
#######################################################
#                                                     #
#                        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   18 (  139),  selected   18 , name T0386TS009_2_1-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   18 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_2_1-D1.T0386_D1.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        33 - 50          4.48     4.48
  LCS_AVERAGE:      8.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        34 - 39          1.84    14.10
  LCS_AVERAGE:      2.45

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        35 - 38          0.78    17.18
  LONGEST_CONTINUOUS_SEGMENT:     4        40 - 43          0.73    11.66
  LONGEST_CONTINUOUS_SEGMENT:     4        47 - 50          0.89    11.23
  LCS_AVERAGE:      1.78

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:  206
LCS_GDT     I      33     I      33      3    5   18     3    3    3    4    7    8    9   10   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     K      34     K      34      3    6   18     3    3    4    4    7    8    9   10   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     N      35     N      35      4    6   18     3    3    4    4    6    8    9   10   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     L      36     L      36      4    6   18     3    3    4    4    7    8    9   10   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     N      37     N      37      4    6   18     3    3    5    6    7    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     A      38     A      38      4    6   18     3    3    4    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     F      39     F      39      3    6   18     3    4    5    6    7    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     L      40     L      40      4    4   18     3    4    4    6    7    7    8   10   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     E      41     E      41      4    4   18     3    4    6    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     K      42     K      42      4    4   18     3    4    6    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     C      43     C      43      4    4   18     3    4    4    4    7    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     S      44     S      44      3    4   18     3    3    4    6    7    7    8    9   10   12   14   18   18   18   18   18   18   18   18   18 
LCS_GDT     H      45     H      45      3    5   18     3    3    6    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     D      46     D      46      3    5   18     1    3    6    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     T      47     T      47      4    5   18     1    3    6    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     A      48     A      48      4    5   18     3    4    6    7    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     K      49     K      49      4    5   18     3    4    4    6    8    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_GDT     A      50     A      50      4    5   18     3    3    4    6    7    8    9   12   12   13   16   18   18   18   18   18   18   18   18   18 
LCS_AVERAGE  LCS_A:   4.32  (   1.78    2.45    8.74 )

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      6      7      8      8      9     12     12     13     16     18     18     18     18     18     18     18     18     18 
GDT PERCENT_CA   1.46   1.94   2.91   3.40   3.88   3.88   4.37   5.83   5.83   6.31   7.77   8.74   8.74   8.74   8.74   8.74   8.74   8.74   8.74   8.74
GDT RMS_LOCAL    0.00   0.66   1.04   1.22   1.63   1.63   2.13   2.89   2.89   3.49   4.24   4.48   4.48   4.48   4.48   4.48   4.48   4.48   4.48   4.48
GDT RMS_ALL_CA  15.56   5.38   7.91   7.87   7.96   7.96   8.07   6.45   6.45   5.00   4.56   4.48   4.48   4.48   4.48   4.48   4.48   4.48   4.48   4.48

#      Molecule1      Molecule2       DISTANCE
LGA    I      33      I      33         12.797
LGA    K      34      K      34         14.164
LGA    N      35      N      35          9.931
LGA    L      36      L      36          9.313
LGA    N      37      N      37          3.399
LGA    A      38      A      38          2.733
LGA    F      39      F      39          3.144
LGA    L      40      L      40          6.876
LGA    E      41      E      41          1.116
LGA    K      42      K      42          3.652
LGA    C      43      C      43          3.966
LGA    S      44      S      44          7.109
LGA    H      45      H      45          2.481
LGA    D      46      D      46          3.802
LGA    T      47      T      47          2.037
LGA    A      48      A      48          1.321
LGA    K      49      K      49          1.554
LGA    A      50      A      50          3.505

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  206    4.0     12    2.89     4.976     4.516     0.401

LGA_LOCAL      RMSD =  2.893  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.446  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  4.484  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.910553 * X  +  -0.356395 * Y  +   0.209463 * Z  +   0.014515
  Y_new =  -0.210471 * X  +  -0.036432 * Y  +  -0.976921 * Z  + 146.987595
  Z_new =   0.355801 * X  +  -0.933625 * Y  +  -0.041838 * Z  +  62.682178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.615579    1.526014  [ DEG:   -92.5658     87.4342 ]
  Theta =  -0.363771   -2.777821  [ DEG:   -20.8426   -159.1574 ]
  Phi   =  -2.914436    0.227157  [ DEG:  -166.9849     13.0151 ]
 
# 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_2_1-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_2_1-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  206   4.0   12   2.89   4.516     4.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_2_1-D1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                                                                       
ATOM    259  N   ILE    33      17.714  82.163  55.290  1.00  0.00             
ATOM    260  CA  ILE    33      18.170  81.717  53.943  1.00  0.00             
ATOM    261  C   ILE    33      18.675  82.892  53.114  1.00  0.00             
ATOM    262  O   ILE    33      18.062  83.959  53.093  1.00  0.00             
ATOM    263  CB  ILE    33      19.283  80.657  54.045  1.00  0.00             
ATOM    264  CG2 ILE    33      18.688  79.257  54.027  1.00  0.00             
ATOM    265  CG1 ILE    33      20.112  80.876  55.313  1.00  0.00             
ATOM    266  CD1 ILE    33      20.320  79.620  56.130  1.00  0.00             
ATOM    267  N   LYS    34      19.798  82.689  52.432  1.00  0.00             
ATOM    268  CA  LYS    34      20.388  83.732  51.600  1.00  0.00             
ATOM    269  C   LYS    34      21.871  83.471  51.358  1.00  0.00             
ATOM    270  O   LYS    34      22.724  84.259  51.764  1.00  0.00             
ATOM    271  CB  LYS    34      19.647  83.835  50.265  1.00  0.00             
ATOM    272  CG  LYS    34      19.112  85.224  49.958  1.00  0.00             
ATOM    273  CD  LYS    34      18.523  85.292  48.559  1.00  0.00             
ATOM    274  CE  LYS    34      17.824  86.621  48.318  1.00  0.00             
ATOM    275  NZ  LYS    34      16.890  86.555  47.160  1.00  0.00             
ATOM    276  N   ASN    35      22.171  82.358  50.695  1.00  0.00             
ATOM    277  CA  ASN    35      23.550  81.992  50.398  1.00  0.00             
ATOM    278  C   ASN    35      24.308  81.621  51.669  1.00  0.00             
ATOM    279  O   ASN    35      24.635  82.486  52.481  1.00  0.00             
ATOM    280  CB  ASN    35      23.593  80.831  49.401  1.00  0.00             
ATOM    281  CG  ASN    35      24.374  81.168  48.147  1.00  0.00             
ATOM    282  OD1 ASN    35      24.869  80.279  47.454  1.00  0.00             
ATOM    283  ND2 ASN    35      24.487  82.458  47.852  1.00  0.00             
ATOM    284  N   LEU    36      24.584  80.332  51.832  1.00  0.00             
ATOM    285  CA  LEU    36      25.303  79.845  53.003  1.00  0.00             
ATOM    286  C   LEU    36      24.730  78.518  53.490  1.00  0.00             
ATOM    287  O   LEU    36      23.751  78.490  54.236  1.00  0.00             
ATOM    288  CB  LEU    36      26.794  79.692  52.691  1.00  0.00             
ATOM    289  CG  LEU    36      27.760  79.978  53.842  1.00  0.00             
ATOM    290  CD1 LEU    36      29.184  79.614  53.452  1.00  0.00             
ATOM    291  CD2 LEU    36      27.335  79.233  55.098  1.00  0.00             
ATOM    292  N   ASN    37      25.346  77.421  53.062  1.00  0.00             
ATOM    293  CA  ASN    37      24.899  76.090  53.454  1.00  0.00             
ATOM    294  C   ASN    37      24.077  75.437  52.347  1.00  0.00             
ATOM    295  O   ASN    37      22.873  75.228  52.496  1.00  0.00             
ATOM    296  CB  ASN    37      26.096  75.206  53.812  1.00  0.00             
ATOM    297  CG  ASN    37      26.117  74.819  55.277  1.00  0.00             
ATOM    298  OD1 ASN    37      27.003  74.094  55.725  1.00  0.00             
ATOM    299  ND2 ASN    37      25.136  75.306  56.030  1.00  0.00             
ATOM    300  N   ALA    38      24.736  75.116  51.238  1.00  0.00             
ATOM    301  CA  ALA    38      24.069  74.486  50.106  1.00  0.00             
ATOM    302  C   ALA    38      22.889  75.324  49.625  1.00  0.00             
ATOM    303  O   ALA    38      21.791  74.807  49.418  1.00  0.00             
ATOM    304  CB  ALA    38      25.052  74.266  48.967  1.00  0.00             
ATOM    305  N   PHE    39      23.122  76.621  49.450  1.00  0.00             
ATOM    306  CA  PHE    39      22.079  77.532  48.994  1.00  0.00             
ATOM    307  C   PHE    39      21.187  77.972  50.151  1.00  0.00             
ATOM    308  O   PHE    39      20.029  77.566  50.243  1.00  0.00             
ATOM    309  CB  PHE    39      22.697  78.755  48.312  1.00  0.00             
ATOM    310  CG  PHE    39      22.207  78.978  46.910  1.00  0.00             
ATOM    311  CD1 PHE    39      21.348  78.075  46.309  1.00  0.00             
ATOM    312  CD2 PHE    39      22.604  80.093  46.192  1.00  0.00             
ATOM    313  CE1 PHE    39      20.897  78.281  45.020  1.00  0.00             
ATOM    314  CE2 PHE    39      22.153  80.299  44.903  1.00  0.00             
ATOM    315  CZ  PHE    39      21.303  79.399  44.315  1.00  0.00             
ATOM    316  N   LEU    40      21.735  78.804  51.031  1.00  0.00             
ATOM    317  CA  LEU    40      20.990  79.300  52.182  1.00  0.00             
ATOM    318  C   LEU    40      20.308  78.161  52.930  1.00  0.00             
ATOM    319  O   LEU    40      19.082  78.120  53.034  1.00  0.00             
ATOM    320  CB  LEU    40      21.915  80.070  53.127  1.00  0.00             
ATOM    321  CG  LEU    40      21.288  81.246  53.879  1.00  0.00             
ATOM    322  CD1 LEU    40      21.964  81.441  55.228  1.00  0.00             
ATOM    323  CD2 LEU    40      19.791  81.038  54.049  1.00  0.00             
ATOM    324  N   GLU    41      21.109  77.236  53.449  1.00  0.00             
ATOM    325  CA  GLU    41      20.584  76.093  54.187  1.00  0.00             
ATOM    326  C   GLU    41      19.802  75.157  53.272  1.00  0.00             
ATOM    327  O   GLU    41      18.571  75.182  53.249  1.00  0.00             
ATOM    328  CB  GLU    41      21.719  75.332  54.874  1.00  0.00             
ATOM    329  CG  GLU    41      21.335  74.714  56.208  1.00  0.00             
ATOM    330  CD  GLU    41      22.541  74.343  57.047  1.00  0.00             
ATOM    331  OE1 GLU    41      23.300  75.256  57.434  1.00  0.00             
ATOM    332  OE2 GLU    41      22.727  73.138  57.319  1.00  0.00             
ATOM    333  N   LYS    42      20.523  74.333  52.521  1.00  0.00             
ATOM    334  CA  LYS    42      19.899  73.388  51.603  1.00  0.00             
ATOM    335  C   LYS    42      19.368  74.094  50.361  1.00  0.00             
ATOM    336  O   LYS    42      18.221  73.890  49.962  1.00  0.00             
ATOM    337  CB  LYS    42      20.892  72.294  51.204  1.00  0.00             
ATOM    338  CG  LYS    42      20.251  70.944  50.928  1.00  0.00             
ATOM    339  CD  LYS    42      21.169  70.052  50.108  1.00  0.00             
ATOM    340  CE  LYS    42      20.453  68.791  49.654  1.00  0.00             
ATOM    341  NZ  LYS    42      21.259  68.021  48.665  1.00  0.00             
ATOM    342  N   CYS    43      20.209  74.923  49.753  1.00  0.00             
ATOM    343  CA  CYS    43      19.825  75.661  48.556  1.00  0.00             
ATOM    344  C   CYS    43      18.544  76.455  48.784  1.00  0.00             
ATOM    345  O   CYS    43      17.465  76.047  48.355  1.00  0.00             
ATOM    346  CB  CYS    43      20.954  76.597  48.118  1.00  0.00             
ATOM    347  SG  CYS    43      21.517  76.348  46.404  1.00  0.00             
ATOM    348  N   SER    44      18.670  77.592  49.460  1.00  0.00             
ATOM    349  CA  SER    44      17.524  78.446  49.745  1.00  0.00             
ATOM    350  C   SER    44      16.464  77.696  50.547  1.00  0.00             
ATOM    351  O   SER    44      15.316  77.580  50.120  1.00  0.00             
ATOM    352  CB  SER    44      17.965  79.700  50.503  1.00  0.00             
ATOM    353  OG  SER    44      17.146  80.809  50.172  1.00  0.00             
ATOM    354  N   HIS    45      16.858  77.187  51.710  1.00  0.00             
ATOM    355  CA  HIS    45      15.945  76.448  52.572  1.00  0.00             
ATOM    356  C   HIS    45      15.683  75.048  52.026  1.00  0.00             
ATOM    357  O   HIS    45      15.997  74.752  50.873  1.00  0.00             
ATOM    358  CB  HIS    45      16.500  76.363  53.994  1.00  0.00             
ATOM    359  CG  HIS    45      15.455  76.489  55.060  1.00  0.00             
ATOM    360  ND1 HIS    45      14.203  77.007  54.816  1.00  0.00             
ATOM    361  CD2 HIS    45      15.479  76.163  56.373  1.00  0.00             
ATOM    362  CE1 HIS    45      13.500  76.995  55.934  1.00  0.00             
ATOM    363  NE2 HIS    45      14.249  76.488  56.894  1.00  0.00             
ATOM    364  N   ASP    46      15.106  74.190  52.862  1.00  0.00             
ATOM    365  CA  ASP    46      14.802  72.821  52.466  1.00  0.00             
ATOM    366  C   ASP    46      14.229  72.024  53.633  1.00  0.00             
ATOM    367  O   ASP    46      14.969  71.395  54.390  1.00  0.00             
ATOM    368  CB  ASP    46      13.824  72.809  51.290  1.00  0.00             
ATOM    369  CG  ASP    46      14.438  72.239  50.026  1.00  0.00             
ATOM    370  OD1 ASP    46      13.944  71.198  49.543  1.00  0.00             
ATOM    371  OD2 ASP    46      15.413  72.833  49.520  1.00  0.00             
ATOM    372  N   THR    47      12.908  72.054  53.772  1.00  0.00             
ATOM    373  CA  THR    47      12.219  71.317  54.870  1.00  0.00             
ATOM    374  C   THR    47      12.003  72.215  56.084  1.00  0.00             
ATOM    375  O   THR    47      12.941  72.512  56.824  1.00  0.00             
ATOM    376  CB  THR    47      10.860  70.758  54.409  1.00  0.00             
ATOM    377  OG1 THR    47      10.203  71.719  53.574  1.00  0.00             
ATOM    378  CG2 THR    47      11.053  69.465  53.632  1.00  0.00             
ATOM    379  N   ALA    48      10.760  72.643  56.283  1.00  0.00             
ATOM    380  CA  ALA    48      10.419  73.507  57.407  1.00  0.00             
ATOM    381  C   ALA    48      10.575  74.979  57.039  1.00  0.00             
ATOM    382  O   ALA    48      11.662  75.425  56.671  1.00  0.00             
ATOM    383  CB  ALA    48       8.998  73.231  57.875  1.00  0.00             
ATOM    384  N   LYS    49       9.482  75.728  57.140  1.00  0.00             
ATOM    385  CA  LYS    49       9.495  77.150  56.818  1.00  0.00             
ATOM    386  C   LYS    49       9.505  77.373  55.310  1.00  0.00             
ATOM    387  O   LYS    49      10.403  78.024  54.774  1.00  0.00             
ATOM    388  CB  LYS    49       8.290  77.852  57.446  1.00  0.00             
ATOM    389  CG  LYS    49       8.601  79.224  58.021  1.00  0.00             
ATOM    390  CD  LYS    49       7.490  79.704  58.939  1.00  0.00             
ATOM    391  CE  LYS    49       7.771  81.103  59.463  1.00  0.00             
ATOM    392  NZ  LYS    49       6.540  81.760  59.982  1.00  0.00             
ATOM    393  N   ALA    50       8.500  76.831  54.629  1.00  0.00             
ATOM    394  CA  ALA    50       8.391  76.970  53.182  1.00  0.00             
ATOM    395  C   ALA    50       9.764  76.921  52.518  1.00  0.00             
ATOM    396  O   ALA    50      10.297  77.947  52.097  1.00  0.00             
ATOM    397  CB  ALA    50       7.494  75.884  52.610  1.00  0.00             
TER
END
