
#######################################################
#                                                     #
#                        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 (  147),  selected   18 , name T0347TS389_2-D2
# Molecule2: number of CA atoms   71 (  561),  selected   18 , name T0347_D2.pdb
# PARAMETERS: T0347TS389_2-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:    14       150 - 170         3.85     8.68
  LCS_AVERAGE:     16.59

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       157 - 170         1.23     8.58
  LCS_AVERAGE:     11.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       157 - 169         0.59     8.57
  LCS_AVERAGE:     10.02

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     A     140     A     140      4    4    4     3    3    4    4    4    4    4    4    4    5    5    5    6    6    6    6    7    8   11   12 
LCS_GDT     G     141     G     141      4    4    4     3    3    4    4    4    4    4    4    4    5    5    5    6    6   13   13   15   15   15   15 
LCS_GDT     G     148     G     148      4    4    4     3    3    4    4    4    4    4    4    4    5    6    7    8   10   11   11   11   11   13   13 
LCS_GDT     Y     149     Y     149      4    4    4     0    3    4    4    4    4   11   11   11   12   12   12   12   12   12   12   13   13   13   13 
LCS_GDT     A     150     A     150      3    3   14     3    3    3    7    8    9   10   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     K     151     K     151      3    3   14     3    3    3    3    3    9   10   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     V     152     V     152      3    3   14     3    3    4    7    8    9   10   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     S     157     S     157     10   11   14     7    9   10   10   10   11   11   11   11   12   12   12   12   13   14   14   15   15   15   15 
LCS_GDT     W     161     W     161     10   11   14     8    9   10   10   10   11   11   11   11   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     A     162     A     162     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     D     163     D     163     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     F     164     F     164     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     L     165     L     165     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     R     166     R     166     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     R     167     R     167     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     R     168     R     168     10   11   14     8    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     I     169     I     169     10   11   14     3    9   10   10   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_GDT     D     170     D     170      3   11   14     0    3    4    7   10   11   11   11   12   12   13   13   13   13   14   14   15   15   15   15 
LCS_AVERAGE  LCS_A:  12.68  (  10.02   11.42   16.59 )

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      8      9     10     10     10     11     11     11     12     12     13     13     13     13     14     14     15     15     15     15 
GDT PERCENT_CA  11.27  12.68  14.08  14.08  14.08  15.49  15.49  15.49  16.90  16.90  18.31  18.31  18.31  18.31  19.72  19.72  21.13  21.13  21.13  21.13
GDT RMS_LOCAL    0.28   0.38   0.59   0.59   0.59   1.23   1.23   1.23   2.75   2.22   3.06   3.06   3.06   3.06   3.85   3.85   4.61   4.61   4.61   4.61
GDT RMS_ALL_CA   8.62   8.68   8.57   8.57   8.57   8.58   8.58   8.58   9.28   9.51   9.08   9.08   9.08   9.08   8.68   8.68   8.31   8.31   8.31   8.31

#      Molecule1      Molecule2       DISTANCE
LGA    A     140      A     140         14.946
LGA    G     141      G     141         12.117
LGA    G     148      G     148         14.374
LGA    Y     149      Y     149          8.092
LGA    A     150      A     150         14.745
LGA    K     151      K     151         15.709
LGA    V     152      V     152         14.158
LGA    S     157      S     157          1.540
LGA    W     161      W     161          0.366
LGA    A     162      A     162          0.624
LGA    D     163      D     163          0.796
LGA    F     164      F     164          0.611
LGA    L     165      L     165          0.741
LGA    R     166      R     166          1.279
LGA    R     167      R     167          0.954
LGA    R     168      R     168          0.655
LGA    I     169      I     169          0.431
LGA    D     170      D     170          3.020

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   71    4.0     11    1.23    15.493    14.772     0.825

LGA_LOCAL      RMSD =  1.233  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.575  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  7.635  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.938522 * X  +   0.296329 * Y  +   0.177101 * Z  +   8.055255
  Y_new =   0.005328 * X  +  -0.500517 * Y  +   0.865710 * Z  +  50.932007
  Z_new =   0.345177 * X  +   0.813432 * Y  +   0.468167 * Z  + -13.158907 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.048552   -2.093040  [ DEG:    60.0776   -119.9224 ]
  Theta =  -0.352428   -2.789165  [ DEG:   -20.1926   -159.8074 ]
  Phi   =   3.135915   -0.005677  [ DEG:   179.6747     -0.3253 ]
 
# 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_2-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS389_2-D2.T0347_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   71   4.0   11   1.23  14.772     7.64
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS389_2-D2
PFRMAT TS
TARGET T0347
MODEL  2
PARENT N/A
ATOM    732  N   ALA   140      31.102  49.641  -2.266  1.00  0.00
ATOM    733  CA  ALA   140      29.690  49.688  -1.910  1.00  0.00
ATOM    734  CB  ALA   140      29.403  50.898  -1.034  1.00  0.00
ATOM    735  O   ALA   140      27.776  49.092  -3.204  1.00  0.00
ATOM    736  C   ALA   140      28.771  49.784  -3.131  1.00  0.00
ATOM    737  N   GLY   141      29.095  50.641  -4.086  1.00  0.00
ATOM    738  CA  GLY   141      28.220  50.831  -5.242  1.00  0.00
ATOM    739  O   GLY   141      26.989  49.144  -6.447  1.00  0.00
ATOM    740  C   GLY   141      28.082  49.528  -6.047  1.00  0.00
ATOM    744  N   GLY   148      23.622  42.873  -3.212  1.00  0.00
ATOM    745  CA  GLY   148      24.268  42.250  -2.048  1.00  0.00
ATOM    746  O   GLY   148      24.270  42.467   0.298  1.00  0.00
ATOM    747  C   GLY   148      24.084  43.014  -0.760  1.00  0.00
ATOM    748  N   TYR   149      23.773  44.304  -0.874  1.00  0.00
ATOM    749  CA  TYR   149      23.515  45.164   0.274  1.00  0.00
ATOM    750  CB  TYR   149      24.693  46.111   0.510  1.00  0.00
ATOM    751  CG  TYR   149      26.002  45.404   0.779  1.00  0.00
ATOM    752  CD1 TYR   149      26.960  45.274  -0.220  1.00  0.00
ATOM    753  CD2 TYR   149      26.278  44.869   2.032  1.00  0.00
ATOM    754  CE1 TYR   149      28.158  44.629   0.018  1.00  0.00
ATOM    755  CE2 TYR   149      27.471  44.221   2.287  1.00  0.00
ATOM    756  CZ  TYR   149      28.414  44.104   1.266  1.00  0.00
ATOM    757  OH  TYR   149      29.607  43.462   1.505  1.00  0.00
ATOM    758  O   TYR   149      21.805  45.978  -1.154  1.00  0.00
ATOM    759  C   TYR   149      22.271  45.956  -0.025  1.00  0.00
ATOM    760  N   ALA   150      31.282  62.165  -1.253  1.00  0.00
ATOM    761  CA  ALA   150      32.722  62.335  -1.006  1.00  0.00
ATOM    762  CB  ALA   150      32.956  63.389   0.064  1.00  0.00
ATOM    763  O   ALA   150      34.436  60.655  -0.978  1.00  0.00
ATOM    764  C   ALA   150      33.331  61.023  -0.537  1.00  0.00
ATOM    765  N   LYS   151      32.606  60.319   0.348  1.00  0.00
ATOM    766  CA  LYS   151      32.965  58.990   0.801  1.00  0.00
ATOM    767  CB  LYS   151      32.927  58.916   2.328  1.00  0.00
ATOM    768  CG  LYS   151      33.885  59.874   3.020  1.00  0.00
ATOM    769  CD  LYS   151      33.848  59.697   4.530  1.00  0.00
ATOM    770  CE  LYS   151      34.871  60.588   5.214  1.00  0.00
ATOM    771  NZ  LYS   151      34.847  60.425   6.695  1.00  0.00
ATOM    772  O   LYS   151      30.915  58.313  -0.334  1.00  0.00
ATOM    773  C   LYS   151      31.968  57.955   0.227  1.00  0.00
ATOM    774  N   VAL   152      32.294  56.677   0.383  1.00  0.00
ATOM    775  CA  VAL   152      31.476  55.587  -0.134  1.00  0.00
ATOM    776  CB  VAL   152      32.205  54.812  -1.247  1.00  0.00
ATOM    777  CG1 VAL   152      32.290  55.652  -2.513  1.00  0.00
ATOM    778  CG2 VAL   152      33.619  54.459  -0.811  1.00  0.00
ATOM    779  O   VAL   152      32.100  54.088   1.611  1.00  0.00
ATOM    780  C   VAL   152      31.177  54.653   1.011  1.00  0.00
ATOM    784  N   SER   157      15.915  46.483   5.319  1.00  0.00
ATOM    785  CA  SER   157      16.859  47.562   5.550  1.00  0.00
ATOM    786  CB  SER   157      18.294  47.069   5.360  1.00  0.00
ATOM    787  OG  SER   157      18.620  46.069   6.308  1.00  0.00
ATOM    788  O   SER   157      16.742  49.885   4.958  1.00  0.00
ATOM    789  C   SER   157      16.620  48.719   4.579  1.00  0.00
ATOM    793  N   TRP   161      15.971  52.605   5.745  1.00  0.00
ATOM    794  CA  TRP   161      16.645  53.757   5.158  1.00  0.00
ATOM    795  CB  TRP   161      17.523  53.324   3.982  1.00  0.00
ATOM    796  CG  TRP   161      18.259  54.456   3.335  1.00  0.00
ATOM    797  CD1 TRP   161      19.461  54.976   3.717  1.00  0.00
ATOM    798  CD2 TRP   161      17.842  55.210   2.190  1.00  0.00
ATOM    799  CE2 TRP   161      18.841  56.170   1.936  1.00  0.00
ATOM    800  CE3 TRP   161      16.721  55.168   1.354  1.00  0.00
ATOM    801  NE1 TRP   161      19.820  56.007   2.883  1.00  0.00
ATOM    802  CZ2 TRP   161      18.753  57.079   0.882  1.00  0.00
ATOM    803  CZ3 TRP   161      16.638  56.070   0.311  1.00  0.00
ATOM    804  CH2 TRP   161      17.645  57.014   0.081  1.00  0.00
ATOM    805  O   TRP   161      15.686  55.952   4.962  1.00  0.00
ATOM    806  C   TRP   161      15.613  54.760   4.657  1.00  0.00
ATOM    807  N   ALA   162      14.637  54.284   3.896  1.00  0.00
ATOM    808  CA  ALA   162      13.635  55.165   3.308  1.00  0.00
ATOM    809  CB  ALA   162      12.695  54.373   2.411  1.00  0.00
ATOM    810  O   ALA   162      12.423  57.017   4.170  1.00  0.00
ATOM    811  C   ALA   162      12.781  55.865   4.351  1.00  0.00
ATOM    812  N   ASP   163      12.467  55.184   5.445  1.00  0.00
ATOM    813  CA  ASP   163      11.709  55.778   6.547  1.00  0.00
ATOM    814  CB  ASP   163      11.456  54.742   7.644  1.00  0.00
ATOM    815  CG  ASP   163      10.429  53.704   7.242  1.00  0.00
ATOM    816  OD1 ASP   163       9.739  53.916   6.223  1.00  0.00
ATOM    817  OD2 ASP   163      10.311  52.679   7.945  1.00  0.00
ATOM    818  O   ASP   163      11.935  58.024   7.379  1.00  0.00
ATOM    819  C   ASP   163      12.488  56.954   7.153  1.00  0.00
ATOM    820  N   PHE   164      13.773  56.752   7.408  1.00  0.00
ATOM    821  CA  PHE   164      14.629  57.822   7.926  1.00  0.00
ATOM    822  CB  PHE   164      16.063  57.318   8.108  1.00  0.00
ATOM    823  CG  PHE   164      17.015  58.370   8.601  1.00  0.00
ATOM    824  CD1 PHE   164      17.054  58.717   9.941  1.00  0.00
ATOM    825  CD2 PHE   164      17.871  59.014   7.723  1.00  0.00
ATOM    826  CE1 PHE   164      17.931  59.685  10.394  1.00  0.00
ATOM    827  CE2 PHE   164      18.748  59.981   8.178  1.00  0.00
ATOM    828  CZ  PHE   164      18.780  60.318   9.506  1.00  0.00
ATOM    829  O   PHE   164      14.469  60.152   7.377  1.00  0.00
ATOM    830  C   PHE   164      14.651  59.005   6.960  1.00  0.00
ATOM    831  N   LEU   165      14.855  58.733   5.677  1.00  0.00
ATOM    832  CA  LEU   165      14.865  59.808   4.708  1.00  0.00
ATOM    833  CB  LEU   165      15.120  59.259   3.303  1.00  0.00
ATOM    834  CG  LEU   165      15.173  60.290   2.172  1.00  0.00
ATOM    835  CD1 LEU   165      16.305  61.281   2.400  1.00  0.00
ATOM    836  CD2 LEU   165      15.402  59.608   0.833  1.00  0.00
ATOM    837  O   LEU   165      13.569  61.812   4.556  1.00  0.00
ATOM    838  C   LEU   165      13.555  60.592   4.638  1.00  0.00
ATOM    839  N   ARG   166      12.430  59.897   4.697  1.00  0.00
ATOM    840  CA  ARG   166      11.126  60.547   4.667  1.00  0.00
ATOM    841  CB  ARG   166      10.009  59.501   4.655  1.00  0.00
ATOM    842  CG  ARG   166       8.610  60.090   4.539  1.00  0.00
ATOM    843  CD  ARG   166       7.549  59.001   4.560  1.00  0.00
ATOM    844  NE  ARG   166       7.519  58.293   5.838  1.00  0.00
ATOM    845  CZ  ARG   166       6.949  58.766   6.942  1.00  0.00
ATOM    846  NH1 ARG   166       6.970  58.052   8.057  1.00  0.00
ATOM    847  NH2 ARG   166       6.361  59.954   6.925  1.00  0.00
ATOM    848  O   ARG   166      10.485  62.569   5.829  1.00  0.00
ATOM    849  C   ARG   166      10.963  61.439   5.916  1.00  0.00
ATOM    850  N   ARG   167      11.361  60.941   7.078  1.00  0.00
ATOM    851  CA  ARG   167      11.280  61.732   8.291  1.00  0.00
ATOM    852  CB  ARG   167      11.746  60.913   9.497  1.00  0.00
ATOM    853  CG  ARG   167      10.786  59.807   9.905  1.00  0.00
ATOM    854  CD  ARG   167      11.343  58.990  11.058  1.00  0.00
ATOM    855  NE  ARG   167      10.445  57.904  11.445  1.00  0.00
ATOM    856  CZ  ARG   167      10.724  57.000  12.375  1.00  0.00
ATOM    857  NH1 ARG   167       9.845  56.048  12.661  1.00  0.00
ATOM    858  NH2 ARG   167      11.883  57.046  13.019  1.00  0.00
ATOM    859  O   ARG   167      11.693  64.067   8.607  1.00  0.00
ATOM    860  C   ARG   167      12.145  62.981   8.227  1.00  0.00
ATOM    861  N   ARG   168      13.368  62.842   7.719  1.00  0.00
ATOM    862  CA  ARG   168      14.275  63.974   7.623  1.00  0.00
ATOM    863  CB  ARG   168      15.678  63.503   7.235  1.00  0.00
ATOM    864  CG  ARG   168      16.722  64.609   7.220  1.00  0.00
ATOM    865  CD  ARG   168      18.118  64.047   7.007  1.00  0.00
ATOM    866  NE  ARG   168      19.133  65.098   6.982  1.00  0.00
ATOM    867  CZ  ARG   168      20.415  64.894   6.698  1.00  0.00
ATOM    868  NH1 ARG   168      21.264  65.912   6.698  1.00  0.00
ATOM    869  NH2 ARG   168      20.843  63.671   6.416  1.00  0.00
ATOM    870  O   ARG   168      13.977  66.170   6.733  1.00  0.00
ATOM    871  C   ARG   168      13.806  64.975   6.568  1.00  0.00
ATOM    872  N   ILE   169      13.189  64.470   5.494  1.00  0.00
ATOM    873  CA  ILE   169      12.553  65.282   4.451  1.00  0.00
ATOM    874  CB  ILE   169      11.944  64.404   3.343  1.00  0.00
ATOM    875  CG1 ILE   169      13.050  63.693   2.558  1.00  0.00
ATOM    876  CG2 ILE   169      11.135  65.252   2.373  1.00  0.00
ATOM    877  CD1 ILE   169      12.543  62.608   1.635  1.00  0.00
ATOM    878  O   ILE   169      11.380  67.340   4.920  1.00  0.00
ATOM    879  C   ILE   169      11.434  66.123   5.078  1.00  0.00
ATOM    880  N   ASP   170      10.545  65.471   5.797  1.00  0.00
ATOM    881  CA  ASP   170       9.426  66.164   6.429  1.00  0.00
ATOM    882  CB  ASP   170       8.531  65.169   7.171  1.00  0.00
ATOM    883  CG  ASP   170       7.233  65.794   7.641  1.00  0.00
ATOM    884  OD1 ASP   170       6.972  66.964   7.288  1.00  0.00
ATOM    885  OD2 ASP   170       6.475  65.114   8.363  1.00  0.00
ATOM    886  O   ASP   170       9.245  68.262   7.566  1.00  0.00
ATOM    887  C   ASP   170       9.873  67.217   7.448  1.00  0.00
TER
END
