
#######################################################
#                                                     #
#                        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 (   85),  selected   17 , name T0289TS239_4_1-D1
# Molecule2: number of CA atoms  233 ( 1850),  selected   17 , name T0289_D1.pdb
# PARAMETERS: T0289TS239_4_1-D1.T0289_D1.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:    11       213 - 223         1.95     9.83
  LONGEST_CONTINUOUS_SEGMENT:    11       216 - 300         4.98     9.89
  LCS_AVERAGE:      4.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       213 - 223         1.95     9.83
  LCS_AVERAGE:      3.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       218 - 223         0.94     9.27
  LCS_AVERAGE:      1.92

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:  233
LCS_GDT     E     213     E     213      3   11   11     3    3    3    7   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     F     214     F     214      3   11   11     3    3    5    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     P     215     P     215      4   11   11     3    5    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     P     216     P     216      4   11   11     3    3    5    8    8   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     C     217     C     217      4   11   11     3    5    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     A     218     A     218      6   11   11     3    5    5    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     I     219     I     219      6   11   11     3    5    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     D     220     D     220      6   11   11     3    5    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     V     221     V     221      6   11   11     3    5    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     Y     222     Y     222      6   11   11     3    5    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     K     223     K     223      6   11   11     3    4    6    9   10   10   11   11   11   11   11   13   13   13   13   14   14   14   14   14 
LCS_GDT     T     298     T     298      3    6   11     3    3    4    5    5    6    6    6    6    6    6    7    7    7    9    9   10   11   11   13 
LCS_GDT     K     299     K     299      3    6   11     3    3    4    5    5    6    6    6    6    6    6   10   11   11   11   12   12   14   14   14 
LCS_GDT     L     300     L     300      4    6   11     4    4    4    5    5    6    7    7    8   10   10   13   13   13   13   14   14   14   14   14 
LCS_GDT     T     301     T     301      4    6    7     4    4    4    5    5    6    6    6    6    6    6   13   13   13   13   14   14   14   14   14 
LCS_GDT     L     302     L     302      4    6    7     4    4    4    5    5    6    6    6    6    6    6    7    7    8   13   14   14   14   14   14 
LCS_GDT     N     303     N     303      4    6    7     4    4    4    5    5    6    6    6    6    6    6    7    7    7    9    9    9    9    9   10 
LCS_AVERAGE  LCS_A:   3.43  (   1.92    3.96    4.42 )

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      9     10     10     11     11     11     11     11     13     13     13     13     14     14     14     14     14 
GDT PERCENT_CA   1.72   2.15   2.58   3.86   4.29   4.29   4.72   4.72   4.72   4.72   4.72   5.58   5.58   5.58   5.58   6.01   6.01   6.01   6.01   6.01
GDT RMS_LOCAL    0.44   0.71   0.86   1.43   1.63   1.63   1.95   1.95   1.95   1.95   1.95   4.34   4.34   4.34   4.34   4.77   4.77   4.77   4.77   4.77
GDT RMS_ALL_CA  20.65   9.48  10.00   9.79   9.61   9.61   9.83   9.83   9.83   9.83   9.83   7.96   7.96   7.96   7.96   7.98   7.98   7.98   7.98   7.98

#      Molecule1      Molecule2       DISTANCE
LGA    E     213      E     213          2.326
LGA    F     214      F     214          2.641
LGA    P     215      P     215          0.592
LGA    P     216      P     216          3.491
LGA    C     217      C     217          1.062
LGA    A     218      A     218          2.003
LGA    I     219      I     219          0.860
LGA    D     220      D     220          1.489
LGA    V     221      V     221          1.784
LGA    Y     222      Y     222          1.389
LGA    K     223      K     223          1.926
LGA    T     298      T     298         22.617
LGA    K     299      K     299         18.928
LGA    L     300      L     300         13.889
LGA    T     301      T     301         13.676
LGA    L     302      L     302         10.655
LGA    N     303      N     303         15.395

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  233    4.0     11    1.95     4.185     4.208     0.537

LGA_LOCAL      RMSD =  1.950  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.828  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  7.591  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.392766 * X  +  -0.559496 * Y  +  -0.729862 * Z  +  62.645798
  Y_new =   0.366159 * X  +  -0.823161 * Y  +   0.433974 * Z  +  63.160515
  Z_new =  -0.843601 * X  +  -0.096796 * Y  +   0.528174 * Z  +  10.439412 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.181253    2.960340  [ DEG:   -10.3850    169.6150 ]
  Theta =   1.003955    2.137638  [ DEG:    57.5224    122.4776 ]
  Phi   =   2.391239   -0.750354  [ DEG:   137.0079    -42.9921 ]
 
# 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: T0289TS239_4_1-D1                             
REMARK     2: T0289_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289TS239_4_1-D1.T0289_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  233   4.0   11   1.95   4.208     7.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS239_4_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0289
PARENT 2bco_A
ATOM    984  N   GLU   213      39.951  23.522  -5.197  1.00  9.99
ATOM    985  CA  GLU   213      40.449  22.322  -4.534  1.00  9.99
ATOM    986  C   GLU   213      39.929  22.195  -3.106  1.00  9.99
ATOM    987  O   GLU   213      39.372  23.141  -2.549  1.00  9.99
ATOM    988  CB  GLU   213      41.984  22.317  -4.538  1.00  9.99
ATOM    989  N   PHE   214      40.116  21.015  -2.519  1.00  9.99
ATOM    990  CA  PHE   214      39.663  20.727  -1.159  1.00  9.99
ATOM    991  C   PHE   214      40.761  20.048  -0.340  1.00  9.99
ATOM    992  O   PHE   214      40.474  19.245   0.547  1.00  9.99
ATOM    993  CB  PHE   214      38.433  19.814  -1.212  1.00  9.99
ATOM    994  N   PRO   215      42.012  20.383  -0.636  1.00  9.99
ATOM    995  CA  PRO   215      43.148  19.790   0.053  1.00  9.99
ATOM    996  C   PRO   215      43.433  20.440   1.410  1.00  9.99
ATOM    997  O   PRO   215      44.061  19.828   2.277  1.00  9.99
ATOM    998  CB  PRO   215      44.389  19.882  -0.841  1.00  9.99
ATOM    999  N   PRO   216      42.969  21.673   1.592  1.00  9.99
ATOM   1000  CA  PRO   216      43.169  22.412   2.843  1.00  9.99
ATOM   1001  C   PRO   216      42.338  21.860   3.997  1.00  9.99
ATOM   1002  O   PRO   216      41.375  21.120   3.794  1.00  9.99
ATOM   1003  CB  PRO   216      42.817  23.886   2.641  1.00  9.99
ATOM   1004  N   CYS   217      42.709  22.239   5.214  1.00  9.99
ATOM   1005  CA  CYS   217      41.997  21.787   6.402  1.00  9.99
ATOM   1006  C   CYS   217      40.801  22.677   6.732  1.00  9.99
ATOM   1007  O   CYS   217      40.725  23.830   6.290  1.00  9.99
ATOM   1008  CB  CYS   217      42.931  21.760   7.612  1.00  9.99
ATOM   1009  N   ALA   218      39.847  22.147   7.515  1.00  9.99
ATOM   1010  CA  ALA   218      38.676  22.947   7.883  1.00  9.99
ATOM   1011  C   ALA   218      39.046  23.989   8.932  1.00  9.99
ATOM   1012  O   ALA   218      39.778  23.689   9.880  1.00  9.99
ATOM   1013  CB  ALA   218      37.704  21.910   8.435  1.00  9.99
ATOM   1014  N   ILE   219      38.563  25.215   8.749  1.00  9.99
ATOM   1015  CA  ILE   219      38.826  26.264   9.725  1.00  9.99
ATOM   1016  C   ILE   219      38.045  25.877  10.978  1.00  9.99
ATOM   1017  O   ILE   219      37.073  25.124  10.902  1.00  9.99
ATOM   1018  CB  ILE   219      38.341  27.621   9.199  1.00  9.99
ATOM   1019  N   ASP   220      38.472  26.366  12.133  1.00  9.99
ATOM   1020  CA  ASP   220      37.764  26.056  13.363  1.00  9.99
ATOM   1021  C   ASP   220      36.424  26.806  13.348  1.00  9.99
ATOM   1022  O   ASP   220      36.367  27.975  12.955  1.00  9.99
ATOM   1023  CB  ASP   220      38.602  26.474  14.586  1.00  9.99
ATOM   1024  N   VAL   221      35.354  26.125  13.747  1.00  9.99
ATOM   1025  CA  VAL   221      34.028  26.731  13.766  1.00  9.99
ATOM   1026  C   VAL   221      33.657  27.042  15.217  1.00  9.99
ATOM   1027  O   VAL   221      33.746  26.175  16.092  1.00  9.99
ATOM   1028  CB  VAL   221      32.987  25.771  13.170  1.00  9.99
ATOM   1029  N   TYR   222      33.249  28.282  15.469  1.00  9.99
ATOM   1030  CA  TYR   222      32.868  28.710  16.812  1.00  9.99
ATOM   1031  C   TYR   222      31.408  29.135  16.814  1.00  9.99
ATOM   1032  O   TYR   222      30.857  29.470  15.775  1.00  9.99
ATOM   1033  CB  TYR   222      33.717  29.904  17.265  1.00  9.99
ATOM   1034  N   LYS   223      30.785  29.099  17.984  1.00  9.99
ATOM   1035  CA  LYS   223      29.401  29.532  18.143  1.00  9.99
ATOM   1036  C   LYS   223      29.422  30.413  19.381  1.00  9.99
ATOM   1037  O   LYS   223      30.356  30.337  20.179  1.00  9.99
ATOM   1038  CB  LYS   223      28.447  28.344  18.358  1.00  9.99
ATOM   1370  N   THR   298      22.731  22.735   2.362  1.00  9.99
ATOM   1371  CA  THR   298      23.664  23.739   1.881  1.00  9.99
ATOM   1372  C   THR   298      23.960  24.863   2.860  1.00  9.99
ATOM   1373  O   THR   298      24.616  25.842   2.503  1.00  9.99
ATOM   1374  CB  THR   298      23.111  24.310   0.564  1.00  9.99
ATOM   1375  N   LYS   299      23.480  24.723   4.091  1.00  9.99
ATOM   1376  CA  LYS   299      23.682  25.724   5.131  1.00  9.99
ATOM   1377  C   LYS   299      24.505  25.131   6.279  1.00  9.99
ATOM   1378  O   LYS   299      24.228  24.019   6.744  1.00  9.99
ATOM   1379  CB  LYS   299      22.318  26.198   5.658  1.00  9.99
ATOM   1380  N   LEU   300      25.515  25.862   6.738  1.00  9.99
ATOM   1381  CA  LEU   300      26.334  25.359   7.833  1.00  9.99
ATOM   1382  C   LEU   300      25.624  25.648   9.149  1.00  9.99
ATOM   1383  O   LEU   300      25.462  26.810   9.531  1.00  9.99
ATOM   1384  CB  LEU   300      27.729  26.008   7.838  1.00  9.99
ATOM   1385  N   THR   301      25.195  24.590   9.833  1.00  9.99
ATOM   1386  CA  THR   301      24.501  24.731  11.109  1.00  9.99
ATOM   1387  C   THR   301      25.243  23.950  12.182  1.00  9.99
ATOM   1388  O   THR   301      26.121  23.147  11.874  1.00  9.99
ATOM   1389  CB  THR   301      23.035  24.197  11.035  1.00  9.99
ATOM   1390  N   LEU   302      24.909  24.190  13.442  1.00  9.99
ATOM   1391  CA  LEU   302      25.565  23.460  14.521  1.00  9.99
ATOM   1392  C   LEU   302      24.602  22.716  15.449  1.00  9.99
ATOM   1393  O   LEU   302      23.413  23.041  15.538  1.00  9.99
ATOM   1394  CB  LEU   302      26.465  24.382  15.343  1.00  9.99
ATOM   1395  N   ASN   303      25.150  21.720  16.145  1.00  9.99
ATOM   1396  CA  ASN   303      24.410  20.857  17.067  1.00  9.99
ATOM   1397  C   ASN   303      23.568  19.835  16.306  1.00  9.99
ATOM   1398  O   ASN   303      24.021  18.677  16.205  1.00  9.99
ATOM   1399  CB  ASN   303      23.507  21.684  17.990  1.00  9.99
TER
END
