
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0301AL044_3-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   23 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_3-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:    12       194 - 214         4.15    12.53
  LCS_AVERAGE:      4.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       208 - 214         1.93    12.79
  LCS_AVERAGE:      2.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       210 - 214         0.73    18.13
  LCS_AVERAGE:      1.41

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     D     187     D     187      0    3    8     0    0    0    0    4    5    5    7    7    7    7    7    7    9   10   13   17   17   18   18 
LCS_GDT     G     189     G     189      4    4    8     3    3    4    4    4    5    5    7    7    7    7    7    8    9   10   15   17   17   18   18 
LCS_GDT     A     190     A     190      4    4    8     3    3    4    4    4    5    5    7    7    7    7    7    8    9   10   15   17   17   18   18 
LCS_GDT     I     191     I     191      4    4    8     3    3    4    4    4    5    6    7    7    7    7    7   11   11   12   15   17   17   18   18 
LCS_GDT     F     192     F     192      4    4    8     3    3    4    4    4    5    6    7    7    7    7    8   11   11   12   15   17   17   18   18 
LCS_GDT     P     193     P     193      3    3    8     3    3    3    3    4    5    6    7    7    7    7    8   11   11   12   15   17   17   18   18 
LCS_GDT     T     194     T     194      3    3   12     3    3    3    3    4    5    6    7    7    7    9    9   11   11   12   15   17   17   18   18 
LCS_GDT     D     200     D     200      0    0   12     0    2    5    5    5    8    8    9    9   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     V     203     V     203      0    3   12     0    1    3    4    6    7    8    9   10   10   11   11   11   11   12   14   17   17   18   18 
LCS_GDT     P     204     P     204      0    3   12     1    1    3    3    4    7    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     G     205     G     205      0    3   12     0    0    3    3    3    3    8    9   10   10   11   11   11   11   12   13   15   17   18   18 
LCS_GDT     T     208     T     208      0    7   12     1    3    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     F     209     F     209      0    7   12     0    2    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     K     210     K     210      5    7   12     3    5    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     A     211     A     211      5    7   12     3    5    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     T     212     T     212      5    7   12     3    5    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     M     213     M     213      5    7   12     3    5    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     I     214     I     214      5    7   12     0    5    5    5    7    8    8    9   10   10   11   11   11   11   12   15   17   17   18   18 
LCS_GDT     E     227     E     227      3    5    5     3    3    3    5    5    5    5    5    5    5    5    5    5    7   10   11   12   15   16   18 
LCS_GDT     I     228     I     228      3    5    5     3    3    3    5    5    5    5    5    5    5    5    5    8    9   10   13   13   15   16   18 
LCS_GDT     G     229     G     229      3    5    5     3    3    3    5    5    5    6    6    8    8    9   10   10   11   12   13   13   15   16   18 
LCS_GDT     Y     230     Y     230      3    5    5     3    3    3    5    5    5    6    7    8    8    9   10   10   11   12   13   13   15   16   18 
LCS_GDT     R     231     R     231      3    5    5     3    3    3    5    5    5    5    5    5    5    8   10   10   11   12   12   13   15   16   18 
LCS_AVERAGE  LCS_A:   2.94  (   1.41    2.46    4.94 )

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      3      5      5      5      7      8      8      9     10     10     11     11     11     11     12     15     17     17     18     18 
GDT PERCENT_CA   1.57   2.62   2.62   2.62   3.66   4.19   4.19   4.71   5.24   5.24   5.76   5.76   5.76   5.76   6.28   7.85   8.90   8.90   9.42   9.42
GDT RMS_LOCAL    0.09   0.73   0.73   0.73   1.93   2.13   2.13   2.52   2.84   2.84   3.25   3.25   3.25   3.25   4.15   6.36   6.88   6.79   7.04   7.04
GDT RMS_ALL_CA  17.98  18.13  18.13  18.13  12.79  13.40  13.40  12.22  12.41  12.41  12.50  12.50  12.50  12.50  12.53  11.57  11.66  11.21  11.59  11.59

#      Molecule1      Molecule2       DISTANCE
LGA    D     187      D     187         13.692
LGA    G     189      G     189         13.396
LGA    A     190      A     190         14.128
LGA    I     191      I     191         15.342
LGA    F     192      F     192         15.546
LGA    P     193      P     193         14.110
LGA    T     194      T     194         11.129
LGA    D     200      D     200          6.775
LGA    V     203      V     203          2.869
LGA    P     204      P     204          5.483
LGA    G     205      G     205          3.835
LGA    T     208      T     208          3.345
LGA    F     209      F     209          2.136
LGA    K     210      K     210          0.991
LGA    A     211      A     211          2.386
LGA    T     212      T     212          1.786
LGA    M     213      M     213          1.869
LGA    I     214      I     214          2.286
LGA    E     227      E     227         21.103
LGA    I     228      I     228         21.065
LGA    G     229      G     229         20.575
LGA    Y     230      Y     230         18.309
LGA    R     231      R     231         16.998

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  191    4.0      9    2.52     4.450     3.937     0.343

LGA_LOCAL      RMSD =  2.523  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.223  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  9.150  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.915832 * X  +  -0.198249 * Y  +  -0.349211 * Z  +  51.388493
  Y_new =   0.341288 * X  +   0.842521 * Y  +   0.416750 * Z  +   0.555824
  Z_new =   0.211598 * X  +  -0.500854 * Y  +   0.839268 * Z  +  -8.974292 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.538045    2.603548  [ DEG:   -30.8277    149.1723 ]
  Theta =  -0.213209   -2.928383  [ DEG:   -12.2160   -167.7840 ]
  Phi   =   0.356712   -2.784881  [ DEG:    20.4381   -159.5619 ]
 
# 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_3-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_3-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  191   4.0    9   2.52   3.937     9.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_3-D2
REMARK Aligment from pdb entry: 1s7j_A
ATOM    257  N   ASP   187      97.893   0.070   4.813  1.00  0.00              
ATOM    258  CA  ASP   187      98.768   0.437   3.724  1.00  0.00              
ATOM    259  C   ASP   187      99.922  -0.564   3.704  1.00  0.00              
ATOM    260  O   ASP   187     100.164  -1.260   4.706  1.00  0.00              
ATOM    261  N   GLY   189     100.556  -0.770   2.525  1.00  0.00              
ATOM    262  CA  GLY   189     101.671  -1.723   2.438  1.00  0.00              
ATOM    263  C   GLY   189     102.885  -1.220   3.240  1.00  0.00              
ATOM    264  O   GLY   189     103.218  -0.038   3.199  1.00  0.00              
ATOM    265  N   ALA   190     103.517  -2.129   3.987  1.00  0.00              
ATOM    266  CA  ALA   190     104.695  -1.777   4.789  1.00  0.00              
ATOM    267  C   ALA   190     105.971  -1.802   3.923  1.00  0.00              
ATOM    268  O   ALA   190     106.634  -2.844   3.800  1.00  0.00              
ATOM    269  N   ILE   191     106.291  -0.668   3.320  1.00  0.00              
ATOM    270  CA  ILE   191     107.474  -0.553   2.478  1.00  0.00              
ATOM    271  C   ILE   191     108.740  -0.544   3.333  1.00  0.00              
ATOM    272  O   ILE   191     108.764   0.050   4.423  1.00  0.00              
ATOM    273  N   PHE   192     109.803  -1.227   2.872  1.00  0.00              
ATOM    274  CA  PHE   192     111.060  -1.277   3.621  1.00  0.00              
ATOM    275  C   PHE   192     111.740   0.088   3.717  1.00  0.00              
ATOM    276  O   PHE   192     112.562   0.317   4.605  1.00  0.00              
ATOM    277  N   PRO   193     111.414   0.986   2.788  1.00  0.00              
ATOM    278  CA  PRO   193     111.984   2.328   2.799  1.00  0.00              
ATOM    279  C   PRO   193     111.405   3.113   3.978  1.00  0.00              
ATOM    280  O   PRO   193     111.924   4.171   4.352  1.00  0.00              
ATOM    281  N   THR   194     110.278   2.617   4.509  1.00  0.00              
ATOM    282  CA  THR   194     109.611   3.225   5.650  1.00  0.00              
ATOM    283  C   THR   194     110.419   2.913   6.903  1.00  0.00              
ATOM    284  O   THR   194     110.765   3.814   7.679  1.00  0.00              
ATOM    285  N   ASP   200     110.703   1.625   7.100  1.00  0.00              
ATOM    286  CA  ASP   200     111.483   1.148   8.239  1.00  0.00              
ATOM    287  C   ASP   200     112.918   1.701   8.200  1.00  0.00              
ATOM    288  O   ASP   200     113.605   1.749   9.223  1.00  0.00              
ATOM    289  N   VAL   203     113.370   2.058   7.003  1.00  0.00              
ATOM    290  CA  VAL   203     114.702   2.608   6.811  1.00  0.00              
ATOM    291  C   VAL   203     114.805   4.004   7.423  1.00  0.00              
ATOM    292  O   VAL   203     115.715   4.281   8.204  1.00  0.00              
ATOM    293  N   PRO   204     112.794   5.410   9.567  1.00  0.00              
ATOM    294  CA  PRO   204     112.501   5.346  11.008  1.00  0.00              
ATOM    295  C   PRO   204     113.642   4.728  11.782  1.00  0.00              
ATOM    296  O   PRO   204     113.894   5.098  12.935  1.00  0.00              
ATOM    297  N   GLY   205     114.295   3.750  11.165  1.00  0.00              
ATOM    298  CA  GLY   205     115.386   3.063  11.810  1.00  0.00              
ATOM    299  C   GLY   205     114.860   2.031  12.790  1.00  0.00              
ATOM    300  O   GLY   205     115.466   1.792  13.843  1.00  0.00              
ATOM    301  N   THR   208     113.733   1.412  12.453  1.00  0.00              
ATOM    302  CA  THR   208     113.139   0.397  13.316  1.00  0.00              
ATOM    303  C   THR   208     112.102  -0.414  12.552  1.00  0.00              
ATOM    304  O   THR   208     111.789  -0.105  11.391  1.00  0.00              
ATOM    305  N   PHE   209     111.596  -1.471  13.177  1.00  0.00              
ATOM    306  CA  PHE   209     110.593  -2.320  12.566  1.00  0.00              
ATOM    307  C   PHE   209     109.175  -1.763  12.727  1.00  0.00              
ATOM    308  O   PHE   209     108.739  -1.423  13.829  1.00  0.00              
ATOM    309  N   LYS   210     105.465  -2.709  12.563  1.00  0.00              
ATOM    310  CA  LYS   210     104.567  -3.862  12.647  1.00  0.00              
ATOM    311  C   LYS   210     103.292  -3.725  11.797  1.00  0.00              
ATOM    312  O   LYS   210     102.808  -4.710  11.227  1.00  0.00              
ATOM    313  N   ALA   211     102.740  -2.517  11.746  1.00  0.00              
ATOM    314  CA  ALA   211     101.523  -2.251  10.986  1.00  0.00              
ATOM    315  C   ALA   211     101.632  -0.887  10.307  1.00  0.00              
ATOM    316  O   ALA   211     102.341  -0.001  10.792  1.00  0.00              
ATOM    317  N   THR   212     100.955  -0.728   9.184  1.00  0.00              
ATOM    318  CA  THR   212     100.982   0.540   8.459  1.00  0.00              
ATOM    319  C   THR   212      99.574   0.921   8.012  1.00  0.00              
ATOM    320  O   THR   212      98.753   0.050   7.711  1.00  0.00              
ATOM    321  N   MET   213      99.285   2.225   8.030  1.00  0.00              
ATOM    322  CA  MET   213      97.980   2.752   7.641  1.00  0.00              
ATOM    323  C   MET   213      98.155   4.146   7.037  1.00  0.00              
ATOM    324  O   MET   213      99.235   4.739   7.129  1.00  0.00              
ATOM    325  N   ILE   214      97.107   4.661   6.399  1.00  0.00              
ATOM    326  CA  ILE   214      97.169   5.990   5.808  1.00  0.00              
ATOM    327  C   ILE   214      95.909   6.809   6.104  1.00  0.00              
ATOM    328  O   ILE   214      94.813   6.267   6.246  1.00  0.00              
ATOM    329  N   GLU   227      96.120   8.093   6.285  1.00  0.00              
ATOM    330  CA  GLU   227      95.060   9.038   6.552  1.00  0.00              
ATOM    331  C   GLU   227      95.637  10.312   6.004  1.00  0.00              
ATOM    332  O   GLU   227      96.093  10.340   4.841  1.00  0.00              
ATOM    333  N   ILE   228      95.638  11.376   6.781  1.00  0.00              
ATOM    334  CA  ILE   228      96.237  12.608   6.314  1.00  0.00              
ATOM    335  C   ILE   228      97.749  12.336   6.313  1.00  0.00              
ATOM    336  O   ILE   228      98.482  12.783   5.422  1.00  0.00              
ATOM    337  N   GLY   229      98.189  11.544   7.304  1.00  0.00              
ATOM    338  CA  GLY   229      99.594  11.173   7.474  1.00  0.00              
ATOM    339  C   GLY   229      99.781   9.678   7.482  1.00  0.00              
ATOM    340  O   GLY   229      98.851   8.917   7.757  1.00  0.00              
ATOM    341  N   TYR   230     101.013   9.246   7.229  1.00  0.00              
ATOM    342  CA  TYR   230     101.336   7.837   7.279  1.00  0.00              
ATOM    343  C   TYR   230     101.180   7.465   8.755  1.00  0.00              
ATOM    344  O   TYR   230     101.400   8.304   9.627  1.00  0.00              
ATOM    345  N   ARG   231     100.839   6.232   9.029  1.00  0.00              
ATOM    346  CA  ARG   231     100.576   5.810  10.391  1.00  0.00              
ATOM    347  C   ARG   231     101.228   4.457  10.659  1.00  0.00              
ATOM    348  O   ARG   231     100.705   3.423  10.257  1.00  0.00              
END
