
#######################################################
#                                                     #
#                        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   31 (  132),  selected   31 , name T0386AL380_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   31 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_3-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         4.70    13.88
  LCS_AVERAGE:     16.01

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       228 - 237         1.60    24.63
  LCS_AVERAGE:      7.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       228 - 234         0.93    25.06
  LCS_AVERAGE:      5.38

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    5    7    8   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     F     229     F     229      7   10   13     4    5    7    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     M     230     M     230      7   10   13     4    5    7    9   10   10   10   11   11   11   12   13   14   15   18   19   19   21   22   24 
LCS_GDT     H     231     H     231      7   10   14     4    5    7    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     T     232     T     232      7   10   14     4    5    7    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     M     233     M     233      7   10   14     4    5    7    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     K     234     K     234      7   10   14     4    5    7    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     N     235     N     235      5   10   14     3    4    5    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     T     236     T     236      5   10   14     3    4    6    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     G     237     G     237      5   10   14     2    4    5    9   10   10   10   11   11   11   15   15   17   18   19   19   20   21   22   26 
LCS_GDT     R     238     R     238      4    6   14     0    4    5    5    6    8    9   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     N     239     N     239      4    6   14     3    4    5    6    7    9   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     V     240     V     240      4    6   14     3    4    5    5    6    9   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     N     241     N     241      4    6   14     3    4    5    6    7    9   10   11   11   11   13   15   17   18   19   19   20   21   23   26 
LCS_GDT     D     242     D     242      3    6   14     3    3    5    6    7    9   10   11   11   11   13   15   17   18   19   19   20   21   23   26 
LCS_GDT     R     243     R     243      3    6   14     3    3    4    4    6    9   10   11   11   11   13   14   15   18   19   19   20   21   23   26 
LCS_GDT     M     246     M     246      3    4   14     0    3    3    3    6    6    7    7    8   10   11   12   14   15   18   19   19   21   23   26 
LCS_GDT     V     247     V     247      3    4   12     3    3    3    4    6    6    7    7    8    9   11   13   14   15   18   19   19   20   22   26 
LCS_GDT     A     248     A     248      3    4   11     3    3    3    4    6    6    7    7    8    9   11   13   14   15   18   19   19   21   23   26 
LCS_GDT     K     249     K     249      4    5   12     3    4    4    4    6    6    7    7    8    9   11   13   14   15   18   19   19   20   23   26 
LCS_GDT     E     250     E     250      4    5   12     3    4    4    4    5    5    5    6    7    8   10   10   11   14   17   18   18   19   20   21 
LCS_GDT     G     251     G     251      4    5   12     3    4    4    4    5    5    5    6    7    8   10   10   11   12   17   17   17   17   19   21 
LCS_GDT     E     252     E     252      4    5   12     3    4    4    4    6    6    7    7    7    9   10   12   14   15   18   19   19   21   23   26 
LCS_GDT     T     253     T     253      3    5   12     0    3    3    3    5    6    7    7    8    9   11   13   14   15   18   19   20   21   23   26 
LCS_GDT     Y     254     Y     254      3    3   12     0    3    3    4    6    6    7    7    7    9   11   13   14   15   18   19   20   21   23   26 
LCS_GDT     T     255     T     255      3    4   12     0    3    3    4    4    6    6    6    7    9   10   12   14   15   19   19   20   21   23   26 
LCS_GDT     G     256     G     256      3    4   12     0    3    4    5    7    9   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     T     257     T     257      3    4   12     3    3    4    6    7    9   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     Y     258     Y     258      3    4   12     3    3    4    6    7    9   10   11   11   11   15   15   17   18   19   19   20   21   23   26 
LCS_GDT     R     259     R     259      3    3   12     3    3    3    3    4    4    5    6    7    7   10   13   14   16   18   19   20   21   22   22 
LCS_GDT     G     260     G     260      3    3   12     3    3    3    3    3    3    5    6    7    7    9   10   11   12   13   13   18   20   22   22 
LCS_AVERAGE  LCS_A:   9.76  (   5.38    7.89   16.01 )

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      7      9     10     10     10     11     11     11     15     15     17     18     19     19     20     21     23     26 
GDT PERCENT_CA   4.94   6.17   8.64  11.11  12.35  12.35  12.35  13.58  13.58  13.58  18.52  18.52  20.99  22.22  23.46  23.46  24.69  25.93  28.40  32.10
GDT RMS_LOCAL    0.09   0.45   0.93   1.44   1.60   1.60   1.60   2.47   2.24   2.24   4.02   4.02   4.67   4.92   5.15   5.11   5.35   5.61   7.55   7.85
GDT RMS_ALL_CA  25.71  24.26  25.06  24.60  24.63  24.63  24.63  11.76  23.34  23.34  12.78  12.78  11.59  11.13  11.02  11.36  11.21  11.33   9.15   9.15

#      Molecule1      Molecule2       DISTANCE
LGA    E     228      E     228          2.822
LGA    F     229      F     229          1.285
LGA    M     230      M     230          3.771
LGA    H     231      H     231          1.872
LGA    T     232      T     232          0.627
LGA    M     233      M     233          3.291
LGA    K     234      K     234          2.180
LGA    N     235      N     235          3.043
LGA    T     236      T     236          3.514
LGA    G     237      G     237          1.833
LGA    R     238      R     238          3.344
LGA    N     239      N     239          8.705
LGA    V     240      V     240         11.768
LGA    N     241      N     241         18.437
LGA    D     242      D     242         19.695
LGA    R     243      R     243         23.476
LGA    M     246      M     246         30.010
LGA    V     247      V     247         27.994
LGA    A     248      A     248         29.961
LGA    K     249      K     249         36.496
LGA    E     250      E     250         38.272
LGA    G     251      G     251         36.143
LGA    E     252      E     252         34.601
LGA    T     253      T     253         35.133
LGA    Y     254      Y     254         30.171
LGA    T     255      T     255         25.423
LGA    G     256      G     256         24.792
LGA    T     257      T     257         23.610
LGA    Y     258      Y     258         18.377
LGA    R     259      R     259         16.489
LGA    G     260      G     260         17.451

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   81    4.0     11    2.24    13.580    12.335     0.470

LGA_LOCAL      RMSD =  2.239  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 21.502  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  9.040  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.627129 * X  +   0.154946 * Y  +   0.763349 * Z  +  24.087055
  Y_new =   0.692727 * X  +   0.337146 * Y  +  -0.637544 * Z  +  63.093887
  Z_new =  -0.356145 * X  +   0.928614 * Y  +   0.104098 * Z  +  22.739624 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.459162   -1.682431  [ DEG:    83.6038    -96.3962 ]
  Theta =   0.364139    2.777453  [ DEG:    20.8636    159.1364 ]
  Phi   =   0.835058   -2.306534  [ DEG:    47.8453   -132.1547 ]
 
# 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_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_3-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   81   4.0   11   2.24  12.335     9.04
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_3-D2
REMARK Aligment from pdb entry: 2g03A
ATOM    569  N   GLU   228       9.608  68.907  80.864  1.00  0.00              
ATOM    570  CA  GLU   228      11.026  69.215  80.884  1.00  0.00              
ATOM    571  C   GLU   228      11.708  68.988  79.525  1.00  0.00              
ATOM    572  O   GLU   228      12.528  69.800  79.088  1.00  0.00              
ATOM    573  N   PHE   229      11.412  67.879  78.862  1.00  0.00              
ATOM    574  CA  PHE   229      11.977  67.644  77.511  1.00  0.00              
ATOM    575  C   PHE   229      11.554  68.699  76.503  1.00  0.00              
ATOM    576  O   PHE   229      12.384  69.175  75.738  1.00  0.00              
ATOM    577  N  AMET   230      10.260  69.041  76.486  1.00  0.00              
ATOM    578  N  BMET   230      10.283  69.088  76.525  1.00  0.00              
ATOM    579  CA AMET   230       9.732  70.109  75.627  1.00  0.00              
ATOM    580  CA BMET   230       9.801  70.086  75.582  1.00  0.00              
ATOM    581  C  AMET   230      10.566  71.366  75.862  1.00  0.00              
ATOM    582  C  BMET   230      10.331  71.490  75.862  1.00  0.00              
ATOM    583  O  AMET   230      11.182  71.912  74.938  1.00  0.00              
ATOM    584  O  BMET   230      10.500  72.286  74.941  1.00  0.00              
ATOM    585  N   HIS   231      10.640  71.783  77.124  1.00  0.00              
ATOM    586  CA  HIS   231      11.225  73.065  77.470  1.00  0.00              
ATOM    587  C   HIS   231      12.706  73.108  77.158  1.00  0.00              
ATOM    588  O   HIS   231      13.186  74.091  76.641  1.00  0.00              
ATOM    589  N   THR   232      13.456  72.073  77.520  1.00  0.00              
ATOM    590  CA  THR   232      14.911  72.135  77.311  1.00  0.00              
ATOM    591  C   THR   232      15.310  71.924  75.843  1.00  0.00              
ATOM    592  O   THR   232      16.219  72.578  75.349  1.00  0.00              
ATOM    593  N   MET   233      14.608  71.039  75.144  1.00  0.00              
ATOM    594  CA  MET   233      14.886  70.763  73.748  1.00  0.00              
ATOM    595  C   MET   233      14.710  72.007  72.890  1.00  0.00              
ATOM    596  O   MET   233      15.455  72.222  71.955  1.00  0.00              
ATOM    597  N   LYS   234      13.692  72.805  73.203  1.00  0.00              
ATOM    598  CA  LYS   234      13.478  74.125  72.593  1.00  0.00              
ATOM    599  C   LYS   234      14.631  75.112  72.810  1.00  0.00              
ATOM    600  O   LYS   234      14.700  76.146  72.154  1.00  0.00              
ATOM    601  N   ASN   235      15.505  74.817  73.761  1.00  0.00              
ATOM    602  CA  ASN   235      16.447  75.812  74.198  1.00  0.00              
ATOM    603  C   ASN   235      17.883  75.298  74.223  1.00  0.00              
ATOM    604  O   ASN   235      18.695  75.804  74.973  1.00  0.00              
ATOM    605  N   THR   236      18.212  74.322  73.383  1.00  0.00              
ATOM    606  CA  THR   236      19.604  73.882  73.279  1.00  0.00              
ATOM    607  C   THR   236      20.328  74.832  72.350  1.00  0.00              
ATOM    608  O   THR   236      19.690  75.482  71.517  1.00  0.00              
ATOM    609  N   GLY   237      21.649  74.935  72.505  1.00  0.00              
ATOM    610  CA  GLY   237      22.486  75.689  71.579  1.00  0.00              
ATOM    611  C   GLY   237      23.749  74.881  71.369  1.00  0.00              
ATOM    612  O   GLY   237      24.211  74.225  72.288  1.00  0.00              
ATOM    613  N   ARG   238      24.326  74.906  70.173  1.00  0.00              
ATOM    614  CA  ARG   238      25.627  74.266  70.037  1.00  0.00              
ATOM    615  C   ARG   238      26.789  75.232  70.178  1.00  0.00              
ATOM    616  O   ARG   238      27.933  74.857  69.964  1.00  0.00              
ATOM    617  N   ASN   239      26.492  76.456  70.591  1.00  0.00              
ATOM    618  CA  ASN   239      27.534  77.453  70.821  1.00  0.00              
ATOM    619  C   ASN   239      28.000  77.307  72.283  1.00  0.00              
ATOM    620  O   ASN   239      27.760  78.184  73.105  1.00  0.00              
ATOM    621  N   VAL   240      28.671  76.195  72.586  1.00  0.00              
ATOM    622  CA  VAL   240      28.790  75.690  73.960  1.00  0.00              
ATOM    623  C   VAL   240      29.781  76.488  74.820  1.00  0.00              
ATOM    624  O   VAL   240      29.783  76.348  76.059  1.00  0.00              
ATOM    625  N   ASN   241      30.605  77.310  74.171  1.00  0.00              
ATOM    626  CA  ASN   241      31.671  78.039  74.850  1.00  0.00              
ATOM    627  C   ASN   241      31.510  79.548  74.727  1.00  0.00              
ATOM    628  O   ASN   241      32.422  80.301  75.030  1.00  0.00              
ATOM    629  N   ASP   242      30.345  79.977  74.280  1.00  0.00              
ATOM    630  CA  ASP   242      30.060  81.385  74.119  1.00  0.00              
ATOM    631  C   ASP   242      29.943  82.090  75.483  1.00  0.00              
ATOM    632  O   ASP   242      29.194  81.654  76.357  1.00  0.00              
ATOM    633  N   ARG   243      30.717  83.156  75.676  1.00  0.00              
ATOM    634  CA  ARG   243      30.729  83.879  76.947  1.00  0.00              
ATOM    635  C   ARG   243      29.330  84.353  77.400  1.00  0.00              
ATOM    636  O   ARG   243      28.997  84.248  78.576  1.00  0.00              
ATOM    637  N   MET   246      28.514  84.841  76.473  1.00  0.00              
ATOM    638  CA  MET   246      27.202  85.361  76.820  1.00  0.00              
ATOM    639  C   MET   246      26.238  84.253  77.266  1.00  0.00              
ATOM    640  O   MET   246      25.500  84.407  78.255  1.00  0.00              
ATOM    641  N   VAL   247      26.250  83.131  76.547  1.00  0.00              
ATOM    642  CA  VAL   247      25.454  81.966  76.911  1.00  0.00              
ATOM    643  C   VAL   247      25.905  81.423  78.260  1.00  0.00              
ATOM    644  O   VAL   247      25.069  81.119  79.112  1.00  0.00              
ATOM    645  N   ALA   248      27.215  81.301  78.470  1.00  0.00              
ATOM    646  CA  ALA   248      27.711  80.810  79.759  1.00  0.00              
ATOM    647  C   ALA   248      27.290  81.763  80.912  1.00  0.00              
ATOM    648  O   ALA   248      26.609  81.359  81.848  1.00  0.00              
ATOM    649  N   LYS   249      27.646  83.032  80.817  1.00  0.00              
ATOM    650  CA  LYS   249      27.420  83.942  81.933  1.00  0.00              
ATOM    651  C   LYS   249      25.965  84.373  82.191  1.00  0.00              
ATOM    652  O   LYS   249      25.570  84.452  83.344  1.00  0.00              
ATOM    653  N   GLU   250      25.186  84.637  81.142  1.00  0.00              
ATOM    654  CA  GLU   250      23.756  84.901  81.308  1.00  0.00              
ATOM    655  C   GLU   250      23.038  83.651  81.798  1.00  0.00              
ATOM    656  O   GLU   250      22.034  83.750  82.509  1.00  0.00              
ATOM    657  N   GLY   251      23.561  82.480  81.426  1.00  0.00              
ATOM    658  CA  GLY   251      23.050  81.202  81.883  1.00  0.00              
ATOM    659  C   GLY   251      23.272  80.959  83.362  1.00  0.00              
ATOM    660  O   GLY   251      22.369  80.510  84.058  1.00  0.00              
ATOM    661  N   GLU   252      24.489  81.208  83.840  1.00  0.00              
ATOM    662  CA  GLU   252      24.814  81.162  85.265  1.00  0.00              
ATOM    663  C   GLU   252      23.915  82.120  86.056  1.00  0.00              
ATOM    664  O   GLU   252      23.389  81.753  87.097  1.00  0.00              
ATOM    665  N   THR   253      23.750  83.345  85.575  1.00  0.00              
ATOM    666  CA  THR   253      22.820  84.266  86.219  1.00  0.00              
ATOM    667  C   THR   253      21.384  83.740  86.297  1.00  0.00              
ATOM    668  O   THR   253      20.721  83.933  87.306  1.00  0.00              
ATOM    669  N   TYR   254      20.906  83.096  85.236  1.00  0.00              
ATOM    670  CA  TYR   254      19.542  82.581  85.223  1.00  0.00              
ATOM    671  C   TYR   254      19.429  81.390  86.172  1.00  0.00              
ATOM    672  O   TYR   254      18.497  81.309  86.949  1.00  0.00              
ATOM    673  N   THR   255      20.398  80.478  86.114  1.00  0.00              
ATOM    674  CA  THR   255      20.477  79.339  87.011  1.00  0.00              
ATOM    675  C   THR   255      20.382  79.727  88.491  1.00  0.00              
ATOM    676  O   THR   255      19.667  79.079  89.272  1.00  0.00              
ATOM    677  N  AGLY   256      21.120  80.766  88.874  1.00  0.00              
ATOM    678  N  BGLY   256      21.125  80.755  88.857  1.00  0.00              
ATOM    679  CA AGLY   256      21.139  81.268  90.256  1.00  0.00              
ATOM    680  CA BGLY   256      21.156  81.253  90.212  1.00  0.00              
ATOM    681  C  AGLY   256      19.833  81.966  90.642  1.00  0.00              
ATOM    682  C  BGLY   256      19.804  81.860  90.607  1.00  0.00              
ATOM    683  O  AGLY   256      19.473  82.036  91.832  1.00  0.00              
ATOM    684  O  BGLY   256      19.399  81.781  91.775  1.00  0.00              
ATOM    685  N   THR   257      19.132  82.481  89.635  1.00  0.00              
ATOM    686  CA  THR   257      17.808  83.084  89.824  1.00  0.00              
ATOM    687  C   THR   257      16.705  82.028  90.133  1.00  0.00              
ATOM    688  O   THR   257      15.774  82.299  90.891  1.00  0.00              
ATOM    689  N   TYR   258      16.840  80.823  89.583  1.00  0.00              
ATOM    690  CA  TYR   258      15.836  79.779  89.733  1.00  0.00              
ATOM    691  C   TYR   258      15.601  79.465  91.192  1.00  0.00              
ATOM    692  O   TYR   258      14.484  79.125  91.587  1.00  0.00              
ATOM    693  N   ARG   259      16.632  79.590  92.018  1.00  0.00              
ATOM    694  CA  ARG   259      16.412  79.238  93.423  1.00  0.00              
ATOM    695  C   ARG   259      16.647  80.391  94.372  1.00  0.00              
ATOM    696  O   ARG   259      16.923  80.163  95.536  1.00  0.00              
ATOM    697  N   GLY   260      16.474  81.622  93.895  1.00  0.00              
ATOM    698  CA  GLY   260      16.702  82.817  94.725  1.00  0.00              
ATOM    699  C   GLY   260      16.200  84.094  94.076  1.00  0.00              
ATOM    700  O   GLY   260      16.676  85.204  94.377  1.00  0.00              
END
