    -6.3767   -173.6233 ]
  Phi   =   2.517833   -0.623760  [ DEG:   144.2612    -35.7388 ]
 
# 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: T0386TS009_1_2                                
REMARK     2: T0386.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_1_2.T0386.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  291   4.0   11   2.44   3.212     4.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_1_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                       
ATOM    586  N   GLN    73       7.108  69.338  43.233  1.00  0.00             
ATOM    587  CA  GLN    73       7.883  68.331  43.948  1.00  0.00             
ATOM    588  C   GLN    73       7.807  68.545  45.456  1.00  0.00             
ATOM    589  O   GLN    73       8.618  68.009  46.211  1.00  0.00             
ATOM    590  CB  GLN    73       7.394  66.926  43.591  1.00  0.00             
ATOM    591  CG  GLN    73       8.479  65.862  43.633  1.00  0.00             
ATOM    592  CD  GLN    73       7.934  64.465  43.411  1.00  0.00             
ATOM    593  OE1 GLN    73       8.674  63.549  43.054  1.00  0.00             
ATOM    594  NE2 GLN    73       6.634  64.298  43.623  1.00  0.00             
ATOM    595  N   GLN    74       6.826  69.332  45.889  1.00  0.00             
ATOM    596  CA  GLN    74       6.642  69.619  47.306  1.00  0.00             
ATOM    597  C   GLN    74       7.956  69.492  48.069  1.00  0.00             
ATOM    598  O   GLN    74       8.277  70.328  48.915  1.00  0.00             
ATOM    599  CB  GLN    74       6.056  71.018  47.499  1.00  0.00             
ATOM    600  CG  GLN    74       6.724  72.093  46.656  1.00  0.00             
ATOM    601  CD  GLN    74       5.766  72.747  45.680  1.00  0.00             
ATOM    602  OE1 GLN    74       5.584  73.964  45.696  1.00  0.00             
ATOM    603  NE2 GLN    74       5.151  71.939  44.825  1.00  0.00             
ATOM    604  N   LEU    75       8.713  68.443  47.765  1.00  0.00             
ATOM    605  CA  LEU    75       9.994  68.206  48.422  1.00  0.00             
ATOM    606  C   LEU    75      10.821  69.485  48.494  1.00  0.00             
ATOM    607  O   LEU    75      11.788  69.652  47.751  1.00  0.00             
ATOM    608  CB  LEU    75       9.779  67.636  49.825  1.00  0.00             
ATOM    609  CG  LEU    75      10.937  66.828  50.414  1.00  0.00             
ATOM    610  CD1 LEU    75      11.080  67.101  51.903  1.00  0.00             
ATOM    611  CD2 LEU    75      12.234  67.134  49.681  1.00  0.00             
ATOM    612  N   PHE    76      10.436  70.382  49.395  1.00  0.00             
ATOM    613  CA  PHE    76      11.141  71.647  49.567  1.00  0.00             
ATOM    614  C   PHE    76      10.556  72.730  48.668  1.00  0.00             
ATOM    615  O   PHE    76      11.009  73.876  48.686  1.00  0.00             
ATOM    616  CB  PHE    76      11.092  72.094  51.029  1.00  0.00             
ATOM    617  CG  PHE    76      11.767  73.410  51.284  1.00  0.00             
ATOM    618  CD1 PHE    76      11.186  74.595  50.867  1.00  0.00             
ATOM    619  CD2 PHE    76      12.984  73.464  51.940  1.00  0.00             
ATOM    620  CE1 PHE    76      11.807  75.807  51.102  1.00  0.00             
ATOM    621  CE2 PHE    76      13.606  74.676  52.175  1.00  0.00             
ATOM    622  CZ  PHE    76      13.023  75.844  51.758  1.00  0.00             
ATOM    623  N   LYS    77       9.550  72.362  47.882  1.00  0.00             
ATOM    624  CA  LYS    77       8.902  73.302  46.975  1.00  0.00             
ATOM    625  C   LYS    77       9.919  73.971  46.056  1.00  0.00             
ATOM    626  O   LYS    77      10.593  74.922  46.450  1.00  0.00             
ATOM    627  CB  LYS    77       7.830  72.592  46.145  1.00  0.00             
ATOM    628  CG  LYS    77       6.608  73.447  45.849  1.00  0.00             
ATOM    629  CD  LYS    77       5.328  72.743  46.270  1.00  0.00             
ATOM    630  CE  LYS    77       4.176  73.092  45.342  1.00  0.00             
ATOM    631  NZ  LYS    77       3.151  72.012  45.298  1.00  0.00             
ATOM    632  N   ASN    78      10.022  73.469  44.830  1.00  0.00             
ATOM    633  CA  ASN    78      10.957  74.016  43.854  1.00  0.00             
ATOM    634  C   ASN    78      12.334  73.375  43.988  1.00  0.00             
ATOM    635  O   ASN    78      13.114  73.354  43.036  1.00  0.00             
ATOM    636  CB  ASN    78      10.422  73.822  42.433  1.00  0.00             
ATOM    637  CG  ASN    78      10.796  74.964  41.509  1.00  0.00             
ATOM    638  OD1 ASN    78      10.774  74.819  40.287  1.00  0.00             
ATOM    639  ND2 ASN    78      11.143  76.106  42.091  1.00  0.00             
ATOM    640  N   THR    79      12.625  72.855  45.176  1.00  0.00             
ATOM    641  CA  THR    79      13.937  72.199  45.442  1.00  0.00             
ATOM    642  C   THR    79      14.161  71.014  44.509  1.00  0.00             
ATOM    643  O   THR    79      13.627  69.927  44.731  1.00  0.00             
ATOM    644  CB  THR    79      15.106  73.190  45.287  1.00  0.00             
ATOM    645  OG1 THR    79      15.102  73.734  43.962  1.00  0.00             
ATOM    646  CG2 THR    79      14.981  74.322  46.295  1.00  0.00             
ATOM    647  N   PHE    80      14.954  71.231  43.465  1.00  0.00             
ATOM    648  CA  PHE    80      15.250  70.182  42.496  1.00  0.00             
ATOM    649  C   PHE    80      13.973  69.502  42.012  1.00  0.00             
ATOM    650  O   PHE    80      13.951  68.292  41.783  1.00  0.00             
ATOM    651  CB  PHE    80      16.024  70.754  41.307  1.00  0.00             
ATOM    652  CG  PHE    80      17.168  69.891  40.857  1.00  0.00             
ATOM    653  CD1 PHE    80      16.976  68.549  40.583  1.00  0.00             
ATOM    654  CD2 PHE    80      18.438  70.423  40.709  1.00  0.00             
ATOM    655  CE1 PHE    80      18.029  67.755  40.170  1.00  0.00             
ATOM    656  CE2 PHE    80      19.491  69.628  40.296  1.00  0.00             
ATOM    657  CZ  PHE    80      19.291  68.301  40.027  1.00  0.00             
ATOM    658  N   GLU    81      12.912  70.287  41.859  1.00  0.00             
ATOM    659  CA  GLU    81      11.631  69.763  41.403  1.00  0.00             
ATOM    660  C   GLU    81      11.402  68.344  41.913  1.00  0.00             
ATOM    661  O   GLU    81      10.949  67.473  41.171  1.00  0.00             
ATOM    662  CB  GLU    81      10.487  70.674  41.854  1.00  0.00             
ATOM    663  CG  GLU    81      10.496  72.048  41.205  1.00  0.00             
ATOM    664  CD  GLU    81       9.155  72.749  41.307  1.00  0.00             
ATOM    665  OE1 GLU    81       8.299  72.282  42.086  1.00  0.00             
ATOM    666  OE2 GLU    81       8.962  73.766  40.607  1.00  0.00             
ATOM    667  N   TRP    82      11.719  68.119  43.184  1.00  0.00             
ATOM    668  CA  TRP    82      11.550  66.806  43.794  1.00  0.00             
ATOM    669  C   TRP    82      10.471  66.000  43.079  1.00  0.00             
ATOM    670  O   TRP    82       9.282  66.291  43.201  1.00  0.00             
ATOM    671  CB  TRP    82      12.873  66.037  43.789  1.00  0.00             
ATOM    672  CG  TRP    82      13.427  65.786  45.158  1.00  0.00             
ATOM    673  CD1 TRP    82      14.544  65.068  45.470  1.00  0.00             
ATOM    674  CD2 TRP    82      12.888  66.255  46.401  1.00  0.00             
ATOM    675  NE1 TRP    82      14.737  65.058  46.831  1.00  0.00             
ATOM    676  CE2 TRP    82      13.732  65.781  47.425  1.00  0.00             
ATOM    677  CE3 TRP    82      11.776  67.027  46.746  1.00  0.00             
ATOM    678  CZ2 TRP    82      13.498  66.053  48.772  1.00  0.00             
ATOM    679  CZ3 TRP    82      11.545  67.296  48.081  1.00  0.00             
ATOM    680  CH2 TRP    82      12.402  66.811  49.082  1.00  0.00             
ATOM    681  N   ALA    83      10.896  64.986  42.332  1.00  0.00             
ATOM    682  CA  ALA    83       9.968  64.136  41.596  1.00  0.00             
ATOM    683  C   ALA    83       9.705  64.687  40.199  1.00  0.00             
ATOM    684  O   ALA    83       8.611  64.530  39.655  1.00  0.00             
ATOM    685  CB  ALA    83      10.506  62.716  41.507  1.00  0.00             
ATOM    686  N   GLY    84      10.714  65.334  39.624  1.00  0.00             
ATOM    687  CA  GLY    84      10.568  65.898  38.294  1.00  0.00             
ATOM    688  C   GLY    84       9.163  66.398  38.029  1.00  0.00             
ATOM    689  O   GLY    84       8.626  66.221  36.934  1.00  0.00             
ATOM    690  N   TYR    85       8.559  67.029  39.031  1.00  0.00             
ATOM    691  CA  TYR    85       7.207  67.558  38.901  1.00  0.00             
ATOM    692  C   TYR    85       6.406  66.775  37.866  1.00  0.00             
ATOM    693  O   TYR    85       5.379  67.245  37.376  1.00  0.00             
ATOM    694  CB  TYR    85       6.489  67.533  40.252  1.00  0.00             
ATOM    695  CG  TYR    85       6.849  66.345  41.114  1.00  0.00             
ATOM    696  CD1 TYR    85       6.836  66.441  42.500  1.00  0.00             
ATOM    697  CD2 TYR    85       7.200  65.129  40.540  1.00  0.00             
ATOM    698  CE1 TYR    85       7.163  65.360  43.296  1.00  0.00             
ATOM    699  CE2 TYR    85       7.530  64.037  41.321  1.00  0.00             
ATOM    700  CZ  TYR    85       7.509  64.162  42.709  1.00  0.00             
ATOM    701  OH  TYR    85       7.836  63.081  43.496  1.00  0.00             
ATOM    702  N   LEU    86       6.881  65.578  37.540  1.00  0.00             
ATOM    703  CA  LEU    86       6.210  64.727  36.564  1.00  0.00             
ATOM    704  C   LEU    86       5.446  65.559  35.540  1.00  0.00             
ATOM    705  O   LEU    86       4.266  65.857  35.724  1.00  0.00             
ATOM    706  CB  LEU    86       7.221  63.822  35.857  1.00  0.00             
ATOM    707  CG  LEU    86       6.730  63.115  34.592  1.00  0.00             
ATOM    708  CD1 LEU    86       7.430  61.776  34.418  1.00  0.00             
ATOM    709  CD2 LEU    86       6.937  63.995  33.370  1.00  0.00             
ATOM    710  N   ARG    87       6.126  65.931  34.461  1.00  0.00             
ATOM    711  CA  ARG    87       5.514  66.729  33.406  1.00  0.00             
ATOM    712  C   ARG    87       5.740  68.220  33.639  1.00  0.00             
ATOM    713  O   ARG    87       4.807  69.019  33.559  1.00  0.00             
ATOM    714  CB  ARG    87       6.064  66.322  32.037  1.00  0.00             
ATOM    715  CG  ARG    87       6.591  67.483  31.209  1.00  0.00             
ATOM    716  CD  ARG    87       6.073  68.813  31.732  1.00  0.00             
ATOM    717  NE  ARG    87       4.827  68.661  32.477  1.00  0.00             
ATOM    718  CZ  ARG    87       4.086  69.676  32.909  1.00  0.00             
ATOM    719  NH1 ARG    87       4.466  70.923  32.669  1.00  0.00             
ATOM    720  NH2 ARG    87       2.967  69.441  33.581  1.00  0.00             
ATOM    721  N   HIS    88       6.985  68.585  33.928  1.00  0.00             
ATOM    722  CA  HIS    88       7.336  69.979  34.175  1.00  0.00             
ATOM    723  C   HIS    88       7.459  70.262  35.668  1.00  0.00             
ATOM    724  O   HIS    88       7.524  71.418  36.087  1.00  0.00             
ATOM    725  CB  HIS    88       8.642  70.337  33.462  1.00  0.00             
ATOM    726  CG  HIS    88       8.635  71.693  32.832  1.00  0.00             
ATOM    727  ND1 HIS    88       7.494  72.458  32.722  1.00  0.00             
ATOM    728  CD2 HIS    88       9.631  72.425  32.278  1.00  0.00             
ATOM    729  CE1 HIS    88       7.787  73.600  32.127  1.00  0.00             
ATOM    730  NE2 HIS    88       9.076  73.606  31.847  1.00  0.00             
TER
END
