
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0301AL044_4-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected   20 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_4-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:    13       200 - 217         4.95    11.73
  LCS_AVERAGE:      5.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       210 - 217         1.63    12.35
  LCS_AVERAGE:      2.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       212 - 217         0.94    13.26
  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     D     187     D     187      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    6    6 
LCS_GDT     T     194     T     194      0    0    3     0    0    0    0    1    1    1    2    3    3    5    6    9    9    9   11   13   13   14   14 
LCS_GDT     D     200     D     200      0    0   13     1    2    4    5    6    7    8    8    9   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     V     203     V     203      3    3   13     3    5    5    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     P     204     P     204      3    3   13     3    3    3    3    5    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     G     205     G     205      3    3   13     3    3    3    3    3    3    3    3    4    5    9   11   11   12   12   13   13   13   14   14 
LCS_GDT     V     206     V     206      0    0   13     0    0    0    0    0    0    4    4    7    8    9   10   10   10   11   13   13   13   14   14 
LCS_GDT     T     208     T     208      0    0   13     0    1    1    1    3    3    6    8   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     K     210     K     210      0    7   13     0    1    1    1    4    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     T     212     T     212      6    7   13     3    5    6    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     M     213     M     213      6    7   13     4    5    6    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     I     214     I     214      6    7   13     4    5    6    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     N     215     N     215      6    7   13     3    5    6    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     A     216     A     216      6    7   13     4    5    6    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     G     217     G     217      6    7   13     4    5    6    6    7    9    9    9   10   10   11   11   11   12   12   13   13   13   14   14 
LCS_GDT     E     227     E     227      3    5    5     3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    7    7   11   11   11 
LCS_GDT     I     228     I     228      3    5    5     3    3    3    4    4    5    5    5    5    5    5    6    7    8    9   10   10   11   11   13 
LCS_GDT     G     229     G     229      3    5    5     3    3    3    4    4    5    5    5    5    5    5    6    7    8    9   10   10   11   11   13 
LCS_GDT     Y     230     Y     230      3    5    5     0    3    3    4    4    5    5    5    5    5    5    5    7    7    9   10   10   11   12   13 
LCS_GDT     R     231     R     231      3    5    5     0    3    3    4    4    5    5    5    5    5    5    5    5    5    6    7    7    8   11   12 
LCS_AVERAGE  LCS_A:   2.97  (   1.57    2.17    5.16 )

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      6      6      7      9      9      9     10     10     11     11     11     12     12     13     13     13     14     14 
GDT PERCENT_CA   2.09   2.62   3.14   3.14   3.66   4.71   4.71   4.71   5.24   5.24   5.76   5.76   5.76   6.28   6.28   6.81   6.81   6.81   7.33   7.33
GDT RMS_LOCAL    0.26   0.53   0.94   0.94   1.47   2.18   2.18   2.18   2.88   2.63   3.32   3.32   3.32   3.88   3.88   4.95   4.95   4.95   5.55   5.55
GDT RMS_ALL_CA  13.64  13.15  13.26  13.26  11.95  11.71  11.71  11.71  11.60  11.77  11.64  11.64  11.64  11.52  11.52  11.73  11.73  11.73  11.88  11.88

#      Molecule1      Molecule2       DISTANCE
LGA    D     187      D     187         22.945
LGA    T     194      T     194         11.257
LGA    D     200      D     200          5.621
LGA    V     203      V     203          2.559
LGA    P     204      P     204          2.835
LGA    G     205      G     205          8.136
LGA    V     206      V     206         13.525
LGA    T     208      T     208          6.542
LGA    K     210      K     210          2.962
LGA    T     212      T     212          2.706
LGA    M     213      M     213          0.987
LGA    I     214      I     214          1.664
LGA    N     215      N     215          1.941
LGA    A     216      A     216          2.064
LGA    G     217      G     217          2.022
LGA    E     227      E     227         22.521
LGA    I     228      I     228         19.150
LGA    G     229      G     229         18.648
LGA    Y     230      Y     230         15.829
LGA    R     231      R     231         14.592

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  191    4.0      9    2.18     4.319     3.944     0.394

LGA_LOCAL      RMSD =  2.183  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.637  Number of atoms =   20 
Std_ALL_ATOMS  RMSD = 10.240  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.320722 * X  +   0.835016 * Y  +  -0.447085 * Z  +  74.144287
  Y_new =  -0.017462 * X  +  -0.466727 * Y  +  -0.884229 * Z  +  38.450844
  Z_new =  -0.947012 * X  +   0.291399 * Y  +  -0.135108 * Z  +  27.140989 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.004947   -1.136646  [ DEG:   114.8750    -65.1250 ]
  Theta =   1.243803    1.897790  [ DEG:    71.2647    108.7353 ]
  Phi   =  -0.054393    3.087199  [ DEG:    -3.1165    176.8835 ]
 
# 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_4-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_4-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  191   4.0    9   2.18   3.944    10.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_4-D2
REMARK Aligment from pdb entry: 1ym5_A
ATOM    277  N   ASP   187     112.255  -1.728   4.249  1.00  0.00              
ATOM    278  CA  ASP   187     113.151  -0.605   4.009  1.00  0.00              
ATOM    279  C   ASP   187     112.585   0.716   4.565  1.00  0.00              
ATOM    280  O   ASP   187     113.240   1.385   5.353  1.00  0.00              
ATOM    281  N   THR   194     111.357   1.049   4.163  1.00  0.00              
ATOM    282  CA  THR   194     110.597   2.144   4.796  1.00  0.00              
ATOM    283  C   THR   194     110.629   2.042   6.309  1.00  0.00              
ATOM    284  O   THR   194     110.878   3.036   7.000  1.00  0.00              
ATOM    285  N   ASP   200     110.419   0.832   6.826  1.00  0.00              
ATOM    286  CA  ASP   200     110.285   0.597   8.258  1.00  0.00              
ATOM    287  C   ASP   200     111.558   0.996   8.952  1.00  0.00              
ATOM    288  O   ASP   200     111.518   1.668   9.985  1.00  0.00              
ATOM    289  N   VAL   203     112.695   0.574   8.382  1.00  0.00              
ATOM    290  CA  VAL   203     114.009   0.722   9.040  1.00  0.00              
ATOM    291  C   VAL   203     114.406   2.187   9.082  1.00  0.00              
ATOM    292  O   VAL   203     114.974   2.675  10.064  1.00  0.00              
ATOM    293  N   PRO   204     114.085   2.880   8.001  1.00  0.00              
ATOM    294  CA  PRO   204     114.281   4.299   7.938  1.00  0.00              
ATOM    295  C   PRO   204     113.452   5.061   8.973  1.00  0.00              
ATOM    296  O   PRO   204     113.981   5.921   9.680  1.00  0.00              
ATOM    297  N   GLY   205     112.150   4.734   9.070  1.00  0.00              
ATOM    298  CA  GLY   205     111.306   5.370  10.087  1.00  0.00              
ATOM    299  C   GLY   205     111.798   5.118  11.476  1.00  0.00              
ATOM    300  O   GLY   205     111.730   5.996  12.337  1.00  0.00              
ATOM    301  N   VAL   206     106.372  -4.288  16.297  1.00  0.00              
ATOM    302  CA  VAL   206     105.608  -4.954  15.273  1.00  0.00              
ATOM    303  C   VAL   206     105.881  -4.185  14.021  1.00  0.00              
ATOM    304  O   VAL   206     106.343  -3.058  14.098  1.00  0.00              
ATOM    305  N   THR   208     105.642  -4.792  12.863  1.00  0.00              
ATOM    306  CA  THR   208     105.776  -4.022  11.634  1.00  0.00              
ATOM    307  C   THR   208     104.795  -2.866  11.527  1.00  0.00              
ATOM    308  O   THR   208     103.574  -3.127  11.501  1.00  0.00              
ATOM    309  N   LYS   210     105.306  -1.614  11.419  1.00  0.00              
ATOM    310  CA  LYS   210     104.421  -0.482  11.022  1.00  0.00              
ATOM    311  C   LYS   210     103.661  -0.765   9.773  1.00  0.00              
ATOM    312  O   LYS   210     104.039  -1.642   9.022  1.00  0.00              
ATOM    313  N   THR   212     102.620  -0.000   9.514  1.00  0.00              
ATOM    314  CA  THR   212     101.905  -0.156   8.266  1.00  0.00              
ATOM    315  C   THR   212     101.301   1.159   7.869  1.00  0.00              
ATOM    316  O   THR   212     101.257   2.091   8.676  1.00  0.00              
ATOM    317  N   MET   213     100.879   1.266   6.615  1.00  0.00              
ATOM    318  CA  MET   213     100.229   2.476   6.136  1.00  0.00              
ATOM    319  C   MET   213      98.705   2.358   6.342  1.00  0.00              
ATOM    320  O   MET   213      98.079   1.395   5.863  1.00  0.00              
ATOM    321  N   ILE   214      98.139   3.310   7.098  1.00  0.00              
ATOM    322  CA  ILE   214      96.697   3.413   7.352  1.00  0.00              
ATOM    323  C   ILE   214      96.097   4.652   6.698  1.00  0.00              
ATOM    324  O   ILE   214      96.565   5.765   6.842  1.00  0.00              
ATOM    325  N   ASN   215      95.074   4.387   5.901  1.00  0.00              
ATOM    326  CA  ASN   215      94.350   5.359   5.133  1.00  0.00              
ATOM    327  C   ASN   215      93.098   5.672   5.949  1.00  0.00              
ATOM    328  O   ASN   215      92.212   4.817   6.110  1.00  0.00              
ATOM    329  N   ALA   216      93.042   6.897   6.472  1.00  0.00              
ATOM    330  CA  ALA   216      92.048   7.257   7.477  1.00  0.00              
ATOM    331  C   ALA   216      91.628   8.686   7.204  1.00  0.00              
ATOM    332  O   ALA   216      91.201   9.410   8.084  1.00  0.00              
ATOM    333  N   GLY   217      91.693   9.070   5.938  1.00  0.00              
ATOM    334  CA  GLY   217      91.690  10.461   5.540  1.00  0.00              
ATOM    335  C   GLY   217      93.109  10.888   5.164  1.00  0.00              
ATOM    336  O   GLY   217      93.438  10.958   3.988  1.00  0.00              
ATOM    337  N   GLU   227      93.962  11.188   6.167  1.00  0.00              
ATOM    338  CA  GLU   227      95.386  11.334   5.970  1.00  0.00              
ATOM    339  C   GLU   227      96.061  10.018   5.775  1.00  0.00              
ATOM    340  O   GLU   227      95.515   8.967   6.143  1.00  0.00              
ATOM    341  N   ILE   228      97.277  10.064   5.226  1.00  0.00              
ATOM    342  CA  ILE   228      98.094   8.842   5.077  1.00  0.00              
ATOM    343  C   ILE   228      99.054   8.753   6.231  1.00  0.00              
ATOM    344  O   ILE   228     100.100   9.426   6.224  1.00  0.00              
ATOM    345  N   GLY   229      98.696   7.916   7.209  1.00  0.00              
ATOM    346  CA  GLY   229      99.434   7.789   8.452  1.00  0.00              
ATOM    347  C   GLY   229     100.189   6.451   8.468  1.00  0.00              
ATOM    348  O   GLY   229      99.629   5.395   8.187  1.00  0.00              
ATOM    349  N   TYR   230     101.452   6.484   8.852  1.00  0.00              
ATOM    350  CA  TYR   230     102.137   5.249   9.231  1.00  0.00              
ATOM    351  C   TYR   230     101.790   5.067  10.663  1.00  0.00              
ATOM    352  O   TYR   230     101.903   6.004  11.436  1.00  0.00              
ATOM    353  N   ARG   231     101.401   3.878  11.057  1.00  0.00              
ATOM    354  CA  ARG   231     101.274   3.585  12.466  1.00  0.00              
ATOM    355  C   ARG   231     102.408   2.677  12.920  1.00  0.00              
ATOM    356  O   ARG   231     102.686   1.687  12.274  1.00  0.00              
END
