
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0382TS009_3_2
# Molecule2: number of CA atoms  121 (  929),  selected   15 , name T0382.pdb
# PARAMETERS: T0382TS009_3_2.T0382.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:    15        34 - 48          4.66     4.66
  LCS_AVERAGE:     12.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        41 - 46          1.87     7.71
  LCS_AVERAGE:      4.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        36 - 39          0.61     6.13
  LCS_AVERAGE:      2.70

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:  121
LCS_GDT     I      34     I      34      3    3   15     3    3    3    5    6    7    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     S      35     S      35      3    5   15     3    3    3    4    4    5    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     R      36     R      36      4    5   15     3    4    4    5    6    7    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     F      37     F      37      4    5   15     3    4    4    5    6    7    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     N      38     N      38      4    5   15     3    4    4    5    6    7    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     R      39     R      39      4    5   15     3    4    4    4    6    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     L      40     L      40      3    5   15     3    3    3    4    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     F      41     F      41      3    6   15     3    3    4    4    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     G      42     G      42      3    6   15     3    3    4    5    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     V      43     V      43      3    6   15     3    3    4    5    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     M      44     M      44      3    6   15     3    3    4    5    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     A      45     A      45      3    6   15     3    3    4    5    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     E      46     E      46      3    6   15     3    3    4    5    5    8    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     I      47     I      47      3    5   15     3    3    4    5    6    7    8    9   10   11   14   14   14   15   15   15   15   15   15   15 
LCS_GDT     A      48     A      48      3    5   15     3    3    3    5    5    7    7    9    9   10   12   13   14   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   6.48  (   2.70    4.35   12.40 )

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      4      5      6      8      8      9     10     11     14     14     14     15     15     15     15     15     15     15 
GDT PERCENT_CA   2.48   3.31   3.31   4.13   4.96   6.61   6.61   7.44   8.26   9.09  11.57  11.57  11.57  12.40  12.40  12.40  12.40  12.40  12.40  12.40
GDT RMS_LOCAL    0.02   0.61   0.61   1.20   1.58   2.34   2.34   2.78   3.16   3.75   4.24   4.24   4.24   4.66   4.66   4.66   4.66   4.66   4.66   4.66
GDT RMS_ALL_CA  18.75   6.13   6.13   9.54   5.41   6.36   6.36   5.53   5.42   4.76   4.86   4.86   4.86   4.66   4.66   4.66   4.66   4.66   4.66   4.66

#      Molecule1      Molecule2       DISTANCE
LGA    I      34      I      34          2.622
LGA    S      35      S      35          3.978
LGA    R      36      R      36          2.235
LGA    F      37      F      37          0.827
LGA    N      38      N      38          1.507
LGA    R      39      R      39          2.243
LGA    L      40      L      40          7.045
LGA    F      41      F      41          7.754
LGA    G      42      G      42          4.842
LGA    V      43      V      43          6.734
LGA    M      44      M      44         10.354
LGA    A      45      A      45          7.657
LGA    E      46      E      46          3.936
LGA    I      47      I      47          2.849
LGA    A      48      A      48          3.878

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  121    4.0      9    2.78     6.818     6.543     0.312

LGA_LOCAL      RMSD =  2.780  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.283  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  4.663  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.826927 * X  +   0.514162 * Y  +  -0.227662 * Z  +  18.874811
  Y_new =  -0.372989 * X  +  -0.804527 * Y  +  -0.462186 * Z  +  34.933823
  Z_new =  -0.420798 * X  +  -0.297278 * Y  +   0.857061 * Z  +  19.686117 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.333873    2.807720  [ DEG:   -19.1295    160.8705 ]
  Theta =   0.434325    2.707268  [ DEG:    24.8850    155.1150 ]
  Phi   =  -2.717862    0.423731  [ DEG:  -155.7220     24.2780 ]
 
# 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: T0382TS009_3_2                                
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_2.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  121   4.0    9   2.78   6.543     4.66
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                       
ATOM    256  N   ILE    34      -1.661  35.178  14.672  1.00  0.00             
ATOM    257  CA  ILE    34      -2.477  33.931  14.696  1.00  0.00             
ATOM    258  C   ILE    34      -3.718  34.068  13.821  1.00  0.00             
ATOM    259  O   ILE    34      -4.642  34.813  14.149  1.00  0.00             
ATOM    260  CB  ILE    34      -1.661  32.713  14.226  1.00  0.00             
ATOM    261  CG2 ILE    34      -0.788  32.189  15.355  1.00  0.00             
ATOM    262  CG1 ILE    34      -0.810  33.079  13.009  1.00  0.00             
ATOM    263  CD1 ILE    34       0.509  32.339  12.940  1.00  0.00             
ATOM    264  N   SER    35      -3.733  33.344  12.706  1.00  0.00             
ATOM    265  CA  SER    35      -4.860  33.384  11.782  1.00  0.00             
ATOM    266  C   SER    35      -4.460  34.010  10.451  1.00  0.00             
ATOM    267  O   SER    35      -5.312  34.467   9.688  1.00  0.00             
ATOM    268  CB  SER    35      -5.417  31.976  11.556  1.00  0.00             
ATOM    269  OG  SER    35      -6.460  31.687  12.471  1.00  0.00             
ATOM    270  N   ARG    36      -3.160  34.026  10.177  1.00  0.00             
ATOM    271  CA  ARG    36      -2.644  34.596   8.937  1.00  0.00             
ATOM    272  C   ARG    36      -3.668  35.521   8.288  1.00  0.00             
ATOM    273  O   ARG    36      -3.408  36.113   7.241  1.00  0.00             
ATOM    274  CB  ARG    36      -1.340  35.352   9.197  1.00  0.00             
ATOM    275  CG  ARG    36      -0.171  34.884   8.345  1.00  0.00             
ATOM    276  CD  ARG    36       0.928  35.932   8.292  1.00  0.00             
ATOM    277  NE  ARG    36       2.170  35.396   7.745  1.00  0.00             
ATOM    278  CZ  ARG    36       2.615  35.647   6.518  1.00  0.00             
ATOM    279  NH1 ARG    36       1.918  36.430   5.706  1.00  0.00             
ATOM    280  NH2 ARG    36       3.758  35.114   6.106  1.00  0.00             
ATOM    281  N   PHE    37      -4.832  35.642   8.918  1.00  0.00             
ATOM    282  CA  PHE    37      -5.896  36.496   8.404  1.00  0.00             
ATOM    283  C   PHE    37      -5.329  37.747   7.744  1.00  0.00             
ATOM    284  O   PHE    37      -5.568  38.001   6.563  1.00  0.00             
ATOM    285  CB  PHE    37      -6.767  35.725   7.408  1.00  0.00             
ATOM    286  CG  PHE    37      -8.239  35.982   7.566  1.00  0.00             
ATOM    287  CD1 PHE    37      -8.729  36.618   8.693  1.00  0.00             
ATOM    288  CD2 PHE    37      -9.133  35.589   6.586  1.00  0.00             
ATOM    289  CE1 PHE    37     -10.082  36.855   8.838  1.00  0.00             
ATOM    290  CE2 PHE    37     -10.487  35.825   6.729  1.00  0.00             
ATOM    291  CZ  PHE    37     -10.963  36.456   7.850  1.00  0.00             
ATOM    292  N   ASN    38      -4.577  38.527   8.514  1.00  0.00             
ATOM    293  CA  ASN    38      -3.974  39.754   8.007  1.00  0.00             
ATOM    294  C   ASN    38      -3.481  39.574   6.574  1.00  0.00             
ATOM    295  O   ASN    38      -2.516  40.214   6.156  1.00  0.00             
ATOM    296  CB  ASN    38      -4.972  40.911   8.078  1.00  0.00             
ATOM    297  CG  ASN    38      -4.779  41.772   9.312  1.00  0.00             
ATOM    298  OD1 ASN    38      -5.374  42.842   9.432  1.00  0.00             
ATOM    299  ND2 ASN    38      -3.944  41.306  10.232  1.00  0.00             
ATOM    300  N   ARG    39      -4.150  38.701   5.829  1.00  0.00             
ATOM    301  CA  ARG    39      -3.782  38.437   4.443  1.00  0.00             
ATOM    302  C   ARG    39      -2.366  38.918   4.147  1.00  0.00             
ATOM    303  O   ARG    39      -1.461  38.755   4.966  1.00  0.00             
ATOM    304  CB  ARG    39      -3.906  36.944   4.133  1.00  0.00             
ATOM    305  CG  ARG    39      -5.171  36.569   3.377  1.00  0.00             
ATOM    306  CD  ARG    39      -5.422  35.071   3.428  1.00  0.00             
ATOM    307  NE  ARG    39      -6.625  34.693   2.694  1.00  0.00             
ATOM    308  CZ  ARG    39      -6.669  34.501   1.379  1.00  0.00             
ATOM    309  NH1 ARG    39      -5.571  34.652   0.651  1.00  0.00             
ATOM    310  NH2 ARG    39      -7.809  34.158   0.796  1.00  0.00             
ATOM    311  N   LEU    40      -2.182  39.512   2.972  1.00  0.00             
ATOM    312  CA  LEU    40      -0.876  40.018   2.566  1.00  0.00             
ATOM    313  C   LEU    40      -1.013  41.267   1.703  1.00  0.00             
ATOM    314  O   LEU    40      -1.429  42.322   2.182  1.00  0.00             
ATOM    315  CB  LEU    40      -0.013  40.319   3.793  1.00  0.00             
ATOM    316  CG  LEU    40       0.917  39.197   4.259  1.00  0.00             
ATOM    317  CD1 LEU    40       2.055  39.756   5.101  1.00  0.00             
ATOM    318  CD2 LEU    40       1.457  38.417   3.070  1.00  0.00             
ATOM    319  N   PHE    41      -0.661  41.141   0.428  1.00  0.00             
ATOM    320  CA  PHE    41      -0.744  42.259  -0.505  1.00  0.00             
ATOM    321  C   PHE    41      -1.703  41.952  -1.650  1.00  0.00             
ATOM    322  O   PHE    41      -2.370  42.846  -2.171  1.00  0.00             
ATOM    323  CB  PHE    41      -1.183  43.532   0.222  1.00  0.00             
ATOM    324  CG  PHE    41      -0.170  44.639   0.170  1.00  0.00             
ATOM    325  CD1 PHE    41       0.781  44.680  -0.835  1.00  0.00             
ATOM    326  CD2 PHE    41      -0.167  45.641   1.126  1.00  0.00             
ATOM    327  CE1 PHE    41       1.712  45.700  -0.883  1.00  0.00             
ATOM    328  CE2 PHE    41       0.764  46.659   1.077  1.00  0.00             
ATOM    329  CZ  PHE    41       1.702  46.692   0.078  1.00  0.00             
ATOM    330  N   GLY    42      -1.769  40.681  -2.035  1.00  0.00             
ATOM    331  CA  GLY    42      -2.651  40.282  -3.117  1.00  0.00             
ATOM    332  C   GLY    42      -3.318  41.467  -3.788  1.00  0.00             
ATOM    333  O   GLY    42      -3.891  41.337  -4.870  1.00  0.00             
ATOM    334  N   VAL    43      -3.245  42.629  -3.147  1.00  0.00             
ATOM    335  CA  VAL    43      -3.859  43.870  -3.699  1.00  0.00             
ATOM    336  C   VAL    43      -3.624  43.979  -5.202  1.00  0.00             
ATOM    337  O   VAL    43      -4.524  44.348  -5.956  1.00  0.00             
ATOM    338  CB  VAL    43      -5.373  43.922  -3.422  1.00  0.00             
ATOM    339  CG1 VAL    43      -5.689  44.997  -2.393  1.00  0.00             
ATOM    340  CG2 VAL    43      -5.876  42.564  -2.956  1.00  0.00             
ATOM    341  N   MET    44      -2.408  43.655  -5.631  1.00  0.00             
ATOM    342  CA  MET    44      -2.052  43.716  -7.044  1.00  0.00             
ATOM    343  C   MET    44      -3.235  44.174  -7.891  1.00  0.00             
ATOM    344  O   MET    44      -3.122  45.120  -8.671  1.00  0.00             
ATOM    345  CB  MET    44      -0.860  44.651  -7.256  1.00  0.00             
ATOM    346  CG  MET    44       0.089  44.206  -8.358  1.00  0.00             
ATOM    347  SD  MET    44       1.125  45.550  -8.967  1.00  0.00             
ATOM    348  CE  MET    44       1.863  44.782 -10.408  1.00  0.00             
ATOM    349  N   ALA    45      -4.367  43.498  -7.732  1.00  0.00             
ATOM    350  CA  ALA    45      -5.572  43.834  -8.481  1.00  0.00             
ATOM    351  C   ALA    45      -6.791  43.897  -7.567  1.00  0.00             
ATOM    352  O   ALA    45      -7.056  44.922  -6.940  1.00  0.00             
ATOM    353  CB  ALA    45      -5.392  45.159  -9.208  1.00  0.00             
ATOM    354  N   GLU    46      -7.529  42.795  -7.498  1.00  0.00             
ATOM    355  CA  GLU    46      -8.721  42.723  -6.660  1.00  0.00             
ATOM    356  C   GLU    46      -8.355  42.474  -5.200  1.00  0.00             
ATOM    357  O   GLU    46      -8.912  43.098  -4.296  1.00  0.00             
ATOM    358  CB  GLU    46      -9.543  44.008  -6.785  1.00  0.00             
ATOM    359  CG  GLU    46     -11.046  43.786  -6.774  1.00  0.00             
ATOM    360  CD  GLU    46     -11.826  45.078  -6.914  1.00  0.00             
ATOM    361  OE1 GLU    46     -12.033  45.527  -8.062  1.00  0.00             
ATOM    362  OE2 GLU    46     -12.232  45.644  -5.877  1.00  0.00             
ATOM    363  N   ILE    47      -7.416  41.560  -4.978  1.00  0.00             
ATOM    364  CA  ILE    47      -6.965  41.221  -3.598  1.00  0.00             
ATOM    365  C   ILE    47      -8.032  41.574  -2.566  1.00  0.00             
ATOM    366  O   ILE    47      -8.807  40.717  -2.142  1.00  0.00             
ATOM    367  CB  ILE    47      -6.616  39.726  -3.470  1.00  0.00             
ATOM    368  CG2 ILE    47      -5.122  39.511  -3.655  1.00  0.00             
ATOM    369  CG1 ILE    47      -7.410  38.904  -4.487  1.00  0.00             
ATOM    370  CD1 ILE    47      -6.595  37.831  -5.175  1.00  0.00             
ATOM    371  N   ALA    48      -8.065  42.841  -2.167  1.00  0.00             
ATOM    372  CA  ALA    48      -9.036  43.309  -1.186  1.00  0.00             
ATOM    373  C   ALA    48     -10.315  43.791  -1.860  1.00  0.00             
ATOM    374  O   ALA    48     -10.273  44.605  -2.784  1.00  0.00             
ATOM    375  CB  ALA    48      -9.353  42.207  -0.186  1.00  0.00             
TER
END
