
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0301AL044_5-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   22 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_5-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:     9       206 - 217         3.78    12.91
  LCS_AVERAGE:      3.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       210 - 217         1.55    11.36
  LCS_AVERAGE:      2.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       212 - 216         0.91    10.95
  LONGEST_CONTINUOUS_SEGMENT:     5       213 - 217         0.66    11.42
  LCS_AVERAGE:      1.57

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    4    6     3    3    5    6    6    7    8   10   11   11   11   11   11   12   13   14   14   15   15   15 
LCS_GDT     G     195     G     195      3    4    6     3    3    3    3    4    4    4    4    5   10   10   11   11   11   13   14   14   15   15   15 
LCS_GDT     N     196     N     196      3    4    6     3    3    3    3    5    6    7    8    9   10   10   11   11   12   13   14   14   15   15   15 
LCS_GDT     L     197     L     197      3    4    6     0    3    3    3    4    4    4    4    5    5    5    5    7    7   13   13   13   14   14   14 
LCS_GDT     D     200     D     200      0    0    6     0    0    1    5    6    7    8    8   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     V     203     V     203      3    3    6     3    4    6    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     P     204     P     204      3    3    4     3    3    3    3    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     G     205     G     205      3    3    4     3    3    3    3    3    3    3    3    3    5   10   11   12   12   13   13   14   15   15   15 
LCS_GDT     V     206     V     206      0    0    9     0    0    0    0    0    0    3    3    3    9   10   10   11   11   13   13   13   14   14   14 
LCS_GDT     T     208     T     208      0    0    9     1    1    1    1    1    1    3    6    9   10   10   11   12   12   13   14   14   15   15   15 
LCS_GDT     K     210     K     210      0    7    9     1    1    1    5    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     T     212     T     212      5    7    9     3    4    5    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     M     213     M     213      5    7    9     3    4    6    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     I     214     I     214      5    7    9     3    4    6    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     N     215     N     215      5    7    9     3    4    6    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     A     216     A     216      5    7    9     3    4    6    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     G     217     G     217      5    7    9     3    4    6    6    7    8    9   10   11   11   11   11   12   12   13   14   14   15   15   15 
LCS_GDT     E     227     E     227      3    4    5     0    3    3    4    4    5    5    5    5    5    5    5    6    6    6    7    9    9   10   11 
LCS_GDT     I     228     I     228      3    4    5     0    3    4    4    4    5    5    5    5    5    5    7    7    8    9    9   11   11   13   14 
LCS_GDT     G     229     G     229      3    4    5     3    3    4    4    4    5    5    5    5    5    6    7    7    8    9    9   11   11   13   13 
LCS_GDT     Y     230     Y     230      3    4    5     3    3    4    4    4    5    5    5    5    5    6    7    7    8    9    9   11   12   13   14 
LCS_GDT     R     231     R     231      3    4    5     3    3    4    4    4    5    5    5    5    5    5    5    5    5    5    6    9    9   11   12 
LCS_AVERAGE  LCS_A:   2.46  (   1.57    2.24    3.57 )

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      4      6      6      7      8      9     10     11     11     11     11     12     12     13     14     14     15     15     15 
GDT PERCENT_CA   1.57   2.09   3.14   3.14   3.66   4.19   4.71   5.24   5.76   5.76   5.76   5.76   6.28   6.28   6.81   7.33   7.33   7.85   7.85   7.85
GDT RMS_LOCAL    0.00   0.41   0.88   0.88   1.40   1.73   2.05   2.38   2.75   2.75   2.75   2.75   4.08   3.69   4.14   4.84   4.68   5.19   5.19   5.19
GDT RMS_ALL_CA  22.16  11.49  11.21  11.21  10.95  10.81  10.61  10.73  10.73  10.73  10.73  10.73  10.33  10.76  10.91  10.71  10.68  10.51  10.51  10.51

#      Molecule1      Molecule2       DISTANCE
LGA    T     194      T     194          3.876
LGA    G     195      G     195          9.699
LGA    N     196      N     196         10.686
LGA    L     197      L     197         15.090
LGA    D     200      D     200          5.701
LGA    V     203      V     203          2.382
LGA    P     204      P     204          3.443
LGA    G     205      G     205          8.544
LGA    V     206      V     206         16.536
LGA    T     208      T     208          9.269
LGA    K     210      K     210          3.350
LGA    T     212      T     212          2.553
LGA    M     213      M     213          0.214
LGA    I     214      I     214          0.897
LGA    N     215      N     215          1.451
LGA    A     216      A     216          0.857
LGA    G     217      G     217          1.650
LGA    E     227      E     227         22.316
LGA    I     228      I     228         18.279
LGA    G     229      G     229         17.786
LGA    Y     230      Y     230         15.012
LGA    R     231      R     231         14.140

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  191    4.0     10    2.38     4.450     4.018     0.403

LGA_LOCAL      RMSD =  2.381  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.726  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  9.459  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.550454 * X  +   0.665712 * Y  +  -0.503814 * Z  + 131.134018
  Y_new =   0.711847 * X  +   0.058946 * Y  +  -0.699857 * Z  +  30.142849
  Z_new =  -0.436205 * X  +  -0.743877 * Y  +  -0.506332 * Z  +  83.701752 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.168428    0.973165  [ DEG:  -124.2418     55.7582 ]
  Theta =   0.451377    2.690216  [ DEG:    25.8620    154.1380 ]
  Phi   =   2.229029   -0.912564  [ DEG:   127.7139    -52.2861 ]
 
# 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_5-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_5-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  191   4.0   10   2.38   4.018     9.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_5-D2
REMARK Aligment from pdb entry: 1t6k_A
ATOM    281  N   THR   194     101.384  -1.165   2.812  1.00  0.00              
ATOM    282  CA  THR   194     102.623  -1.113   3.572  1.00  0.00              
ATOM    283  C   THR   194     103.225   0.299   3.497  1.00  0.00              
ATOM    284  O   THR   194     103.177   0.946   2.445  1.00  0.00              
ATOM    285  N   GLY   195     103.822   0.759   4.588  1.00  0.00              
ATOM    286  CA  GLY   195     104.481   2.067   4.576  1.00  0.00              
ATOM    287  C   GLY   195     105.729   2.037   3.642  1.00  0.00              
ATOM    288  O   GLY   195     106.022   3.002   2.879  1.00  0.00              
ATOM    289  N   ASN   196     106.478   0.949   3.740  1.00  0.00              
ATOM    290  CA  ASN   196     107.696   0.815   2.931  1.00  0.00              
ATOM    291  C   ASN   196     108.878   1.727   3.281  1.00  0.00              
ATOM    292  O   ASN   196     109.761   1.938   2.420  1.00  0.00              
ATOM    293  N   LEU   197     108.918   2.255   4.512  1.00  0.00              
ATOM    294  CA  LEU   197     110.034   2.994   5.053  1.00  0.00              
ATOM    295  C   LEU   197     110.298   2.463   6.447  1.00  0.00              
ATOM    296  O   LEU   197     110.499   3.238   7.362  1.00  0.00              
ATOM    297  N   ASP   200     110.361   1.148   6.596  1.00  0.00              
ATOM    298  CA  ASP   200     110.483   0.564   7.924  1.00  0.00              
ATOM    299  C   ASP   200     111.752   0.909   8.612  1.00  0.00              
ATOM    300  O   ASP   200     111.674   1.288   9.741  1.00  0.00              
ATOM    301  N   VAL   203     112.935   0.781   7.978  1.00  0.00              
ATOM    302  CA  VAL   203     114.132   0.997   8.752  1.00  0.00              
ATOM    303  C   VAL   203     114.225   2.473   9.218  1.00  0.00              
ATOM    304  O   VAL   203     114.675   2.736  10.310  1.00  0.00              
ATOM    305  N   PRO   204     113.771   3.392   8.385  1.00  0.00              
ATOM    306  CA  PRO   204     113.787   4.822   8.710  1.00  0.00              
ATOM    307  C   PRO   204     112.884   5.100   9.924  1.00  0.00              
ATOM    308  O   PRO   204     113.273   5.784  10.877  1.00  0.00              
ATOM    309  N   GLY   205     111.684   4.545   9.875  1.00  0.00              
ATOM    310  CA  GLY   205     110.692   4.809  10.930  1.00  0.00              
ATOM    311  C   GLY   205     111.152   4.176  12.229  1.00  0.00              
ATOM    312  O   GLY   205     111.190   4.827  13.238  1.00  0.00              
ATOM    313  N   VAL   206     103.878  -6.412  14.396  1.00  0.00              
ATOM    314  CA  VAL   206     102.999  -6.627  13.230  1.00  0.00              
ATOM    315  C   VAL   206     103.473  -5.753  12.055  1.00  0.00              
ATOM    316  O   VAL   206     104.249  -4.824  12.279  1.00  0.00              
ATOM    317  N   THR   208     103.049  -6.037  10.812  1.00  0.00              
ATOM    318  CA  THR   208     103.487  -5.264   9.637  1.00  0.00              
ATOM    319  C   THR   208     103.263  -3.758   9.802  1.00  0.00              
ATOM    320  O   THR   208     102.237  -3.357  10.313  1.00  0.00              
ATOM    321  N   LYS   210     104.228  -2.947   9.355  1.00  0.00              
ATOM    322  CA  LYS   210     104.075  -1.490   9.505  1.00  0.00              
ATOM    323  C   LYS   210     103.252  -1.002   8.321  1.00  0.00              
ATOM    324  O   LYS   210     103.747  -0.947   7.179  1.00  0.00              
ATOM    325  N   THR   212     102.003  -0.656   8.579  1.00  0.00              
ATOM    326  CA  THR   212     101.099  -0.324   7.496  1.00  0.00              
ATOM    327  C   THR   212     100.541   1.045   7.760  1.00  0.00              
ATOM    328  O   THR   212     100.377   1.432   8.910  1.00  0.00              
ATOM    329  N   MET   213     100.251   1.746   6.677  1.00  0.00              
ATOM    330  CA  MET   213      99.718   3.100   6.782  1.00  0.00              
ATOM    331  C   MET   213      98.294   3.112   6.268  1.00  0.00              
ATOM    332  O   MET   213      98.026   2.639   5.164  1.00  0.00              
ATOM    333  N   ILE   214      97.379   3.675   7.090  1.00  0.00              
ATOM    334  CA  ILE   214      95.948   3.696   6.802  1.00  0.00              
ATOM    335  C   ILE   214      95.497   5.080   6.462  1.00  0.00              
ATOM    336  O   ILE   214      96.011   6.054   7.049  1.00  0.00              
ATOM    337  N   ASN   215      94.536   5.165   5.543  1.00  0.00              
ATOM    338  CA  ASN   215      93.994   6.458   5.134  1.00  0.00              
ATOM    339  C   ASN   215      92.515   6.494   5.336  1.00  0.00              
ATOM    340  O   ASN   215      91.813   5.651   4.813  1.00  0.00              
ATOM    341  N   ALA   216      92.034   7.484   6.107  1.00  0.00              
ATOM    342  CA  ALA   216      90.606   7.775   6.168  1.00  0.00              
ATOM    343  C   ALA   216      90.313   9.294   6.208  1.00  0.00              
ATOM    344  O   ALA   216      89.335   9.709   6.805  1.00  0.00              
ATOM    345  N   GLY   217      91.148  10.074   5.533  1.00  0.00              
ATOM    346  CA  GLY   217      91.183  11.526   5.737  1.00  0.00              
ATOM    347  C   GLY   217      92.606  11.825   6.104  1.00  0.00              
ATOM    348  O   GLY   217      93.459  12.045   5.187  1.00  0.00              
ATOM    349  N   GLU   227      92.909  11.771   7.414  1.00  0.00              
ATOM    350  CA  GLU   227      94.287  11.718   7.848  1.00  0.00              
ATOM    351  C   GLU   227      94.888  10.348   7.451  1.00  0.00              
ATOM    352  O   GLU   227      94.157   9.483   6.963  1.00  0.00              
ATOM    353  N   ILE   228      96.198  10.215   7.614  1.00  0.00              
ATOM    354  CA  ILE   228      96.894   8.918   7.442  1.00  0.00              
ATOM    355  C   ILE   228      97.534   8.529   8.796  1.00  0.00              
ATOM    356  O   ILE   228      98.085   9.359   9.526  1.00  0.00              
ATOM    357  N   GLY   229      97.438   7.245   9.149  1.00  0.00              
ATOM    358  CA  GLY   229      97.983   6.752  10.416  1.00  0.00              
ATOM    359  C   GLY   229      98.761   5.462  10.152  1.00  0.00              
ATOM    360  O   GLY   229      98.208   4.560   9.498  1.00  0.00              
ATOM    361  N   TYR   230     100.009   5.439  10.614  1.00  0.00              
ATOM    362  CA  TYR   230     100.884   4.277  10.492  1.00  0.00              
ATOM    363  C   TYR   230     100.917   3.600  11.813  1.00  0.00              
ATOM    364  O   TYR   230     100.933   4.277  12.822  1.00  0.00              
ATOM    365  N   ARG   231     100.896   2.258  11.822  1.00  0.00              
ATOM    366  CA  ARG   231     100.897   1.493  13.065  1.00  0.00              
ATOM    367  C   ARG   231     102.124   0.676  13.265  1.00  0.00              
ATOM    368  O   ARG   231     102.509  -0.088  12.365  1.00  0.00              
END
