
#######################################################
#                                                     #
#                        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   30 (  147),  selected   30 , name T0386TS278_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   30 , name T0386_D2.pdb
# PARAMETERS: T0386TS278_1-D2.T0386_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:    13       235 - 248         4.74    13.16
  LCS_AVERAGE:     13.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       222 - 228         1.67    14.19
  LCS_AVERAGE:      6.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       224 - 228         0.97    11.37
  LCS_AVERAGE:      4.53

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:   81
LCS_GDT     K     222     K     222      4    7    9     3    4    4    6    7    7    9   11   11   11   12   14   15   15   16   17   19   19   19   21 
LCS_GDT     I     223     I     223      4    7    9     3    4    4    6    7    8   10   11   13   13   14   14   15   16   16   18   19   19   20   21 
LCS_GDT     R     224     R     224      5    7    9     3    4    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     L     225     L     225      5    7    9     4    5    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     L     226     L     226      5    7    9     4    5    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     K     227     K     227      5    7    9     4    5    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     E     228     E     228      5    7   12     4    5    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     N     235     N     235      3    5   13     0    3    3    4    4    5    7    7   10   10   11   11   11   11   12   14   17   18   20   22 
LCS_GDT     T     236     T     236      3    5   13     1    3    4    4    6    7    8    9   10   11   12   13   13   15   15   16   17   18   20   22 
LCS_GDT     G     237     G     237      3    5   13     0    3    3    4    4    7    8    9   10   10   11   13   14   15   15   16   17   18   20   22 
LCS_GDT     R     238     R     238      4    6   13     1    4    5    5    7    7    8   10   11   12   14   14   15   15   16   18   19   19   20   22 
LCS_GDT     N     239     N     239      4    6   13     3    5    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     V     240     V     240      4    6   13     3    4    6    7    9    9   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     N     241     N     241      4    6   13     3    4    5    5    7    8   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     D     242     D     242      3    6   13     3    3    6    6    7    8   10   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     R     243     R     243      3    6   13     3    3    4    4    7    7    8   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     P     244     P     244      3    3   13     3    3    3    3    5    7    8   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     V     245     V     245      3    3   13     3    3    3    3    5    6    8   11   13   13   14   14   15   16   16   18   19   19   20   22 
LCS_GDT     V     247     V     247      3    3   13     3    3    4    4    4    5    5    5    6    7    9   11   13   14   15   17   18   19   20   22 
LCS_GDT     A     248     A     248      3    3   13     3    3    4    4    4    5    5    5    7    8    8   11   13   14   15   17   18   19   20   22 
LCS_GDT     K     249     K     249      4    5   11     3    4    4    4    5    6    7    7    8    9   11   12   13   13   14   17   18   18   20   21 
LCS_GDT     E     250     E     250      4    5   10     3    4    4    4    5    6    7    7    8    9   11   12   13   13   14   15   16   18   18   21 
LCS_GDT     G     251     G     251      4    5   10     3    4    4    4    5    6    7    7    8    9   11   12   13   13   14   15   17   18   20   21 
LCS_GDT     E     252     E     252      4    5   10     3    4    4    4    5    6    7    7    8    9   12   13   15   16   16   18   19   19   20   22 
LCS_GDT     T     253     T     253      3    5   10     0    3    3    4    5    6    7    7    8    8    9   12   13   16   16   18   19   19   20   22 
LCS_GDT     Y     254     Y     254      3    3   10     2    4    6    7    9    9   10   11   12   13   13   14   14   16   16   18   19   19   20   22 
LCS_GDT     T     255     T     255      3    3   10     0    3    6    6    9    9   10   11   12   13   13   14   14   16   16   18   19   19   20   22 
LCS_GDT     Y     258     Y     258      3    3   10     3    3    3    3    3    7    8    9    9   11   12   13   14   15   15   16   17   18   20   22 
LCS_GDT     R     259     R     259      3    3   10     3    3    3    3    3    3    3    3    4    5    6    8    9    9   12   14   15   18   19   20 
LCS_GDT     G     260     G     260      3    3    7     3    3    3    3    3    3    3    3    3    5    5    8    8   11   12   13   13   13   18   20 
LCS_AVERAGE  LCS_A:   8.16  (   4.53    6.26   13.70 )

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      4      5      6      7      9      9     10     11     13     13     14     14     15     16     16     18     19     19     20     22 
GDT PERCENT_CA   4.94   6.17   7.41   8.64  11.11  11.11  12.35  13.58  16.05  16.05  17.28  17.28  18.52  19.75  19.75  22.22  23.46  23.46  24.69  27.16
GDT RMS_LOCAL    0.09   0.50   0.94   1.21   1.64   1.64   1.98   2.34   3.06   3.06   3.31   3.31   3.63   4.28   4.16   5.12   5.27   5.27   6.31   7.18
GDT RMS_ALL_CA  11.28  10.64  10.66  10.19  10.27  10.27  10.28  10.49  12.32  12.32  12.73  12.73  12.83   9.74   9.91   9.72   9.85   9.85  10.84   9.32

#      Molecule1      Molecule2       DISTANCE
LGA    K     222      K     222          3.762
LGA    I     223      I     223          3.347
LGA    R     224      R     224          3.259
LGA    L     225      L     225          0.561
LGA    L     226      L     226          0.471
LGA    K     227      K     227          0.808
LGA    E     228      E     228          0.899
LGA    N     235      N     235         12.396
LGA    T     236      T     236         10.592
LGA    G     237      G     237          8.879
LGA    R     238      R     238          5.596
LGA    N     239      N     239          1.547
LGA    V     240      V     240          2.192
LGA    N     241      N     241          6.692
LGA    D     242      D     242          8.400
LGA    R     243      R     243          9.150
LGA    P     244      P     244         12.677
LGA    V     245      V     245          9.906
LGA    V     247      V     247         15.309
LGA    A     248      A     248         16.861
LGA    K     249      K     249         18.390
LGA    E     250      E     250         18.446
LGA    G     251      G     251         18.185
LGA    E     252      E     252         14.321
LGA    T     253      T     253          8.905
LGA    Y     254      Y     254          3.979
LGA    T     255      T     255          2.063
LGA    Y     258      Y     258         10.870
LGA    R     259      R     259         16.452
LGA    G     260      G     260         18.343

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30   81    4.0     11    2.34    12.654    11.343     0.450

LGA_LOCAL      RMSD =  2.342  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.703  Number of atoms =   30 
Std_ALL_ATOMS  RMSD =  9.233  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.833499 * X  +   0.531570 * Y  +   0.150706 * Z  +  -0.382143
  Y_new =   0.552437 * X  +  -0.806500 * Y  +  -0.210643 * Z  + 114.740028
  Z_new =   0.009573 * X  +   0.258827 * Y  +  -0.965876 * Z  +  56.224102 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.879773   -0.261820  [ DEG:   164.9988    -15.0012 ]
  Theta =  -0.009573   -3.132020  [ DEG:    -0.5485   -179.4515 ]
  Phi   =   0.585316   -2.556277  [ DEG:    33.5361   -146.4639 ]
 
# 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: T0386TS278_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS278_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30   81   4.0   11   2.34  11.343     9.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS278_1-D2
PFRMAT TS
TARGET T0386
MODEL  1
PARENT 2g03_A
ATOM    693  N   LYS   222       2.689  59.391  79.040  1.00  1.50           386
ATOM    694  CA  LYS   222       3.797  59.630  80.009  1.00  1.50           386
ATOM    695  C   LYS   222       5.102  59.871  79.281  1.00  1.50           386
ATOM    696  O   LYS   222       5.837  60.797  79.574  1.00  1.50           386
ATOM    697  CB  LYS   222       3.941  58.456  80.975  1.00  1.50           386
ATOM    698  N   ILE   223       5.381  59.044  78.285  1.00  1.50           386
ATOM    699  CA  ILE   223       6.609  59.186  77.527  1.00  1.50           386
ATOM    700  C   ILE   223       6.662  60.487  76.709  1.00  1.50           386
ATOM    701  O   ILE   223       7.695  61.159  76.658  1.00  1.50           386
ATOM    702  CB  ILE   223       6.816  57.941  76.635  1.00  1.50           386
ATOM    703  N   ARG   224       5.575  60.840  76.036  1.00  1.50           386
ATOM    704  CA  ARG   224       5.540  62.124  75.295  1.00  1.50           386
ATOM    705  C   ARG   224       5.717  63.331  76.198  1.00  1.50           386
ATOM    706  O   ARG   224       6.467  64.238  75.857  1.00  1.50           386
ATOM    707  CB  ARG   224       4.242  62.253  74.490  1.00  1.50           386
ATOM    708  N   LEU   225       7.229  63.431  79.103  1.00  1.50           386
ATOM    709  CA  LEU   225       8.570  63.446  79.656  1.00  1.50           386
ATOM    710  C   LEU   225       9.599  63.848  78.620  1.00  1.50           386
ATOM    711  O   LEU   225      10.484  64.619  78.916  1.00  1.50           386
ATOM    712  CB  LEU   225       8.907  62.071  80.265  1.00  1.50           386
ATOM    713  N   LEU   226       9.532  63.289  77.416  1.00  1.50           386
ATOM    714  CA  LEU   226      10.576  63.596  76.426  1.00  1.50           386
ATOM    715  C   LEU   226      10.413  64.988  75.800  1.00  1.50           386
ATOM    716  O   LEU   226      11.394  65.682  75.569  1.00  1.50           386
ATOM    717  CB  LEU   226      10.682  62.511  75.359  1.00  1.50           386
ATOM    718  N   LYS   227       9.174  65.405  75.562  1.00  1.50           386
ATOM    719  CA  LYS   227       8.895  66.705  74.984  1.00  1.50           386
ATOM    720  C   LYS   227       9.408  67.830  75.871  1.00  1.50           386
ATOM    721  O   LYS   227       9.887  68.832  75.382  1.00  1.50           386
ATOM    722  CB  LYS   227       7.401  66.861  74.733  1.00  1.50           386
ATOM    723  N   GLU   228       9.268  67.661  77.184  1.00  1.50           386
ATOM    724  CA  GLU   228       9.856  68.561  78.185  1.00  1.50           386
ATOM    725  C   GLU   228      11.385  68.663  78.118  1.00  1.50           386
ATOM    726  O   GLU   228      11.978  69.555  78.715  1.00  1.50           386
ATOM    727  CB  GLU   228       9.500  68.030  79.576  1.00  1.50           386
ATOM    728  N   ASN   235      12.022  67.724  77.435  1.00  1.50           386
ATOM    729  CA  ASN   235      13.450  67.602  77.550  1.00  1.50           386
ATOM    730  C   ASN   235      14.150  67.539  76.195  1.00  1.50           386
ATOM    731  O   ASN   235      15.227  66.987  76.096  1.00  1.50           386
ATOM    732  CB  ASN   235      13.796  66.394  78.439  1.00  1.50           386
ATOM    733  N   THR   236      13.563  68.133  75.160  1.00  1.50           386
ATOM    734  CA  THR   236      14.253  68.210  73.872  1.00  1.50           386
ATOM    735  C   THR   236      15.204  69.385  73.920  1.00  1.50           386
ATOM    736  O   THR   236      14.998  70.312  74.708  1.00  1.50           386
ATOM    737  CB  THR   236      13.280  68.340  72.696  1.00  1.50           386
ATOM    738  N   GLY   237      16.257  69.341  73.101  1.00  1.50           386
ATOM    739  CA  GLY   237      17.161  70.473  72.931  1.00  1.50           386
ATOM    740  C   GLY   237      17.492  70.555  71.456  1.00  1.50           386
ATOM    741  O   GLY   237      17.586  69.533  70.796  1.00  1.50           386
ATOM    742  N   ARG   238      17.670  71.752  70.911  1.00  1.50           386
ATOM    743  CA  ARG   238      18.155  71.807  69.540  1.00  1.50           386
ATOM    744  C   ARG   238      19.660  71.977  69.441  1.00  1.50           386
ATOM    745  O   ARG   238      20.191  72.162  68.355  1.00  1.50           386
ATOM    746  CB  ARG   238      17.446  72.878  68.721  1.00  1.50           386
ATOM    747  N   ASN   239      20.343  71.860  70.571  1.00  1.50           386
ATOM    748  CA  ASN   239      21.800  71.945  70.590  1.00  1.50           386
ATOM    749  C   ASN   239      22.350  70.522  70.364  1.00  1.50           386
ATOM    750  O   ASN   239      22.931  69.927  71.264  1.00  1.50           386
ATOM    751  CB  ASN   239      22.218  72.479  71.951  1.00  1.50           386
ATOM    752  N   VAL   240      22.163  69.998  69.153  1.00  1.50           386
ATOM    753  CA  VAL   240      22.207  68.552  68.899  1.00  1.50           386
ATOM    754  C   VAL   240      23.631  67.975  68.897  1.00  1.50           386
ATOM    755  O   VAL   240      23.802  66.742  68.966  1.00  1.50           386
ATOM    756  CB  VAL   240      21.496  68.170  67.559  1.00  1.50           386
ATOM    757  N   ASN   241      24.629  68.854  68.823  1.00  1.50           386
ATOM    758  CA  ASN   241      26.022  68.441  68.696  1.00  1.50           386
ATOM    759  C   ASN   241      26.877  68.920  69.861  1.00  1.50           386
ATOM    760  O   ASN   241      28.095  68.867  69.806  1.00  1.50           386
ATOM    761  CB  ASN   241      26.629  68.966  67.386  1.00  1.50           386
ATOM    762  N   ASP   242      26.227  69.387  70.910  1.00  1.50           386
ATOM    763  CA  ASP   242      26.917  69.870  72.085  1.00  1.50           386
ATOM    764  C   ASP   242      27.588  68.716  72.851  1.00  1.50           386
ATOM    765  O   ASP   242      26.946  67.719  73.179  1.00  1.50           386
ATOM    766  CB  ASP   242      25.924  70.615  72.946  1.00  1.50           386
ATOM    767  N   ARG   243      28.890  68.838  73.099  1.00  1.50           386
ATOM    768  CA  ARG   243      29.647  67.786  73.778  1.00  1.50           386
ATOM    769  C   ARG   243      29.049  67.379  75.142  1.00  1.50           386
ATOM    770  O   ARG   243      28.989  66.195  75.459  1.00  1.50           386
ATOM    771  CB  ARG   243      31.131  68.169  73.910  1.00  1.50           386
ATOM    772  N   PRO   244      28.586  68.346  75.927  1.00  1.50           386
ATOM    773  CA  PRO   244      28.059  68.058  77.250  1.00  1.50           386
ATOM    774  C   PRO   244      26.728  67.296  77.191  1.00  1.50           386
ATOM    775  O   PRO   244      26.509  66.332  77.945  1.00  1.50           386
ATOM    776  CB  PRO   244      27.906  69.344  78.049  1.00  1.50           386
ATOM    777  N   VAL   245      25.842  67.717  76.288  1.00  1.50           386
ATOM    778  CA  VAL   245      24.577  67.031  76.061  1.00  1.50           386
ATOM    779  C   VAL   245      24.830  65.621  75.548  1.00  1.50           386
ATOM    780  O   VAL   245      24.207  64.671  76.026  1.00  1.50           386
ATOM    781  CB  VAL   245      23.654  67.840  75.102  1.00  1.50           386
ATOM    782  N   VAL   247      25.737  65.467  74.585  1.00  1.50           386
ATOM    783  CA  VAL   247      26.044  64.130  74.069  1.00  1.50           386
ATOM    784  C   VAL   247      26.616  63.222  75.194  1.00  1.50           386
ATOM    785  O   VAL   247      26.057  62.176  75.506  1.00  1.50           386
ATOM    786  CB  VAL   247      27.009  64.179  72.855  1.00  1.50           386
ATOM    787  N   ALA   248      27.689  63.646  75.835  1.00  1.50           386
ATOM    788  CA  ALA   248      28.365  62.776  76.789  1.00  1.50           386
ATOM    789  C   ALA   248      27.657  62.543  78.136  1.00  1.50           386
ATOM    790  O   ALA   248      27.669  61.423  78.623  1.00  1.50           386
ATOM    791  CB  ALA   248      29.849  63.158  76.920  1.00  1.50           386
ATOM    792  N   LYS   249      27.048  63.576  78.719  1.00  1.50           386
ATOM    793  CA  LYS   249      26.227  63.394  79.918  1.00  1.50           386
ATOM    794  C   LYS   249      24.989  62.569  79.594  1.00  1.50           386
ATOM    795  O   LYS   249      24.482  61.844  80.454  1.00  1.50           386
ATOM    796  CB  LYS   249      25.829  64.726  80.552  1.00  1.50           386
ATOM    797  N   GLU   250      24.512  62.674  78.350  1.00  1.50           386
ATOM    798  CA  GLU   250      23.398  61.888  77.859  1.00  1.50           386
ATOM    799  C   GLU   250      23.711  60.410  77.734  1.00  1.50           386
ATOM    800  O   GLU   250      22.913  59.572  78.135  1.00  1.50           386
ATOM    801  CB  GLU   250      22.958  62.435  76.499  1.00  1.50           386
ATOM    802  N   GLY   251      24.854  60.083  77.135  1.00  1.50           386
ATOM    803  CA  GLY   251      25.360  58.712  77.072  1.00  1.50           386
ATOM    804  C   GLY   251      25.513  58.127  78.481  1.00  1.50           386
ATOM    805  O   GLY   251      25.113  56.998  78.726  1.00  1.50           386
ATOM    806  N   GLU   252      26.102  58.883  79.399  1.00  1.50           386
ATOM    807  CA  GLU   252      26.177  58.429  80.783  1.00  1.50           386
ATOM    808  C   GLU   252      24.812  58.138  81.414  1.00  1.50           386
ATOM    809  O   GLU   252      24.677  57.168  82.146  1.00  1.50           386
ATOM    810  CB  GLU   252      26.939  59.397  81.659  1.00  1.50           386
ATOM    811  N   THR   253      21.908  57.455  79.755  1.00  1.50           386
ATOM    812  CA  THR   253      21.403  56.313  79.014  1.00  1.50           386
ATOM    813  C   THR   253      21.906  54.971  79.557  1.00  1.50           386
ATOM    814  O   THR   253      21.129  54.013  79.698  1.00  1.50           386
ATOM    815  CB  THR   253      21.807  56.446  77.544  1.00  1.50           386
ATOM    816  N   TYR   254      23.206  54.899  79.837  1.00  1.50           386
ATOM    817  CA  TYR   254      23.844  53.686  80.369  1.00  1.50           386
ATOM    818  C   TYR   254      23.447  53.404  81.820  1.00  1.50           386
ATOM    819  O   TYR   254      23.486  52.248  82.280  1.00  1.50           386
ATOM    820  CB  TYR   254      25.391  53.717  80.184  1.00  1.50           386
ATOM    821  N   THR   255      23.068  54.462  82.532  1.00  1.50           386
ATOM    822  CA  THR   255      22.553  54.347  83.900  1.00  1.50           386
ATOM    823  C   THR   255      21.127  53.723  83.956  1.00  1.50           386
ATOM    824  O   THR   255      20.797  52.999  84.896  1.00  1.50           386
ATOM    825  CB  THR   255      22.592  55.742  84.518  1.00  1.50           386
ATOM    826  N   TYR   258      20.312  53.968  82.932  1.00  1.50           386
ATOM    827  CA  TYR   258      18.931  53.505  82.906  1.00  1.50           386
ATOM    828  C   TYR   258      18.864  52.003  83.045  1.00  1.50           386
ATOM    829  O   TYR   258      17.919  51.469  83.629  1.00  1.50           386
ATOM    830  CB  TYR   258      18.205  53.915  81.633  1.00  1.50           386
ATOM    831  N   ARG   259      19.865  51.297  82.533  1.00  1.50           386
ATOM    832  CA  ARG   259      19.772  49.838  82.627  1.00  1.50           386
ATOM    833  C   ARG   259      20.905  49.216  83.412  1.00  1.50           386
ATOM    834  O   ARG   259      21.200  48.051  83.218  1.00  1.50           386
ATOM    835  CB  ARG   259      19.546  49.148  81.251  1.00  1.50           386
ATOM    836  N   GLY   260      21.492  49.969  84.341  1.00  1.50           386
ATOM    837  CA  GLY   260      22.622  49.472  85.144  1.00  1.50           386
ATOM    838  C   GLY   260      22.966  50.383  86.309  1.00  1.50           386
ATOM    839  O   GLY   260      24.105  50.393  86.809  1.00  1.50           386
TER
END
