
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0301AL044_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   27 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_2-D2.T0301_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:    20       194 - 218         4.78    11.28
  LONGEST_CONTINUOUS_SEGMENT:    20       195 - 219         4.97    11.14
  LCS_AVERAGE:      8.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       210 - 217         1.81    15.66
  LCS_AVERAGE:      2.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       212 - 216         0.66    17.44
  LCS_AVERAGE:      1.73

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:  191
LCS_GDT     T     194     T     194      3    5   20     2    3    3    4    4    7    8   12   13   15   16   19   19   20   20   20   21   21   21   21 
LCS_GDT     G     195     G     195      3    5   20     2    3    3    4    5    7    8   12   13   15   16   17   18   20   20   20   21   21   21   21 
LCS_GDT     N     196     N     196      3    5   20     0    3    3    4    5    7    8   12   13   15   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     L     197     L     197      4    5   20     4    5    5    5    6    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     V     198     V     198      4    5   20     4    5    5    5    6    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     D     199     D     199      4    5   20     4    5    5    5    6    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     D     200     D     200      4    5   20     4    5    5    5    6    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     V     203     V     203      3    5   20     0    3    4    4    5    5    8   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     P     204     P     204      3    5   20     3    3    4    4    5    5    8   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     G     205     G     205      3    5   20     3    3    4    4    5    5    6    9   13   14   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     V     206     V     206      3    5   20     3    3    4    4    5    5    8   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     T     208     T     208      0    5   20     0    2    4    4    6    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     K     210     K     210      0    7   20     2    5    5    5    7    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     T     212     T     212      5    7   20     4    4    5    5    7    7    8   11   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     M     213     M     213      5    7   20     4    4    5    5    7    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     I     214     I     214      5    7   20     4    4    5    5    7    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     N     215     N     215      5    7   20     4    4    5    5    7    7    9   12   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     A     216     A     216      5    7   20     3    4    5    5    7    7    8   10   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     G     217     G     217      3    7   20     3    3    4    5    7    7    8   11   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     I     218     I     218      3    4   20     3    3    3    5    6    6    8   11   13   16   17   19   19   20   20   20   21   21   21   21 
LCS_GDT     P     219     P     219      3    4   20     3    3    3    3    4    4    4    5    5    5    5    7   12   13   17   20   21   21   21   21 
LCS_GDT     T     220     T     220      3    4    6     3    3    3    3    4    4    4    5    5    5    5    5    6    6    7    7   11   13   15   16 
LCS_GDT     E     227     E     227      3    5    6     0    3    3    4    4    5    5    5    5    5    5    5    5    5    6    6    6    6    7    7 
LCS_GDT     I     228     I     228      3    5    6     1    3    3    4    4    5    5    5    5    5    5    5    5    7    7    9   10   11   14   15 
LCS_GDT     G     229     G     229      3    5    6     3    3    3    4    4    5    5    5    5    5    5    5    5    7    7    9   14   14   15   15 
LCS_GDT     Y     230     Y     230      3    5    6     3    3    3    4    4    5    5    5    5    6    8    8   11   12   12   12   14   14   16   16 
LCS_GDT     R     231     R     231      3    5    6     3    3    3    3    4    5    5    5    5    6    8   10   11   12   12   12   14   14   16   16 
LCS_AVERAGE  LCS_A:   4.47  (   1.73    2.83    8.84 )

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      5      5      7      7      9     12     13     16     17     19     19     20     20     20     21     21     21     21 
GDT PERCENT_CA   2.09   2.62   2.62   2.62   3.66   3.66   4.71   6.28   6.81   8.38   8.90   9.95   9.95  10.47  10.47  10.47  10.99  10.99  10.99  10.99
GDT RMS_LOCAL    0.25   0.51   0.51   0.51   1.81   1.81   2.49   3.47   3.63   3.99   4.16   4.58   4.58   4.78   4.78   4.78   5.04   5.04   5.04   5.04
GDT RMS_ALL_CA  17.26  13.55  13.55  13.55  15.66  15.66  14.20  15.04  14.59  11.60  11.50  11.29  11.29  11.28  11.28  11.28  11.13  11.13  11.13  11.13

#      Molecule1      Molecule2       DISTANCE
LGA    T     194      T     194          5.695
LGA    G     195      G     195          7.560
LGA    N     196      N     196          6.906
LGA    L     197      L     197          3.749
LGA    V     198      V     198          3.070
LGA    D     199      D     199          3.839
LGA    D     200      D     200          3.263
LGA    V     203      V     203          3.772
LGA    P     204      P     204          3.840
LGA    G     205      G     205          5.429
LGA    V     206      V     206          3.993
LGA    T     208      T     208          3.583
LGA    K     210      K     210          2.753
LGA    T     212      T     212          4.776
LGA    M     213      M     213          3.259
LGA    I     214      I     214          3.852
LGA    N     215      N     215          3.320
LGA    A     216      A     216          8.385
LGA    G     217      G     217          9.658
LGA    I     218      I     218         10.285
LGA    P     219      P     219         11.061
LGA    T     220      T     220         17.560
LGA    E     227      E     227         31.547
LGA    I     228      I     228         26.977
LGA    G     229      G     229         26.898
LGA    Y     230      Y     230         23.394
LGA    R     231      R     231         22.933

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  191    4.0     12    3.42     5.497     5.039     0.341

LGA_LOCAL      RMSD =  3.423  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.996  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  9.367  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.023133 * X  +   0.837516 * Y  +   0.545923 * Z  +  29.532698
  Y_new =  -0.962845 * X  +  -0.128301 * Y  +   0.237629 * Z  +  62.730370
  Z_new =   0.269061 * X  +  -0.531137 * Y  +   0.803430 * Z  + -47.075542 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.584129    2.557463  [ DEG:   -33.4682    146.5318 ]
  Theta =  -0.272418   -2.869175  [ DEG:   -15.6084   -164.3916 ]
  Phi   =  -1.546775    1.594817  [ DEG:   -88.6237     91.3763 ]
 
# 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: T0301AL044_2-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_2-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  191   4.0   12   3.42   5.039     9.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_2-D2
REMARK Aligment from pdb entry: 1tm0_A
ATOM    269  N   THR   194      95.537   3.041  -0.735  1.00  0.00              
ATOM    270  CA  THR   194      95.658   2.021   0.296  1.00  0.00              
ATOM    271  C   THR   194      95.202   2.569   1.645  1.00  0.00              
ATOM    272  O   THR   194      95.263   3.771   1.885  1.00  0.00              
ATOM    273  N   GLY   195      94.741   1.682   2.519  1.00  0.00              
ATOM    274  CA  GLY   195      94.283   2.065   3.853  1.00  0.00              
ATOM    275  C   GLY   195      94.821   1.074   4.878  1.00  0.00              
ATOM    276  O   GLY   195      94.709  -0.133   4.690  1.00  0.00              
ATOM    277  N   ASN   196      95.396   1.581   5.964  1.00  0.00              
ATOM    278  CA  ASN   196      95.942   0.711   7.004  1.00  0.00              
ATOM    279  C   ASN   196      96.722  -0.436   6.375  1.00  0.00              
ATOM    280  O   ASN   196      96.281  -1.584   6.401  1.00  0.00              
ATOM    281  N   LEU   197      97.872  -0.124   5.794  1.00  0.00              
ATOM    282  CA  LEU   197      98.697  -1.149   5.183  1.00  0.00              
ATOM    283  C   LEU   197     100.061  -1.121   5.851  1.00  0.00              
ATOM    284  O   LEU   197     100.585  -0.054   6.163  1.00  0.00              
ATOM    285  N   VAL   198     100.647  -2.299   6.099  1.00  0.00              
ATOM    286  CA  VAL   198     101.961  -2.352   6.741  1.00  0.00              
ATOM    287  C   VAL   198     102.978  -1.587   5.908  1.00  0.00              
ATOM    288  O   VAL   198     102.780  -1.393   4.711  1.00  0.00              
ATOM    289  N   ASP   199     104.062  -1.154   6.544  1.00  0.00              
ATOM    290  CA  ASP   199     105.105  -0.401   5.856  1.00  0.00              
ATOM    291  C   ASP   199     106.476  -0.635   6.491  1.00  0.00              
ATOM    292  O   ASP   199     106.770  -0.121   7.570  1.00  0.00              
ATOM    293  N   ASP   200     107.312  -1.417   5.812  1.00  0.00              
ATOM    294  CA  ASP   200     108.655  -1.733   6.297  1.00  0.00              
ATOM    295  C   ASP   200     109.588  -0.523   6.229  1.00  0.00              
ATOM    296  O   ASP   200     110.264  -0.295   5.225  1.00  0.00              
ATOM    297  N   VAL   203     109.623   0.249   7.310  1.00  0.00              
ATOM    298  CA  VAL   203     110.471   1.430   7.376  1.00  0.00              
ATOM    299  C   VAL   203     111.808   1.112   8.038  1.00  0.00              
ATOM    300  O   VAL   203     111.858   0.706   9.200  1.00  0.00              
ATOM    301  N   PRO   204     112.894   1.299   7.295  1.00  0.00              
ATOM    302  CA  PRO   204     114.223   1.029   7.825  1.00  0.00              
ATOM    303  C   PRO   204     114.514   1.924   9.029  1.00  0.00              
ATOM    304  O   PRO   204     115.507   1.729   9.728  1.00  0.00              
ATOM    305  N   GLY   205     113.646   2.905   9.269  1.00  0.00              
ATOM    306  CA  GLY   205     113.839   3.808  10.392  1.00  0.00              
ATOM    307  C   GLY   205     113.787   3.097  11.733  1.00  0.00              
ATOM    308  O   GLY   205     114.802   2.974  12.418  1.00  0.00              
ATOM    309  N   VAL   206     112.597   2.640  12.113  1.00  0.00              
ATOM    310  CA  VAL   206     112.411   1.923  13.368  1.00  0.00              
ATOM    311  C   VAL   206     111.029   1.286  13.406  1.00  0.00              
ATOM    312  O   VAL   206     110.023   1.945  13.156  1.00  0.00              
ATOM    313  N   THR   208     110.999  -0.007  13.715  1.00  0.00              
ATOM    314  CA  THR   208     109.744  -0.730  13.785  1.00  0.00              
ATOM    315  C   THR   208     108.974  -0.707  12.482  1.00  0.00              
ATOM    316  O   THR   208     109.468  -0.233  11.458  1.00  0.00              
ATOM    317  N   LYS   210     107.759  -1.241  12.518  1.00  0.00              
ATOM    318  CA  LYS   210     106.903  -1.265  11.343  1.00  0.00              
ATOM    319  C   LYS   210     105.608  -0.558  11.723  1.00  0.00              
ATOM    320  O   LYS   210     105.084  -0.768  12.820  1.00  0.00              
ATOM    321  N   THR   212     105.105   0.289  10.827  1.00  0.00              
ATOM    322  CA  THR   212     103.869   1.037  11.067  1.00  0.00              
ATOM    323  C   THR   212     102.909   0.902   9.895  1.00  0.00              
ATOM    324  O   THR   212     103.325   0.615   8.773  1.00  0.00              
ATOM    325  N   MET   213     101.623   1.114  10.154  1.00  0.00              
ATOM    326  CA  MET   213     100.617   1.027   9.104  1.00  0.00              
ATOM    327  C   MET   213     100.271   2.431   8.627  1.00  0.00              
ATOM    328  O   MET   213     100.152   3.344   9.439  1.00  0.00              
ATOM    329  N   ILE   214     100.113   2.601   7.317  1.00  0.00              
ATOM    330  CA  ILE   214      99.773   3.904   6.751  1.00  0.00              
ATOM    331  C   ILE   214      98.720   3.786   5.653  1.00  0.00              
ATOM    332  O   ILE   214      98.328   2.682   5.270  1.00  0.00              
ATOM    333  N   ASN   215      98.261   4.933   5.155  1.00  0.00              
ATOM    334  CA  ASN   215      97.266   4.980   4.085  1.00  0.00              
ATOM    335  C   ASN   215      97.685   5.966   2.995  1.00  0.00              
ATOM    336  O   ASN   215      98.195   7.043   3.295  1.00  0.00              
ATOM    337  N   ALA   216      97.482   5.589   1.733  1.00  0.00              
ATOM    338  CA  ALA   216      97.840   6.457   0.610  1.00  0.00              
ATOM    339  C   ALA   216      96.580   7.028  -0.026  1.00  0.00              
ATOM    340  O   ALA   216      95.598   6.319  -0.212  1.00  0.00              
ATOM    341  N   GLY   217      96.611   8.316  -0.348  1.00  0.00              
ATOM    342  CA  GLY   217      95.459   8.971  -0.958  1.00  0.00              
ATOM    343  C   GLY   217      95.866   9.947  -2.058  1.00  0.00              
ATOM    344  O   GLY   217      97.049  10.152  -2.306  1.00  0.00              
ATOM    345  N   ILE   218      94.874  10.539  -2.717  1.00  0.00              
ATOM    346  CA  ILE   218      95.112  11.505  -3.789  1.00  0.00              
ATOM    347  C   ILE   218      94.006  12.536  -3.820  1.00  0.00              
ATOM    348  O   ILE   218      92.847  12.203  -4.036  1.00  0.00              
ATOM    349  N   PRO   219      94.374  13.790  -3.600  1.00  0.00              
ATOM    350  CA  PRO   219      93.403  14.863  -3.615  1.00  0.00              
ATOM    351  C   PRO   219      94.035  16.031  -4.325  1.00  0.00              
ATOM    352  O   PRO   219      94.066  17.140  -3.810  1.00  0.00              
ATOM    353  N   THR   220      94.542  15.766  -5.524  1.00  0.00              
ATOM    354  CA  THR   220      95.201  16.796  -6.295  1.00  0.00              
ATOM    355  C   THR   220      96.663  16.417  -6.399  1.00  0.00              
ATOM    356  O   THR   220      97.381  16.885  -7.275  1.00  0.00              
ATOM    357  N   GLU   227      97.104  15.560  -5.487  1.00  0.00              
ATOM    358  CA  GLU   227      98.479  15.086  -5.477  1.00  0.00              
ATOM    359  C   GLU   227      98.539  13.802  -4.640  1.00  0.00              
ATOM    360  O   GLU   227      97.642  13.533  -3.828  1.00  0.00              
ATOM    361  N   ILE   228      99.584  13.007  -4.853  1.00  0.00              
ATOM    362  CA  ILE   228      99.743  11.744  -4.138  1.00  0.00              
ATOM    363  C   ILE   228     100.354  11.942  -2.765  1.00  0.00              
ATOM    364  O   ILE   228     101.407  12.549  -2.627  1.00  0.00              
ATOM    365  N   GLY   229      99.678  11.427  -1.747  1.00  0.00              
ATOM    366  CA  GLY   229     100.148  11.558  -0.381  1.00  0.00              
ATOM    367  C   GLY   229     100.103  10.227   0.324  1.00  0.00              
ATOM    368  O   GLY   229      99.412   9.294  -0.091  1.00  0.00              
ATOM    369  N   TYR   230     100.852  10.152   1.416  1.00  0.00              
ATOM    370  CA  TYR   230     100.893   8.965   2.246  1.00  0.00              
ATOM    371  C   TYR   230     100.682   9.513   3.658  1.00  0.00              
ATOM    372  O   TYR   230     101.580  10.113   4.248  1.00  0.00              
ATOM    373  N   ARG   231      99.460   9.347   4.164  1.00  0.00              
ATOM    374  CA  ARG   231      99.089   9.842   5.486  1.00  0.00              
ATOM    375  C   ARG   231      99.512   8.853   6.567  1.00  0.00              
ATOM    376  O   ARG   231      99.302   7.641   6.444  1.00  0.00              
END
