
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0319AL381_5
# Molecule2: number of CA atoms  135 ( 1055),  selected   17 , name T0319.pdb
# PARAMETERS: T0319AL381_5.T0319.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:    16       103 - 118         4.79     6.26
  LCS_AVERAGE:     11.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       108 - 118         0.76     8.05
  LCS_AVERAGE:      6.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       108 - 118         0.76     8.05
  LCS_AVERAGE:      6.54

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:  135
LCS_GDT     Q     102     Q     102      5    6    8     3    4    5    5    6    6    6    6    6    7    7    7    7    7    8    8    9    9    9    9 
LCS_GDT     T     103     T     103      5    6   16     3    4    5    5    6    6    6    6    6    7    7    7    7    8    8   10   11   16   16   16 
LCS_GDT     S     104     S     104      5    6   16     3    4    5    5    6    6    6    6    6    7    7    7   11   15   15   15   15   16   16   16 
LCS_GDT     I     105     I     105      5    6   16     3    4    5    5    6    9   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     A     106     A     106      5    6   16     3    4    5    5    6    7    8    9    9   12   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     E     107     E     107      4    6   16     3    3    4    4    6    9   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     G     108     G     108     11   11   16     3    9   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     E     109     E     109     11   11   16     7   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     M     110     M     110     11   11   16     8   10   11   11   11   11   11   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     K     111     K     111     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     C     112     C     112     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     R     113     R     113     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     N     114     N     114     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     C     115     C     115     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     G     116     G     116     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     H     117     H     117     11   11   16     8   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_GDT     I     118     I     118     11   11   16     3   10   11   11   11   11   12   13   13   13   14   14   14   15   15   15   15   16   16   16 
LCS_AVERAGE  LCS_A:   8.29  (   6.54    6.84   11.50 )

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      8     10     11     11     11     11     12     13     13     13     14     14     14     15     15     15     15     16     16     16 
GDT PERCENT_CA   5.93   7.41   8.15   8.15   8.15   8.15   8.89   9.63   9.63   9.63  10.37  10.37  10.37  11.11  11.11  11.11  11.11  11.85  11.85  11.85
GDT RMS_LOCAL    0.34   0.51   0.76   0.76   0.76   0.76   2.33   2.43   2.43   2.43   3.03   3.03   3.03   3.83   3.83   3.83   3.83   4.79   4.79   4.79
GDT RMS_ALL_CA   8.78   8.49   8.05   8.05   8.05   8.05   6.79   6.85   6.85   6.85   6.66   6.66   6.66   6.50   6.50   6.50   6.50   6.26   6.26   6.26

#      Molecule1      Molecule2       DISTANCE
LGA    Q     102      Q     102         19.046
LGA    T     103      T     103         13.166
LGA    S     104      S     104         10.397
LGA    I     105      I     105          3.624
LGA    A     106      A     106          6.957
LGA    E     107      E     107          3.615
LGA    G     108      G     108          3.046
LGA    E     109      E     109          3.157
LGA    M     110      M     110          3.764
LGA    K     111      K     111          1.942
LGA    C     112      C     112          0.663
LGA    R     113      R     113          1.582
LGA    N     114      N     114          1.900
LGA    C     115      C     115          2.424
LGA    G     116      G     116          1.901
LGA    H     117      H     117          1.274
LGA    I     118      I     118          1.148

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  135    4.0     13    2.43     9.074     8.536     0.513

LGA_LOCAL      RMSD =  2.434  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.752  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  6.143  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.398813 * X  +   0.135215 * Y  +   0.907009 * Z  +  10.147050
  Y_new =   0.262034 * X  +   0.964635 * Y  +  -0.028589 * Z  +   8.279679
  Z_new =  -0.878798 * X  +   0.226266 * Y  +  -0.420140 * Z  +  15.272491 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.647583   -0.494009  [ DEG:   151.6953    -28.3047 ]
  Theta =   1.073338    2.068255  [ DEG:    61.4977    118.5023 ]
  Phi   =   2.560287   -0.581305  [ DEG:   146.6936    -33.3063 ]
 
# 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: T0319AL381_5                                  
REMARK     2: T0319.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_5.T0319.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  135   4.0   13   2.43   8.536     6.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_5
REMARK Aligment from pdb entry: 1pft
ATOM      1  N   GLN   102       9.865   2.814   9.418  1.00  0.00              
ATOM      2  CA  GLN   102      11.249   3.014   9.010  1.00  0.00              
ATOM      3  C   GLN   102      11.797   4.307   9.607  1.00  0.00              
ATOM      4  O   GLN   102      11.039   5.189  10.006  1.00  0.00              
ATOM      5  N   THR   103      13.113   4.336   9.789  1.00  0.00              
ATOM      6  CA  THR   103      13.764   5.396  10.546  1.00  0.00              
ATOM      7  C   THR   103      14.373   6.427   9.601  1.00  0.00              
ATOM      8  O   THR   103      14.449   6.205   8.394  1.00  0.00              
ATOM      9  N   SER   104      14.614   7.619  10.140  1.00  0.00              
ATOM     10  CA  SER   104      15.031   8.759   9.344  1.00  0.00              
ATOM     11  C   SER   104      16.095   9.570  10.111  1.00  0.00              
ATOM     12  O   SER   104      15.787  10.551  10.804  1.00  0.00              
ATOM     13  N   ILE   105      17.346   9.069  10.057  1.00  0.00              
ATOM     14  CA  ILE   105      18.459   9.610  10.878  1.00  0.00              
ATOM     15  C   ILE   105      18.759  11.084  10.602  1.00  0.00              
ATOM     16  O   ILE   105      19.580  11.694  11.285  1.00  0.00              
ATOM     17  N   ALA   106      18.285  11.544   9.448  1.00  0.00              
ATOM     18  CA  ALA   106      18.576  12.891   8.977  1.00  0.00              
ATOM     19  C   ALA   106      17.752  13.912   9.765  1.00  0.00              
ATOM     20  O   ALA   106      18.297  14.882  10.288  1.00  0.00              
ATOM     21  N   GLU   107      16.520  13.515  10.074  1.00  0.00              
ATOM     22  CA  GLU   107      15.620  14.353  10.849  1.00  0.00              
ATOM     23  C   GLU   107      15.547  13.863  12.293  1.00  0.00              
ATOM     24  O   GLU   107      15.095  14.585  13.180  1.00  0.00              
ATOM     25  N   GLY   108      15.843  12.581  12.474  1.00  0.00              
ATOM     26  CA  GLY   108      15.586  11.899  13.735  1.00  0.00              
ATOM     27  C   GLY   108      14.150  11.384  13.778  1.00  0.00              
ATOM     28  O   GLY   108      13.471  11.496  14.797  1.00  0.00              
ATOM     29  N   GLU   109      13.668  10.946  12.620  1.00  0.00              
ATOM     30  CA  GLU   109      12.251  10.653  12.438  1.00  0.00              
ATOM     31  C   GLU   109      12.038   9.144  12.332  1.00  0.00              
ATOM     32  O   GLU   109      12.957   8.404  11.984  1.00  0.00              
ATOM     33  N   MET   110      10.780   8.737  12.457  1.00  0.00              
ATOM     34  CA  MET   110      10.372   7.377  12.130  1.00  0.00              
ATOM     35  C   MET   110       9.012   7.385  11.438  1.00  0.00              
ATOM     36  O   MET   110       8.016   7.825  12.007  1.00  0.00              
ATOM     37  N   LYS   111       9.008   6.947  10.185  1.00  0.00              
ATOM     38  CA  LYS   111       7.847   7.102   9.321  1.00  0.00              
ATOM     39  C   LYS   111       7.190   5.739   9.082  1.00  0.00              
ATOM     40  O   LYS   111       7.833   4.703   9.242  1.00  0.00              
ATOM     41  N   CYS   112       6.015   5.781   8.466  1.00  0.00              
ATOM     42  CA  CYS   112       5.411   4.594   7.869  1.00  0.00              
ATOM     43  C   CYS   112       6.164   4.204   6.600  1.00  0.00              
ATOM     44  O   CYS   112       6.603   5.066   5.841  1.00  0.00              
ATOM     45  N   ARG   113       6.146   2.909   6.305  1.00  0.00              
ATOM     46  CA  ARG   113       6.666   2.397   5.047  1.00  0.00              
ATOM     47  C   ARG   113       5.522   2.137   4.066  1.00  0.00              
ATOM     48  O   ARG   113       5.638   1.292   3.180  1.00  0.00              
ATOM     49  N   ASN   114       4.358   2.685   4.406  1.00  0.00              
ATOM     50  CA  ASN   114       3.141   2.431   3.654  1.00  0.00              
ATOM     51  C   ASN   114       2.463   3.736   3.261  1.00  0.00              
ATOM     52  O   ASN   114       2.640   4.223   2.142  1.00  0.00              
ATOM     53  N   CYS   115       1.929   4.433   4.269  1.00  0.00              
ATOM     54  CA  CYS   115       1.095   5.600   4.005  1.00  0.00              
ATOM     55  C   CYS   115       1.925   6.873   3.911  1.00  0.00              
ATOM     56  O   CYS   115       1.384   7.955   3.664  1.00  0.00              
ATOM     57  N   GLY   116       3.164   6.780   4.403  1.00  0.00              
ATOM     58  CA  GLY   116       4.075   7.915   4.370  1.00  0.00              
ATOM     59  C   GLY   116       4.144   8.615   5.727  1.00  0.00              
ATOM     60  O   GLY   116       4.758   9.682   5.842  1.00  0.00              
ATOM     61  N   HIS   117       3.213   8.222   6.597  1.00  0.00              
ATOM     62  CA  HIS   117       2.963   8.939   7.839  1.00  0.00              
ATOM     63  C   HIS   117       4.169   8.816   8.770  1.00  0.00              
ATOM     64  O   HIS   117       4.473   7.722   9.248  1.00  0.00              
ATOM     65  N   ILE   118       4.652   9.970   9.225  1.00  0.00              
ATOM     66  CA  ILE   118       5.613  10.027  10.315  1.00  0.00              
ATOM     67  C   ILE   118       5.010   9.423  11.585  1.00  0.00              
ATOM     68  O   ILE   118       3.794   9.450  11.772  1.00  0.00              
END
