
#######################################################
#                                                     #
#                        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_2_2
# Molecule2: number of CA atoms  121 (  929),  selected   15 , name T0382.pdb
# PARAMETERS: T0382TS009_2_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          4.28     4.28
  LCS_AVERAGE:     12.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        34 - 39          1.49    15.24
  LONGEST_CONTINUOUS_SEGMENT:     6        41 - 46          1.94     6.22
  LCS_AVERAGE:      4.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        34 - 38          0.86    16.14
  LCS_AVERAGE:      3.31

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      5    6   15     3    4    5    5    6    6    7    7    7    7   11   11   14   14   15   15   15   15   15   15 
LCS_GDT     S      35     S      35      5    6   15     3    4    5    5    6    6    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     R      36     R      36      5    6   15     3    4    6    7    8    8    9   10   10   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     F      37     F      37      5    6   15     3    5    6    7    8    8    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     N      38     N      38      5    6   15     3    4    6    6    7    7    8   10   11   12   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     R      39     R      39      4    6   15     3    3    4    5    7    7    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     L      40     L      40      3    4   15     3    5    6    7    8    8    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     F      41     F      41      3    6   15     3    4    6    6    8    8    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     G      42     G      42      3    6   15     3    3    4    4    6    6    9    9   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     V      43     V      43      4    6   15     3    5    6    7    8    8    8   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     M      44     M      44      4    6   15     3    4    6    7    8    8    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     A      45     A      45      4    6   15     3    5    6    7    8    8    9   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     E      46     E      46      4    6   15     3    5    6    7    8    8    8   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     I      47     I      47      3    5   15     3    3    3    4    6    6    7   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_GDT     A      48     A      48      3    4   15     3    3    3    4    5    6    8   10   11   13   13   14   14   14   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   6.80  (   3.31    4.68   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      5      6      7      8      8      9     10     11     13     13     14     14     14     15     15     15     15     15     15 
GDT PERCENT_CA   2.48   4.13   4.96   5.79   6.61   6.61   7.44   8.26   9.09  10.74  10.74  11.57  11.57  11.57  12.40  12.40  12.40  12.40  12.40  12.40
GDT RMS_LOCAL    0.01   0.90   0.92   1.21   1.48   1.48   3.06   3.06   3.14   3.71   3.61   3.90   3.90   3.90   4.28   4.28   4.28   4.28   4.28   4.28
GDT RMS_ALL_CA   9.69   5.02   5.22   5.15   5.15   5.15   5.43   4.57   4.83   4.32   4.63   4.44   4.44   4.44   4.28   4.28   4.28   4.28   4.28   4.28

#      Molecule1      Molecule2       DISTANCE
LGA    I      34      I      34         10.564
LGA    S      35      S      35          6.432
LGA    R      36      R      36          8.363
LGA    F      37      F      37          3.540
LGA    N      38      N      38          3.401
LGA    R      39      R      39          2.653
LGA    L      40      L      40          4.566
LGA    F      41      F      41          2.763
LGA    G      42      G      42          4.429
LGA    V      43      V      43          1.821
LGA    M      44      M      44          3.497
LGA    A      45      A      45          3.069
LGA    E      46      E      46          2.204
LGA    I      47      I      47          3.820
LGA    A      48      A      48          3.476

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  121    4.0     10    3.04     7.645     7.188     0.319

LGA_LOCAL      RMSD =  3.039  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.890  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  4.280  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.805233 * X  +   0.479344 * Y  +  -0.349039 * Z  + -46.116436
  Y_new =   0.400187 * X  +  -0.004960 * Y  +   0.916420 * Z  +  63.501453
  Z_new =   0.437550 * X  +  -0.877613 * Y  +  -0.195821 * Z  +  17.107393 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.790329    1.351263  [ DEG:  -102.5783     77.4217 ]
  Theta =  -0.452872   -2.688721  [ DEG:   -25.9476   -154.0524 ]
  Phi   =   0.461231   -2.680362  [ DEG:    26.4266   -153.5734 ]
 
# 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_2_2                                
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_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   10   3.04   7.188     4.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_2
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    256  N   ILE    34      -3.372  43.520   6.741  1.00  0.00             
ATOM    257  CA  ILE    34      -2.166  43.276   5.899  1.00  0.00             
ATOM    258  C   ILE    34      -1.312  42.150   6.472  1.00  0.00             
ATOM    259  O   ILE    34      -0.286  42.397   7.107  1.00  0.00             
ATOM    260  CB  ILE    34      -2.550  42.927   4.449  1.00  0.00             
ATOM    261  CG2 ILE    34      -2.868  44.190   3.665  1.00  0.00             
ATOM    262  CG1 ILE    34      -3.739  41.964   4.430  1.00  0.00             
ATOM    263  CD1 ILE    34      -4.658  42.153   3.242  1.00  0.00             
ATOM    264  N   SER    35      -1.742  40.913   6.247  1.00  0.00             
ATOM    265  CA  SER    35      -1.019  39.747   6.741  1.00  0.00             
ATOM    266  C   SER    35      -1.153  39.615   8.254  1.00  0.00             
ATOM    267  O   SER    35      -1.404  38.526   8.772  1.00  0.00             
ATOM    268  CB  SER    35      -1.521  38.475   6.054  1.00  0.00             
ATOM    269  OG  SER    35      -0.758  38.185   4.896  1.00  0.00             
ATOM    270  N   ARG    36      -0.985  40.730   8.957  1.00  0.00             
ATOM    271  CA  ARG    36      -1.087  40.740  10.412  1.00  0.00             
ATOM    272  C   ARG    36      -2.333  39.998  10.882  1.00  0.00             
ATOM    273  O   ARG    36      -2.286  39.232  11.845  1.00  0.00             
ATOM    274  CB  ARG    36       0.163  40.122  11.042  1.00  0.00             
ATOM    275  CG  ARG    36       0.867  41.024  12.040  1.00  0.00             
ATOM    276  CD  ARG    36       1.782  40.228  12.956  1.00  0.00             
ATOM    277  NE  ARG    36       2.687  41.090  13.709  1.00  0.00             
ATOM    278  CZ  ARG    36       2.543  41.380  14.999  1.00  0.00             
ATOM    279  NH1 ARG    36       1.526  40.873  15.682  1.00  0.00             
ATOM    280  NH2 ARG    36       3.416  42.174  15.602  1.00  0.00             
ATOM    281  N   PHE    37      -3.448  40.231  10.198  1.00  0.00             
ATOM    282  CA  PHE    37      -4.709  39.586  10.544  1.00  0.00             
ATOM    283  C   PHE    37      -4.676  38.097  10.213  1.00  0.00             
ATOM    284  O   PHE    37      -3.973  37.323  10.862  1.00  0.00             
ATOM    285  CB  PHE    37      -5.024  39.787  12.028  1.00  0.00             
ATOM    286  CG  PHE    37      -6.465  40.109  12.303  1.00  0.00             
ATOM    287  CD1 PHE    37      -7.318  40.471  11.274  1.00  0.00             
ATOM    288  CD2 PHE    37      -6.970  40.049  13.590  1.00  0.00             
ATOM    289  CE1 PHE    37      -8.644  40.767  11.528  1.00  0.00             
ATOM    290  CE2 PHE    37      -8.295  40.345  13.844  1.00  0.00             
ATOM    291  CZ  PHE    37      -9.132  40.703  12.819  1.00  0.00             
ATOM    292  N   ASN    38      -5.441  37.705   9.199  1.00  0.00             
ATOM    293  CA  ASN    38      -5.500  36.310   8.780  1.00  0.00             
ATOM    294  C   ASN    38      -4.486  36.021   7.679  1.00  0.00             
ATOM    295  O   ASN    38      -4.850  35.596   6.582  1.00  0.00             
ATOM    296  CB  ASN    38      -5.261  35.381   9.973  1.00  0.00             
ATOM    297  CG  ASN    38      -6.551  34.864  10.576  1.00  0.00             
ATOM    298  OD1 ASN    38      -6.538  33.968  11.421  1.00  0.00             
ATOM    299  ND2 ASN    38      -7.673  35.426  10.143  1.00  0.00             
ATOM    300  N   ARG    39      -3.213  36.255   7.978  1.00  0.00             
ATOM    301  CA  ARG    39      -2.143  36.021   7.014  1.00  0.00             
ATOM    302  C   ARG    39      -2.449  36.691   5.679  1.00  0.00             
ATOM    303  O   ARG    39      -2.571  36.024   4.652  1.00  0.00             
ATOM    304  CB  ARG    39      -0.808  36.525   7.562  1.00  0.00             
ATOM    305  CG  ARG    39       0.089  35.430   8.118  1.00  0.00             
ATOM    306  CD  ARG    39       1.205  36.010   8.972  1.00  0.00             
ATOM    307  NE  ARG    39       2.084  34.971   9.501  1.00  0.00             
ATOM    308  CZ  ARG    39       3.091  34.430   8.823  1.00  0.00             
ATOM    309  NH1 ARG    39       3.348  34.829   7.584  1.00  0.00             
ATOM    310  NH2 ARG    39       3.839  33.490   9.385  1.00  0.00             
ATOM    311  N   LEU    40      -2.570  38.015   5.700  1.00  0.00             
ATOM    312  CA  LEU    40      -2.862  38.777   4.492  1.00  0.00             
ATOM    313  C   LEU    40      -4.221  38.399   3.914  1.00  0.00             
ATOM    314  O   LEU    40      -4.431  38.461   2.703  1.00  0.00             
ATOM    315  CB  LEU    40      -2.811  40.279   4.781  1.00  0.00             
ATOM    316  CG  LEU    40      -1.474  40.975   4.521  1.00  0.00             
ATOM    317  CD1 LEU    40      -1.675  42.471   4.332  1.00  0.00             
ATOM    318  CD2 LEU    40      -0.778  40.366   3.313  1.00  0.00             
ATOM    319  N   PHE    41      -5.141  38.008   4.791  1.00  0.00             
ATOM    320  CA  PHE    41      -6.482  37.620   4.370  1.00  0.00             
ATOM    321  C   PHE    41      -6.507  37.226   2.896  1.00  0.00             
ATOM    322  O   PHE    41      -7.508  37.422   2.208  1.00  0.00             
ATOM    323  CB  PHE    41      -7.001  36.466   5.231  1.00  0.00             
ATOM    324  CG  PHE    41      -8.240  36.801   6.012  1.00  0.00             
ATOM    325  CD1 PHE    41      -9.081  37.820   5.599  1.00  0.00             
ATOM    326  CD2 PHE    41      -8.565  36.096   7.158  1.00  0.00             
ATOM    327  CE1 PHE    41     -10.220  38.129   6.317  1.00  0.00             
ATOM    328  CE2 PHE    41      -9.705  36.405   7.876  1.00  0.00             
ATOM    329  CZ  PHE    41     -10.531  37.417   7.460  1.00  0.00             
ATOM    330  N   GLY    42      -5.398  36.670   2.420  1.00  0.00             
ATOM    331  CA  GLY    42      -5.316  36.260   1.031  1.00  0.00             
ATOM    332  C   GLY    42      -5.540  37.411   0.071  1.00  0.00             
ATOM    333  O   GLY    42      -6.328  37.303  -0.869  1.00  0.00             
ATOM    334  N   VAL    43      -4.847  38.520   0.306  1.00  0.00             
ATOM    335  CA  VAL    43      -4.977  39.724  -0.563  1.00  0.00             
ATOM    336  C   VAL    43      -6.329  39.751  -1.270  1.00  0.00             
ATOM    337  O   VAL    43      -6.999  40.783  -1.309  1.00  0.00             
ATOM    338  CB  VAL    43      -4.805  41.025   0.243  1.00  0.00             
ATOM    339  CG1 VAL    43      -3.492  41.704  -0.115  1.00  0.00             
ATOM    340  CG2 VAL    43      -4.875  40.739   1.736  1.00  0.00             
ATOM    341  N   MET    44      -6.721  38.611  -1.828  1.00  0.00             
ATOM    342  CA  MET    44      -7.993  38.502  -2.533  1.00  0.00             
ATOM    343  C   MET    44      -8.773  39.811  -2.472  1.00  0.00             
ATOM    344  O   MET    44      -9.538  40.133  -3.380  1.00  0.00             
ATOM    345  CB  MET    44      -7.764  38.094  -3.990  1.00  0.00             
ATOM    346  CG  MET    44      -8.839  37.183  -4.557  1.00  0.00             
ATOM    347  SD  MET    44      -8.869  37.178  -6.360  1.00  0.00             
ATOM    348  CE  MET    44     -10.391  36.285  -6.671  1.00  0.00             
ATOM    349  N   ALA    45      -8.572  40.563  -1.394  1.00  0.00             
ATOM    350  CA  ALA    45      -9.255  41.838  -1.211  1.00  0.00             
ATOM    351  C   ALA    45      -8.978  42.784  -2.374  1.00  0.00             
ATOM    352  O   ALA    45      -9.742  43.716  -2.625  1.00  0.00             
ATOM    353  CB  ALA    45     -10.754  41.619  -1.058  1.00  0.00             
ATOM    354  N   GLU    46      -7.880  42.538  -3.081  1.00  0.00             
ATOM    355  CA  GLU    46      -7.499  43.367  -4.217  1.00  0.00             
ATOM    356  C   GLU    46      -8.593  44.372  -4.559  1.00  0.00             
ATOM    357  O   GLU    46      -8.322  45.433  -5.123  1.00  0.00             
ATOM    358  CB  GLU    46      -6.184  44.097  -3.933  1.00  0.00             
ATOM    359  CG  GLU    46      -5.265  44.214  -5.138  1.00  0.00             
ATOM    360  CD  GLU    46      -3.969  44.930  -4.814  1.00  0.00             
ATOM    361  OE1 GLU    46      -3.030  44.267  -4.326  1.00  0.00             
ATOM    362  OE2 GLU    46      -3.891  46.154  -5.048  1.00  0.00             
ATOM    363  N   ILE    47      -9.831  44.033  -4.212  1.00  0.00             
ATOM    364  CA  ILE    47     -10.994  44.923  -4.485  1.00  0.00             
ATOM    365  C   ILE    47     -10.761  45.765  -5.736  1.00  0.00             
ATOM    366  O   ILE    47     -11.609  45.818  -6.627  1.00  0.00             
ATOM    367  CB  ILE    47     -12.295  44.118  -4.656  1.00  0.00             
ATOM    368  CG2 ILE    47     -13.066  44.068  -3.346  1.00  0.00             
ATOM    369  CG1 ILE    47     -11.986  42.705  -5.155  1.00  0.00             
ATOM    370  CD1 ILE    47     -12.789  41.624  -4.466  1.00  0.00             
ATOM    371  N   ALA    48      -9.607  46.421  -5.796  1.00  0.00             
ATOM    372  CA  ALA    48      -9.262  47.261  -6.937  1.00  0.00             
ATOM    373  C   ALA    48      -9.185  46.442  -8.221  1.00  0.00             
ATOM    374  O   ALA    48     -10.044  45.599  -8.482  1.00  0.00             
ATOM    375  CB  ALA    48     -10.271  48.387  -7.092  1.00  0.00             
TER
END
