
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0386AL380_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   33 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_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:    14       231 - 246         4.79    12.79
  LCS_AVERAGE:     15.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       228 - 237         1.54    24.26
  LCS_AVERAGE:      7.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       228 - 234         0.78    24.77
  LCS_AVERAGE:      5.31

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:   81
LCS_GDT     E     228     E     228      7   10   13     4    6    7    8   10   10   10   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     F     229     F     229      7   10   13     4    6    7    9   10   10   10   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     M     230     M     230      7   10   13     4    6    7    9   10   10   10   11   11   11   11   14   14   15   18   18   21   21   22   25 
LCS_GDT     H     231     H     231      7   10   14     4    6    7    9   10   10   10   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     T     232     T     232      7   10   14     4    6    7    9   10   10   10   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     M     233     M     233      7   10   14     4    5    7    9   10   10   10   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     K     234     K     234      7   10   14     4    6    7    9   10   10   10   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     N     235     N     235      4   10   14     3    4    5    9   10   10   10   11   11   11   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     T     236     T     236      4   10   14     3    5    7    9   10   10   11   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     G     237     G     237      4   10   14     3    4    5    9   10   10   11   11   12   12   15   16   17   18   19   19   21   21   22   25 
LCS_GDT     R     238     R     238      4    6   14     0    4    4    6    7    8   11   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     N     239     N     239      4    6   14     3    4    5    6    7    9   11   11   11   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     V     240     V     240      4    6   14     3    4    4    6    7    9   11   11   11   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     N     241     N     241      4    6   14     3    4    5    6    7    9   11   11   11   12   14   16   17   18   19   19   21   22   23   25 
LCS_GDT     D     242     D     242      3    6   14     3    3    5    6    7    9   11   11   11   12   14   16   17   18   19   19   21   22   23   25 
LCS_GDT     R     243     R     243      3    6   14     3    4    4    5    7    9   11   11   11   12   14   15   17   18   19   19   21   22   23   25 
LCS_GDT     M     246     M     246      3    3   14     0    3    4    5    6    6    6    7    9   10   11   12   13   14   14   17   19   22   23   25 
LCS_GDT     V     247     V     247      3    3   12     1    3    4    5    6    6    6    6    7    8   10   12   13   15   16   17   19   19   21   25 
LCS_GDT     A     248     A     248      3    3   11     3    3    4    5    6    6    6    6    7    8   10   12   13   15   16   17   19   22   23   25 
LCS_GDT     K     249     K     249      4    5   12     3    4    4    4    5    5    6    6    7    8   10   12   13   15   16   17   19   21   23   25 
LCS_GDT     E     250     E     250      4    5   12     3    4    4    4    5    5    5    6    7    8   10   11   13   14   16   17   17   18   20   21 
LCS_GDT     G     251     G     251      4    5   12     3    4    4    4    5    5    6    6    7    8   10   10   13   14   15   15   16   18   18   20 
LCS_GDT     E     252     E     252      4    5   12     3    4    4    4    5    5    6    6    7    8   10   11   13   15   16   17   19   19   23   25 
LCS_GDT     T     253     T     253      3    5   12     0    3    3    3    5    5    6    6    7    8   10   12   13   15   16   17   21   22   23   25 
LCS_GDT     Y     254     Y     254      3    3   12     0    3    3    3    4    4    6    6    7    8   10   12   13   15   16   19   21   22   23   25 
LCS_GDT     T     255     T     255      3    4   12     0    3    3    3    6    6    6    6    7    8   10   12   13   15   16   19   21   22   23   25 
LCS_GDT     G     256     G     256      3    4   12     0    3    4    6    7    9   11   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     T     257     T     257      3    4   12     3    3    5    6    7    9   11   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     Y     258     Y     258      4    5   12     3    3    4    6    7    9   11   11   12   12   15   16   17   18   19   19   21   22   23   25 
LCS_GDT     R     259     R     259      4    5   12     3    3    4    4    5    6    6    6    6    8   10   11   15   18   19   19   21   21   22   22 
LCS_GDT     G     260     G     260      4    5   12     3    3    4    4    5    6    6    6    6    8   10   11   13   18   19   19   21   21   22   25 
LCS_GDT     A     261     A     261      4    5   11     0    3    4    4    5    6    6    6    6    8   10   11   13   14   15   15   17   19   22   22 
LCS_GDT     G     262     G     262      3    5   11     0    3    3    3    4    6    6    6    6    6   10   11   13   14   15   15   16   17   17   17 
LCS_AVERAGE  LCS_A:   9.68  (   5.31    7.86   15.86 )

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      6      7      9     10     10     11     11     12     12     15     16     17     18     19     19     21     22     23     25 
GDT PERCENT_CA   4.94   7.41   8.64  11.11  12.35  12.35  13.58  13.58  14.81  14.81  18.52  19.75  20.99  22.22  23.46  23.46  25.93  27.16  28.40  30.86
GDT RMS_LOCAL    0.13   0.68   0.78   1.39   1.54   1.54   2.33   2.33   3.11   2.90   3.99   4.40   4.54   4.72   4.93   4.93   5.50   6.98   7.22   7.55
GDT RMS_ALL_CA  25.32  24.83  24.77  24.25  24.26  24.26  12.23  12.23  13.82  11.78  12.84  11.65  11.35  11.54  11.72  11.72  11.78  10.05   9.98   9.87

#      Molecule1      Molecule2       DISTANCE
LGA    E     228      E     228          2.711
LGA    F     229      F     229          1.420
LGA    M     230      M     230          3.651
LGA    H     231      H     231          1.932
LGA    T     232      T     232          0.809
LGA    M     233      M     233          3.521
LGA    K     234      K     234          2.037
LGA    N     235      N     235          2.880
LGA    T     236      T     236          3.622
LGA    G     237      G     237          1.860
LGA    R     238      R     238          3.717
LGA    N     239      N     239          8.771
LGA    V     240      V     240         11.221
LGA    N     241      N     241         17.740
LGA    D     242      D     242         19.353
LGA    R     243      R     243         22.148
LGA    M     246      M     246         30.085
LGA    V     247      V     247         28.601
LGA    A     248      A     248         28.575
LGA    K     249      K     249         34.886
LGA    E     250      E     250         37.156
LGA    G     251      G     251         34.826
LGA    E     252      E     252         32.615
LGA    T     253      T     253         33.417
LGA    Y     254      Y     254         29.022
LGA    T     255      T     255         24.000
LGA    G     256      G     256         23.185
LGA    T     257      T     257         22.350
LGA    Y     258      Y     258         17.398
LGA    R     259      R     259         15.527
LGA    G     260      G     260         16.625
LGA    A     261      A     261         19.081
LGA    G     262      G     262         21.031

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   81    4.0     11    2.26    13.889    12.680     0.466

LGA_LOCAL      RMSD =  2.261  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 20.654  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  9.513  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.791947 * X  +  -0.325156 * Y  +   0.516812 * Z  +  43.381729
  Y_new =  -0.608824 * X  +  -0.484848 * Y  +   0.627898 * Z  +  94.664459
  Z_new =   0.046411 * X  +  -0.811909 * Y  +  -0.581936 * Z  + 163.387482 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.192676    0.948917  [ DEG:  -125.6311     54.3689 ]
  Theta =  -0.046427   -3.095165  [ DEG:    -2.6601   -177.3399 ]
  Phi   =  -0.655405    2.486187  [ DEG:   -37.5520    142.4480 ]
 
# 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: T0386AL380_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   81   4.0   11   2.26  12.680     9.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_1-D2
REMARK Aligment from pdb entry: 2f6sB
ATOM    541  N   GLU   228       9.447  68.788  80.843  1.00  0.00              
ATOM    542  CA  GLU   228      10.873  69.104  80.906  1.00  0.00              
ATOM    543  C   GLU   228      11.588  68.839  79.586  1.00  0.00              
ATOM    544  O   GLU   228      12.447  69.633  79.190  1.00  0.00              
ATOM    545  N   PHE   229      11.203  67.766  78.884  1.00  0.00              
ATOM    546  CA  PHE   229      11.751  67.494  77.557  1.00  0.00              
ATOM    547  C   PHE   229      11.507  68.654  76.610  1.00  0.00              
ATOM    548  O   PHE   229      12.441  69.148  75.960  1.00  0.00              
ATOM    549  N   MET   230      10.259  69.094  76.544  1.00  0.00              
ATOM    550  CA  MET   230       9.868  70.126  75.599  1.00  0.00              
ATOM    551  C   MET   230      10.592  71.402  75.937  1.00  0.00              
ATOM    552  O   MET   230      11.038  72.116  75.062  1.00  0.00              
ATOM    553  N   HIS   231      10.730  71.673  77.223  1.00  0.00              
ATOM    554  CA  HIS   231      11.315  72.913  77.666  1.00  0.00              
ATOM    555  C   HIS   231      12.821  72.971  77.400  1.00  0.00              
ATOM    556  O   HIS   231      13.335  73.999  76.957  1.00  0.00              
ATOM    557  N   THR   232      13.527  71.877  77.651  1.00  0.00              
ATOM    558  CA  THR   232      14.941  71.823  77.305  1.00  0.00              
ATOM    559  C   THR   232      15.149  71.804  75.799  1.00  0.00              
ATOM    560  O   THR   232      16.012  72.512  75.279  1.00  0.00              
ATOM    561  N   MET   233      14.335  71.035  75.081  1.00  0.00              
ATOM    562  CA  MET   233      14.514  70.943  73.635  1.00  0.00              
ATOM    563  C   MET   233      14.407  72.294  72.912  1.00  0.00              
ATOM    564  O   MET   233      15.124  72.536  71.947  1.00  0.00              
ATOM    565  N   LYS   234      13.532  73.168  73.398  1.00  0.00              
ATOM    566  CA  LYS   234      13.325  74.498  72.840  1.00  0.00              
ATOM    567  C   LYS   234      14.558  75.405  72.955  1.00  0.00              
ATOM    568  O   LYS   234      14.569  76.491  72.403  1.00  0.00              
ATOM    569  N   ASN   235      15.556  75.001  73.726  1.00  0.00              
ATOM    570  CA  ASN   235      16.603  75.926  74.128  1.00  0.00              
ATOM    571  C   ASN   235      17.992  75.308  74.126  1.00  0.00              
ATOM    572  O   ASN   235      18.793  75.558  75.023  1.00  0.00              
ATOM    573  N   THR   236      18.271  74.478  73.143  1.00  0.00              
ATOM    574  CA  THR   236      19.599  73.926  72.992  1.00  0.00              
ATOM    575  C   THR   236      20.443  74.903  72.191  1.00  0.00              
ATOM    576  O   THR   236      19.915  75.691  71.408  1.00  0.00              
ATOM    577  N   GLY   237      21.756  74.842  72.383  1.00  0.00              
ATOM    578  CA  GLY   237      22.694  75.658  71.610  1.00  0.00              
ATOM    579  C   GLY   237      23.898  74.818  71.230  1.00  0.00              
ATOM    580  O   GLY   237      24.269  73.901  71.965  1.00  0.00              
ATOM    581  N   ARG   238      24.498  75.145  70.089  1.00  0.00              
ATOM    582  CA  ARG   238      25.716  74.500  69.599  1.00  0.00              
ATOM    583  C   ARG   238      26.937  75.237  70.076  1.00  0.00              
ATOM    584  O   ARG   238      28.070  74.806  69.835  1.00  0.00              
ATOM    585  N   ASN   239      26.686  76.361  70.739  1.00  0.00              
ATOM    586  CA  ASN   239      27.732  77.245  71.223  1.00  0.00              
ATOM    587  C   ASN   239      28.257  76.721  72.551  1.00  0.00              
ATOM    588  O   ASN   239      28.094  77.297  73.617  1.00  0.00              
ATOM    589  N   VAL   240      28.941  75.609  72.426  1.00  0.00              
ATOM    590  CA  VAL   240      29.174  74.675  73.485  1.00  0.00              
ATOM    591  C   VAL   240      30.368  74.992  74.398  1.00  0.00              
ATOM    592  O   VAL   240      30.445  74.492  75.537  1.00  0.00              
ATOM    593  N   ASN   241      31.267  75.842  73.911  1.00  0.00              
ATOM    594  CA  ASN   241      32.531  76.128  74.579  1.00  0.00              
ATOM    595  C   ASN   241      32.693  77.577  74.953  1.00  0.00              
ATOM    596  O   ASN   241      33.685  77.938  75.586  1.00  0.00              
ATOM    597  N   ASP   242      31.746  78.411  74.538  1.00  0.00              
ATOM    598  CA  ASP   242      31.816  79.831  74.813  1.00  0.00              
ATOM    599  C   ASP   242      31.711  80.152  76.318  1.00  0.00              
ATOM    600  O   ASP   242      30.640  79.994  76.920  1.00  0.00              
ATOM    601  N   ARG   243      32.819  80.595  76.943  1.00  0.00              
ATOM    602  CA  ARG   243      32.808  80.831  78.401  1.00  0.00              
ATOM    603  C   ARG   243      31.653  81.720  78.907  1.00  0.00              
ATOM    604  O   ARG   243      30.997  81.356  79.900  1.00  0.00              
ATOM    605  N   MET   246      31.372  82.843  78.246  1.00  0.00              
ATOM    606  CA  MET   246      30.291  83.705  78.741  1.00  0.00              
ATOM    607  C   MET   246      28.875  83.110  78.576  1.00  0.00              
ATOM    608  O   MET   246      28.048  83.277  79.468  1.00  0.00              
ATOM    609  N   VAL   247      28.608  82.402  77.472  1.00  0.00              
ATOM    610  CA  VAL   247      27.361  81.648  77.329  1.00  0.00              
ATOM    611  C   VAL   247      27.190  80.670  78.509  1.00  0.00              
ATOM    612  O   VAL   247      26.143  80.642  79.177  1.00  0.00              
ATOM    613  N   ALA   248      28.240  79.899  78.783  1.00  0.00              
ATOM    614  CA  ALA   248      28.231  78.970  79.901  1.00  0.00              
ATOM    615  C   ALA   248      28.021  79.694  81.245  1.00  0.00              
ATOM    616  O   ALA   248      27.270  79.226  82.100  1.00  0.00              
ATOM    617  N   LYS   249      28.668  80.840  81.426  1.00  0.00              
ATOM    618  CA  LYS   249      28.563  81.559  82.694  1.00  0.00              
ATOM    619  C   LYS   249      27.175  82.160  82.887  1.00  0.00              
ATOM    620  O   LYS   249      26.640  82.101  83.986  1.00  0.00              
ATOM    621  N   GLU   250      26.578  82.687  81.820  1.00  0.00              
ATOM    622  CA  GLU   250      25.194  83.150  81.879  1.00  0.00              
ATOM    623  C   GLU   250      24.230  82.043  82.288  1.00  0.00              
ATOM    624  O   GLU   250      23.314  82.296  83.070  1.00  0.00              
ATOM    625  N   GLY   251      24.436  80.830  81.764  1.00  0.00              
ATOM    626  CA  GLY   251      23.635  79.667  82.141  1.00  0.00              
ATOM    627  C   GLY   251      23.803  79.265  83.612  1.00  0.00              
ATOM    628  O   GLY   251      22.827  78.916  84.295  1.00  0.00              
ATOM    629  N   GLU   252      25.030  79.324  84.117  1.00  0.00              
ATOM    630  CA  GLU   252      25.267  78.964  85.499  1.00  0.00              
ATOM    631  C   GLU   252      24.691  80.009  86.447  1.00  0.00              
ATOM    632  O   GLU   252      24.152  79.673  87.492  1.00  0.00              
ATOM    633  N   THR   253      24.789  81.269  86.061  1.00  0.00              
ATOM    634  CA  THR   253      24.167  82.332  86.828  1.00  0.00              
ATOM    635  C   THR   253      22.663  82.063  86.961  1.00  0.00              
ATOM    636  O   THR   253      22.109  82.133  88.065  1.00  0.00              
ATOM    637  N   TYR   254      22.017  81.713  85.851  1.00  0.00              
ATOM    638  CA  TYR   254      20.595  81.422  85.881  1.00  0.00              
ATOM    639  C   TYR   254      20.308  80.172  86.718  1.00  0.00              
ATOM    640  O   TYR   254      19.301  80.107  87.440  1.00  0.00              
ATOM    641  N   THR   255      21.195  79.183  86.611  1.00  0.00              
ATOM    642  CA  THR   255      21.063  77.949  87.363  1.00  0.00              
ATOM    643  C   THR   255      21.038  78.242  88.872  1.00  0.00              
ATOM    644  O   THR   255      20.288  77.619  89.619  1.00  0.00              
ATOM    645  N   GLY   256      21.850  79.201  89.308  1.00  0.00              
ATOM    646  CA  GLY   256      21.852  79.594  90.704  1.00  0.00              
ATOM    647  C   GLY   256      20.650  80.463  91.042  1.00  0.00              
ATOM    648  O   GLY   256      20.121  80.395  92.135  1.00  0.00              
ATOM    649  N   THR   257      20.209  81.273  90.100  1.00  0.00              
ATOM    650  CA  THR   257      18.983  82.029  90.295  1.00  0.00              
ATOM    651  C   THR   257      17.785  81.091  90.591  1.00  0.00              
ATOM    652  O   THR   257      16.902  81.444  91.374  1.00  0.00              
ATOM    653  N   TYR   258      17.771  79.896  89.986  1.00  0.00              
ATOM    654  CA  TYR   258      16.674  78.946  90.193  1.00  0.00              
ATOM    655  C   TYR   258      16.570  78.556  91.663  1.00  0.00              
ATOM    656  O   TYR   258      15.500  78.209  92.144  1.00  0.00              
ATOM    657  N   ARG   259      17.696  78.600  92.363  1.00  0.00              
ATOM    658  CA  ARG   259      17.758  78.242  93.764  1.00  0.00              
ATOM    659  C   ARG   259      17.401  79.419  94.693  1.00  0.00              
ATOM    660  O   ARG   259      17.312  79.242  95.903  1.00  0.00              
ATOM    661  N   GLY   260      17.209  80.612  94.137  1.00  0.00              
ATOM    662  CA  GLY   260      16.851  81.784  94.949  1.00  0.00              
ATOM    663  C   GLY   260      17.902  82.889  95.021  1.00  0.00              
ATOM    664  O   GLY   260      17.676  83.931  95.653  1.00  0.00              
ATOM    665  N   ALA   261      19.053  82.680  94.383  1.00  0.00              
ATOM    666  CA  ALA   261      20.114  83.693  94.396  1.00  0.00              
ATOM    667  C   ALA   261      19.951  84.749  93.280  1.00  0.00              
ATOM    668  O   ALA   261      20.194  84.456  92.098  1.00  0.00              
ATOM    669  N   GLY   262      19.563  85.972  93.661  1.00  0.00              
ATOM    670  CA  GLY   262      19.204  87.023  92.700  1.00  0.00              
ATOM    671  C   GLY   262      20.242  88.115  92.575  1.00  0.00              
ATOM    672  O   GLY   262      21.434  87.828  92.461  1.00  0.00              
END
