
#######################################################
#                                                     #
#                        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   35 (  140),  selected   31 , name T0320AL044_5-D2
# Molecule2: number of CA atoms   73 (  604),  selected   31 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_5-D2.T0320_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       243 - 266         4.81    16.93
  LCS_AVERAGE:     14.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       245 - 251         1.79    17.61
  LCS_AVERAGE:      6.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       235 - 239         0.90    28.37
  LONGEST_CONTINUOUS_SEGMENT:     5       243 - 247         0.65    21.28
  LONGEST_CONTINUOUS_SEGMENT:     5       247 - 251         0.17    23.02
  LCS_AVERAGE:      4.90

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:   73
LCS_GDT     N     233     N     233      4    4   10     4    4    4    5    5    5    7    8   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     P     234     P     234      4    4   10     4    4    4    4    5    5    6    7   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     H     235     H     235      5    5   10     4    4    5    5    5    5    6    6    9   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     L     236     L     236      5    5   10     4    4    5    5    5    5    7    8   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     R     237     R     237      5    5   10     3    4    5    5    5    5    7    8   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     K     238     K     238      5    5   11     1    4    5    5    5    5    7    8   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     D     239     D     239      5    5   11     0    4    5    5    5    5    6    7   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     S     240     S     240      3    4   11     0    3    3    3    3    4    5    5    6    7    8   10   10   12   15   15   16   17   20   23 
LCS_GDT     N     241     N     241      3    4   11     0    3    3    3    3    4    5    5    6    7    8   10   12   13   15   15   16   17   20   23 
LCS_GDT     N     242     N     242      3    4   12     0    3    4    4    5    5    7    7    8    8    9   11   14   15   16   16   17   19   20   23 
LCS_GDT     P     243     P     243      5    6   13     4    5    5    5    6    8   10   11   11   11   12   13   14   15   16   16   17   17   19   21 
LCS_GDT     A     244     A     244      5    6   13     4    5    5    5    7    8   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     L     245     L     245      5    7   13     4    5    5    5    7    7   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     H     246     H     246      5    7   13     4    5    5    5    7    8   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     F     247     F     247      5    7   13     5    5    5    6    6    7   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     E     248     E     248      5    7   13     5    5    5    6    7    8   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     W     249     W     249      5    7   13     5    5    5    6    7    8   10   11   11   11   12   13   14   15   16   16   17   18   20   23 
LCS_GDT     E     250     E     250      5    7   13     5    5    5    6    7    8   10   11   11   11   12   13   14   15   16   16   17   17   18   22 
LCS_GDT     I     251     I     251      5    7   13     5    5    5    6    6    7   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     G     256     G     256      3    3   13     1    2    3    3    3    3    3    4    4    6    7    7    7    8    8   10   12   13   15   18 
LCS_GDT     R     263     R     263      3    3   13     1    2    3    6    6    7    9    9   10   11   12   13   13   15   16   16   17   18   19   22 
LCS_GDT     S     264     S     264      3    3   13     0    0    3    3    3    3    5    5    5    7    7    7   12   13   15   16   17   17   18   21 
LCS_GDT     A     266     A     266      3    3   13     1    2    3    3    3    3    5    5    6    7    7   11   13   15   16   16   17   18   19   22 
LCS_GDT     N     268     N     268      3    3    8     0    3    4    5    5    5    7    8   10   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     T     269     T     269      3    3    8     0    3    3    3    3    5    7    8   10   11   11   13   14   15   16   17   18   19   20   23 
LCS_GDT     S     270     S     270      3    3    8     1    3    4    5    5    8   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     P     271     P     271      3    3    8     3    3    3    4    7    8   10   11   11   11   12   13   14   15   16   17   18   19   20   23 
LCS_GDT     V     274     V     274      0    0    6     0    2    4    4    4    5    6    7   11   11   11   12   14   15   15   17   18   19   20   23 
LCS_GDT     V     275     V     275      0    3    6     1    1    2    2    3    3    3    3    4    4    7   10   12   13   13   15   16   17   20   23 
LCS_GDT     D     276     D     276      0    3    6     0    0    0    0    3    3    3    3    3    4    8    9   10   12   12   12   12   13   15   16 
LCS_GDT     F     280     F     280      0    3    5     0    1    2    2    3    3    3    4    5    7    8    9   10   12   12   12   14   14   15   17 
LCS_AVERAGE  LCS_A:   8.54  (   4.90    6.14   14.58 )

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      5      5      5      6      7      8     10     11     11     11     12     13     14     15     16     17     18     19     20     23 
GDT PERCENT_CA   6.85   6.85   6.85   8.22   9.59  10.96  13.70  15.07  15.07  15.07  16.44  17.81  19.18  20.55  21.92  23.29  24.66  26.03  27.40  31.51
GDT RMS_LOCAL    0.17   0.17   0.17   1.19   1.86   2.13   2.46   2.65   2.65   2.65   3.08   3.60   3.90   4.42   4.87   5.99   6.20   6.62   6.95   7.76
GDT RMS_ALL_CA  23.02  23.02  23.02  21.55  14.62  14.19  14.39  14.36  14.36  14.36  14.46  14.79  14.04  13.44  14.05  11.72  11.67  11.50  11.32  11.00

#      Molecule1      Molecule2       DISTANCE
LGA    N     233      N     233         24.333
LGA    P     234      P     234         27.218
LGA    H     235      H     235         22.872
LGA    L     236      L     236         22.293
LGA    R     237      R     237         22.627
LGA    K     238      K     238         22.634
LGA    D     239      D     239         23.663
LGA    S     240      S     240         15.538
LGA    N     241      N     241         12.408
LGA    N     242      N     242         10.372
LGA    P     243      P     243          3.419
LGA    A     244      A     244          2.161
LGA    L     245      L     245          2.651
LGA    H     246      H     246          1.026
LGA    F     247      F     247          3.932
LGA    E     248      E     248          2.187
LGA    W     249      W     249          1.644
LGA    E     250      E     250          2.256
LGA    I     251      I     251          3.294
LGA    G     256      G     256         11.073
LGA    R     263      R     263          8.460
LGA    S     264      S     264         11.438
LGA    A     266      A     266         10.036
LGA    N     268      N     268          6.529
LGA    T     269      T     269          8.048
LGA    S     270      S     270          3.612
LGA    P     271      P     271          1.077
LGA    V     274      V     274          6.748
LGA    V     275      V     275         16.070
LGA    D     276      D     276         22.480
LGA    F     280      F     280         23.114

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35   73    4.0     11    2.65    13.356    11.395     0.399

LGA_LOCAL      RMSD =  2.655  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.362  Number of atoms =   31 
Std_ALL_ATOMS  RMSD = 10.586  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.584680 * X  +   0.338216 * Y  +  -0.737400 * Z  + -20.151918
  Y_new =  -0.806232 * X  +   0.343319 * Y  +  -0.481790 * Z  +  61.069290
  Z_new =   0.090214 * X  +   0.876209 * Y  +   0.473412 * Z  + -34.175858 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.075434   -2.066159  [ DEG:    61.6178   -118.3822 ]
  Theta =  -0.090337   -3.051256  [ DEG:    -5.1759   -174.8241 ]
  Phi   =  -0.943357    2.198236  [ DEG:   -54.0503    125.9497 ]
 
# 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: T0320AL044_5-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_5-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35   73   4.0   11   2.65  11.395    10.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_5-D2
REMARK Aligment from pdb entry: 1wxe_A
ATOM    697  N   ASN   233       6.570  24.247  23.193  1.00  0.00              
ATOM    698  CA  ASN   233       5.479  25.145  22.824  1.00  0.00              
ATOM    699  C   ASN   233       6.124  26.158  21.889  1.00  0.00              
ATOM    700  O   ASN   233       7.340  26.358  21.945  1.00  0.00              
ATOM    701  N   PRO   234       5.320  26.811  21.055  1.00  0.00              
ATOM    702  CA  PRO   234       5.852  27.722  20.046  1.00  0.00              
ATOM    703  C   PRO   234       6.374  26.613  19.152  1.00  0.00              
ATOM    704  O   PRO   234       7.489  26.123  19.330  1.00  0.00              
ATOM    705  N   HIS   235       5.522  26.209  18.217  1.00  0.00              
ATOM    706  CA  HIS   235       5.754  25.092  17.311  1.00  0.00              
ATOM    707  C   HIS   235       4.955  24.037  18.052  1.00  0.00              
ATOM    708  O   HIS   235       5.522  23.125  18.649  1.00  0.00              
ATOM    709  N   LEU   236       3.635  24.200  18.052  1.00  0.00              
ATOM    710  CA  LEU   236       2.769  23.258  18.740  1.00  0.00              
ATOM    711  C   LEU   236       2.876  21.862  18.164  1.00  0.00              
ATOM    712  O   LEU   236       1.876  21.164  18.016  1.00  0.00              
ATOM    713  N   ARG   237       4.102  21.464  17.844  1.00  0.00              
ATOM    714  CA  ARG   237       4.395  20.157  17.270  1.00  0.00              
ATOM    715  C   ARG   237       5.749  19.681  17.798  1.00  0.00              
ATOM    716  O   ARG   237       6.564  20.489  18.237  1.00  0.00              
ATOM    717  N   LYS   238       5.984  18.374  17.759  1.00  0.00              
ATOM    718  CA  LYS   238       7.253  17.820  18.229  1.00  0.00              
ATOM    719  C   LYS   238       8.214  17.701  17.059  1.00  0.00              
ATOM    720  O   LYS   238       7.817  17.855  15.903  1.00  0.00              
ATOM    721  N   ASP   239       9.482  17.436  17.357  1.00  0.00              
ATOM    722  CA  ASP   239      10.470  17.274  16.301  1.00  0.00              
ATOM    723  C   ASP   239      10.148  16.051  15.450  1.00  0.00              
ATOM    724  O   ASP   239      10.480  16.013  14.266  1.00  0.00              
ATOM    725  N   SER   240       8.862  13.753  10.353  1.00  0.00              
ATOM    726  CA  SER   240       7.947  12.933   9.555  1.00  0.00              
ATOM    727  C   SER   240       7.416  13.743   8.376  1.00  0.00              
ATOM    728  O   SER   240       7.381  13.268   7.239  1.00  0.00              
ATOM    729  N   ASN   241       7.007  14.978   8.652  1.00  0.00              
ATOM    730  CA  ASN   241       6.485  15.860   7.611  1.00  0.00              
ATOM    731  C   ASN   241       7.540  16.031   6.521  1.00  0.00              
ATOM    732  O   ASN   241       7.247  15.890   5.326  1.00  0.00              
ATOM    733  N   ASN   242       8.767  16.335   6.941  1.00  0.00              
ATOM    734  CA  ASN   242       9.875  16.534   6.014  1.00  0.00              
ATOM    735  C   ASN   242      10.214  15.283   5.211  1.00  0.00              
ATOM    736  O   ASN   242      10.764  15.383   4.118  1.00  0.00              
ATOM    737  N   PRO   243       8.024  13.322   4.019  1.00  0.00              
ATOM    738  CA  PRO   243       6.895  13.076   3.135  1.00  0.00              
ATOM    739  C   PRO   243       5.825  12.146   3.671  1.00  0.00              
ATOM    740  O   PRO   243       4.987  11.646   2.913  1.00  0.00              
ATOM    741  N   ALA   244       5.840  11.916   4.977  1.00  0.00              
ATOM    742  CA  ALA   244       4.871  11.029   5.599  1.00  0.00              
ATOM    743  C   ALA   244       3.524  11.691   5.823  1.00  0.00              
ATOM    744  O   ALA   244       3.405  12.915   5.845  1.00  0.00              
ATOM    745  N   LEU   245       2.507  10.856   5.977  1.00  0.00              
ATOM    746  CA  LEU   245       1.152  11.317   6.212  1.00  0.00              
ATOM    747  C   LEU   245       1.033  11.615   7.704  1.00  0.00              
ATOM    748  O   LEU   245       1.192  10.724   8.534  1.00  0.00              
ATOM    749  N   HIS   246       0.784  12.873   8.044  1.00  0.00              
ATOM    750  CA  HIS   246       0.649  13.259   9.442  1.00  0.00              
ATOM    751  C   HIS   246      -0.753  13.813   9.662  1.00  0.00              
ATOM    752  O   HIS   246      -1.459  14.125   8.702  1.00  0.00              
ATOM    753  N   PHE   247      -1.187  13.916  10.927  1.00  0.00              
ATOM    754  CA  PHE   247      -2.529  14.452  11.187  1.00  0.00              
ATOM    755  C   PHE   247      -2.659  15.813  10.495  1.00  0.00              
ATOM    756  O   PHE   247      -1.709  16.595  10.471  1.00  0.00              
ATOM    757  N   GLU   248      -3.824  16.096   9.926  1.00  0.00              
ATOM    758  CA  GLU   248      -4.021  17.354   9.216  1.00  0.00              
ATOM    759  C   GLU   248      -3.788  18.592  10.076  1.00  0.00              
ATOM    760  O   GLU   248      -3.250  19.589   9.595  1.00  0.00              
ATOM    761  N   TRP   249      -4.190  18.537  11.342  1.00  0.00              
ATOM    762  CA  TRP   249      -4.000  19.680  12.235  1.00  0.00              
ATOM    763  C   TRP   249      -2.507  19.946  12.417  1.00  0.00              
ATOM    764  O   TRP   249      -2.080  21.092  12.558  1.00  0.00              
ATOM    765  N   GLU   250      -1.718  18.875  12.410  1.00  0.00              
ATOM    766  CA  GLU   250      -0.268  18.976  12.559  1.00  0.00              
ATOM    767  C   GLU   250       0.334  19.598  11.301  1.00  0.00              
ATOM    768  O   GLU   250       1.212  20.463  11.380  1.00  0.00              
ATOM    769  N   ILE   251      -0.142  19.154  10.141  1.00  0.00              
ATOM    770  CA  ILE   251       0.333  19.688   8.870  1.00  0.00              
ATOM    771  C   ILE   251       0.032  21.185   8.778  1.00  0.00              
ATOM    772  O   ILE   251       0.874  21.963   8.331  1.00  0.00              
ATOM    773  N   GLY   256      -1.165  21.587   9.205  1.00  0.00              
ATOM    774  CA  GLY   256      -1.550  22.996   9.155  1.00  0.00              
ATOM    775  C   GLY   256      -0.658  23.862  10.041  1.00  0.00              
ATOM    776  O   GLY   256      -0.304  24.978   9.669  1.00  0.00              
ATOM    777  N   ALA   259      -0.303  23.350  11.213  1.00  0.00              
ATOM    778  CA  ALA   259       0.544  24.096  12.139  1.00  0.00              
ATOM    779  C   ALA   259       1.921  24.326  11.528  1.00  0.00              
ATOM    780  O   ALA   259       2.430  25.448  11.514  1.00  0.00              
ATOM    781  N   GLU   260       1.738  26.733   8.697  1.00  0.00              
ATOM    782  CA  GLU   260       1.482  28.094   9.161  1.00  0.00              
ATOM    783  C   GLU   260       2.810  28.751   9.530  1.00  0.00              
ATOM    784  O   GLU   260       3.071  29.902   9.165  1.00  0.00              
ATOM    785  N   GLY   261       3.646  28.012  10.255  1.00  0.00              
ATOM    786  CA  GLY   261       4.957  28.507  10.658  1.00  0.00              
ATOM    787  C   GLY   261       5.816  28.793   9.433  1.00  0.00              
ATOM    788  O   GLY   261       6.511  29.805   9.371  1.00  0.00              
ATOM    789  N   GLU   262       5.774  27.885   8.465  1.00  0.00              
ATOM    790  CA  GLU   262       6.556  28.043   7.249  1.00  0.00              
ATOM    791  C   GLU   262       6.193  29.333   6.524  1.00  0.00              
ATOM    792  O   GLU   262       7.067  30.125   6.176  1.00  0.00              
ATOM    793  N   ARG   263       4.899  29.534   6.302  1.00  0.00              
ATOM    794  CA  ARG   263       4.408  30.719   5.612  1.00  0.00              
ATOM    795  C   ARG   263       4.714  31.997   6.387  1.00  0.00              
ATOM    796  O   ARG   263       5.111  33.012   5.813  1.00  0.00              
ATOM    797  N   SER   264       4.534  31.933   7.699  1.00  0.00              
ATOM    798  CA  SER   264       4.775  33.076   8.567  1.00  0.00              
ATOM    799  C   SER   264       6.231  33.532   8.601  1.00  0.00              
ATOM    800  O   SER   264       6.509  34.714   8.808  1.00  0.00              
ATOM    801  N   ALA   266       7.161  32.610   8.379  1.00  0.00              
ATOM    802  CA  ALA   266       8.577  32.952   8.453  1.00  0.00              
ATOM    803  C   ALA   266       9.376  32.988   7.152  1.00  0.00              
ATOM    804  O   ALA   266      10.599  32.871   7.175  1.00  0.00              
ATOM    805  N   ASN   268       8.703  33.168   6.022  1.00  0.00              
ATOM    806  CA  ASN   268       9.409  33.228   4.747  1.00  0.00              
ATOM    807  C   ASN   268      10.409  34.395   4.730  1.00  0.00              
ATOM    808  O   ASN   268      11.474  34.301   4.113  1.00  0.00              
ATOM    809  N   THR   269      10.080  35.485   5.418  1.00  0.00              
ATOM    810  CA  THR   269      10.977  36.640   5.457  1.00  0.00              
ATOM    811  C   THR   269      12.353  36.301   6.052  1.00  0.00              
ATOM    812  O   THR   269      13.341  36.982   5.773  1.00  0.00              
ATOM    813  N   SER   270      12.425  35.255   6.873  1.00  0.00              
ATOM    814  CA  SER   270      13.694  34.857   7.486  1.00  0.00              
ATOM    815  C   SER   270      14.595  34.065   6.539  1.00  0.00              
ATOM    816  O   SER   270      15.805  33.968   6.757  1.00  0.00              
ATOM    817  N   PRO   271      14.005  33.491   5.497  1.00  0.00              
ATOM    818  CA  PRO   271      14.763  32.679   4.555  1.00  0.00              
ATOM    819  C   PRO   271      15.066  33.388   3.233  1.00  0.00              
ATOM    820  O   PRO   271      15.542  32.759   2.289  1.00  0.00              
ATOM    821  N   VAL   274      14.797  34.691   3.181  1.00  0.00              
ATOM    822  CA  VAL   274      15.029  35.502   1.985  1.00  0.00              
ATOM    823  C   VAL   274      15.729  36.811   2.349  1.00  0.00              
ATOM    824  O   VAL   274      15.684  37.244   3.496  1.00  0.00              
ATOM    825  N   VAL   275      13.240  42.553   1.968  1.00  0.00              
ATOM    826  CA  VAL   275      12.172  42.785   1.003  1.00  0.00              
ATOM    827  C   VAL   275      12.283  44.115   0.257  1.00  0.00              
ATOM    828  O   VAL   275      12.528  45.157   0.861  1.00  0.00              
ATOM    829  N   ASP   276      10.755  46.538  -3.427  1.00  0.00              
ATOM    830  CA  ASP   276       9.566  46.801  -4.235  1.00  0.00              
ATOM    831  C   ASP   276       9.360  45.762  -5.334  1.00  0.00              
ATOM    832  O   ASP   276       8.280  45.671  -5.903  1.00  0.00              
ATOM    833  N   PHE   280      10.389  44.969  -5.618  1.00  0.00              
ATOM    834  CA  PHE   280      10.297  43.957  -6.667  1.00  0.00              
ATOM    835  C   PHE   280       9.727  42.619  -6.205  1.00  0.00              
ATOM    836  O   PHE   280       9.310  41.803  -7.031  1.00  0.00              
END
