
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0298AL242_4-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected   15 , name T0298_D2.pdb
# PARAMETERS: T0298AL242_4-D2.T0298_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:    15       130 - 144         3.22     3.22
  LCS_AVERAGE:      8.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       132 - 144         0.89     3.98
  LCS_AVERAGE:      6.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       132 - 144         0.89     3.98
  LCS_AVERAGE:      6.06

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:  186
LCS_GDT     C     130     C     130      0    3   15     1    1    1    2    3    3    4    4    4    8    9   11   12   13   15   15   15   15   15   15 
LCS_GDT     A     131     A     131      0    3   15     0    0    0    0    3    3    8   10   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     V     132     V     132     13   13   15     3    5   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     A     133     A     133     13   13   15     5    8   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     A     134     A     134     13   13   15     6   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     E     135     E     135     13   13   15     6   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     136     L     136     13   13   15     6   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     C     137     C     137     13   13   15     6   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     E     138     E     138     13   13   15     5   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     V     139     V     139     13   13   15     6   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     140     L     140     13   13   15     6   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     A     141     A     141     13   13   15     5   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     P     142     P     142     13   13   15     3    5   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     143     L     143     13   13   15     5   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_GDT     L     144     L     144     13   13   15     5   10   13   13   13   13   13   13   13   14   14   14   14   14   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   6.80  (   6.06    6.27    8.06 )

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      6     10     13     13     13     13     13     13     13     14     14     14     14     14     15     15     15     15     15     15 
GDT PERCENT_CA   3.23   5.38   6.99   6.99   6.99   6.99   6.99   6.99   6.99   7.53   7.53   7.53   7.53   7.53   8.06   8.06   8.06   8.06   8.06   8.06
GDT RMS_LOCAL    0.28   0.63   0.89   0.89   0.89   0.89   0.89   0.89   0.89   2.29   2.29   2.29   2.29   2.29   3.22   3.22   3.22   3.22   3.22   3.22
GDT RMS_ALL_CA   3.93   4.10   3.98   3.98   3.98   3.98   3.98   3.98   3.98   3.39   3.39   3.39   3.39   3.39   3.22   3.22   3.22   3.22   3.22   3.22

#      Molecule1      Molecule2       DISTANCE
LGA    C     130      C     130         11.861
LGA    A     131      A     131          9.313
LGA    V     132      V     132          1.305
LGA    A     133      A     133          1.131
LGA    A     134      A     134          0.176
LGA    E     135      E     135          0.679
LGA    L     136      L     136          0.395
LGA    C     137      C     137          0.806
LGA    E     138      E     138          1.236
LGA    V     139      V     139          0.771
LGA    L     140      L     140          0.813
LGA    A     141      A     141          0.475
LGA    P     142      P     142          1.343
LGA    L     143      L     143          0.370
LGA    L     144      L     144          0.982

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  186    4.0     13    0.89     6.855     6.848     1.319

LGA_LOCAL      RMSD =  0.886  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.980  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  3.220  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.954193 * X  +   0.185624 * Y  +   0.234645 * Z  + -68.955063
  Y_new =  -0.162365 * X  +   0.980006 * Y  +  -0.115006 * Z  +  44.360874
  Z_new =  -0.251302 * X  +   0.071640 * Y  +   0.965254 * Z  +   0.321104 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.074083   -3.067510  [ DEG:     4.2446   -175.7554 ]
  Theta =   0.254025    2.887568  [ DEG:    14.5546    165.4454 ]
  Phi   =  -0.168545    2.973048  [ DEG:    -9.6569    170.3431 ]
 
# 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: T0298AL242_4-D2                               
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298AL242_4-D2.T0298_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  186   4.0   13   0.89   6.848     3.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0298AL242_4-D2
REMARK Aligment from pdb entry: 1brm_A
ATOM    505  N   CYS   130      -9.396  74.320  12.297  1.00  0.00              
ATOM    506  CA  CYS   130      -9.955  73.408  11.321  1.00  0.00              
ATOM    507  C   CYS   130      -9.424  72.021  11.632  1.00  0.00              
ATOM    508  O   CYS   130      -8.331  71.888  12.184  1.00  0.00              
ATOM    509  N   ALA   131     -10.175  70.984  11.279  1.00  0.00              
ATOM    510  CA  ALA   131      -9.724  69.635  11.572  1.00  0.00              
ATOM    511  C   ALA   131      -9.032  68.876  10.454  1.00  0.00              
ATOM    512  O   ALA   131      -8.655  69.440   9.427  1.00  0.00              
ATOM    513  N   VAL   132      -9.978  72.062   4.167  1.00  0.00              
ATOM    514  CA  VAL   132      -9.009  73.035   4.656  1.00  0.00              
ATOM    515  C   VAL   132      -9.547  74.440   4.963  1.00  0.00              
ATOM    516  O   VAL   132      -9.812  74.775   6.118  1.00  0.00              
ATOM    517  N   ALA   133      -9.716  75.245   3.919  1.00  0.00              
ATOM    518  CA  ALA   133     -10.154  76.630   4.054  1.00  0.00              
ATOM    519  C   ALA   133     -11.621  76.937   4.331  1.00  0.00              
ATOM    520  O   ALA   133     -11.922  77.733   5.216  1.00  0.00              
ATOM    521  N   ALA   134     -12.531  76.333   3.584  1.00  0.00              
ATOM    522  CA  ALA   134     -13.946  76.616   3.771  1.00  0.00              
ATOM    523  C   ALA   134     -14.376  76.799   5.221  1.00  0.00              
ATOM    524  O   ALA   134     -15.009  77.791   5.548  1.00  0.00              
ATOM    525  N   GLU   135     -14.025  75.854   6.111  1.00  0.00              
ATOM    526  CA  GLU   135     -14.434  76.011   7.516  1.00  0.00              
ATOM    527  C   GLU   135     -13.935  77.314   8.156  1.00  0.00              
ATOM    528  O   GLU   135     -14.626  77.910   8.983  1.00  0.00              
ATOM    529  N   LEU   136     -12.737  77.746   7.779  1.00  0.00              
ATOM    530  CA  LEU   136     -12.168  78.984   8.305  1.00  0.00              
ATOM    531  C   LEU   136     -12.989  80.175   7.798  1.00  0.00              
ATOM    532  O   LEU   136     -13.495  80.981   8.582  1.00  0.00              
ATOM    533  N   CYS   137     -13.121  80.260   6.480  1.00  0.00              
ATOM    534  CA  CYS   137     -13.870  81.325   5.822  1.00  0.00              
ATOM    535  C   CYS   137     -15.222  81.586   6.480  1.00  0.00              
ATOM    536  O   CYS   137     -15.620  82.736   6.655  1.00  0.00              
ATOM    537  N   GLU   138     -15.917  80.513   6.850  1.00  0.00              
ATOM    538  CA  GLU   138     -17.233  80.618   7.472  1.00  0.00              
ATOM    539  C   GLU   138     -17.176  80.973   8.953  1.00  0.00              
ATOM    540  O   GLU   138     -18.080  81.626   9.473  1.00  0.00              
ATOM    541  N   VAL   139     -16.129  80.535   9.642  1.00  0.00              
ATOM    542  CA  VAL   139     -16.005  80.859  11.057  1.00  0.00              
ATOM    543  C   VAL   139     -15.815  82.366  11.136  1.00  0.00              
ATOM    544  O   VAL   139     -16.424  83.039  11.965  1.00  0.00              
ATOM    545  N   LEU   140     -14.971  82.886  10.251  1.00  0.00              
ATOM    546  CA  LEU   140     -14.698  84.315  10.194  1.00  0.00              
ATOM    547  C   LEU   140     -15.991  85.089   9.959  1.00  0.00              
ATOM    548  O   LEU   140     -16.222  86.125  10.577  1.00  0.00              
ATOM    549  N   ALA   141     -16.835  84.586   9.066  1.00  0.00              
ATOM    550  CA  ALA   141     -18.097  85.249   8.777  1.00  0.00              
ATOM    551  C   ALA   141     -18.955  85.378  10.034  1.00  0.00              
ATOM    552  O   ALA   141     -19.593  86.408  10.258  1.00  0.00              
ATOM    553  N   PRO   142     -18.964  84.330  10.850  1.00  0.00              
ATOM    554  CA  PRO   142     -19.734  84.309  12.089  1.00  0.00              
ATOM    555  C   PRO   142     -19.291  85.397  13.063  1.00  0.00              
ATOM    556  O   PRO   142     -20.117  86.068  13.683  1.00  0.00              
ATOM    557  N   LEU   143     -17.978  85.559  13.193  1.00  0.00              
ATOM    558  CA  LEU   143     -17.399  86.535  14.108  1.00  0.00              
ATOM    559  C   LEU   143     -17.357  87.966  13.569  1.00  0.00              
ATOM    560  O   LEU   143     -17.223  88.916  14.342  1.00  0.00              
ATOM    561  N   LEU   144     -17.479  88.120  12.255  1.00  0.00              
ATOM    562  CA  LEU   144     -17.434  89.443  11.637  1.00  0.00              
ATOM    563  C   LEU   144     -18.468  90.398  12.218  1.00  0.00              
ATOM    564  O   LEU   144     -18.280  91.621  12.045  1.00  0.00              
END
