
#######################################################
#                                                     #
#                        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   18 (   90),  selected   18 , name T0289TS239_5_1-D1
# Molecule2: number of CA atoms  233 ( 1850),  selected   18 , name T0289_D1.pdb
# PARAMETERS: T0289TS239_5_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:    12       212 - 223         2.01     9.68
  LCS_AVERAGE:      4.72

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       212 - 222         1.92     9.91
  LONGEST_CONTINUOUS_SEGMENT:    11       213 - 223         1.95     9.57
  LCS_AVERAGE:      4.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       218 - 223         0.94     9.09
  LCS_AVERAGE:      1.96

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     K     212     K     212      4   11   12     3    4    4    7   11   11   12   12   12   12   12   12   12   13   14   14   15   15   15   15 
LCS_GDT     E     213     E     213      4   11   12     3    4    4    7   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     F     214     F     214      4   11   12     3    4    5    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     P     215     P     215      4   11   12     3    5    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     P     216     P     216      4   11   12     3    3    5    8    8   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     C     217     C     217      4   11   12     3    5    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     A     218     A     218      6   11   12     3    5    5    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     I     219     I     219      6   11   12     3    5    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     D     220     D     220      6   11   12     3    5    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     V     221     V     221      6   11   12     3    5    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     Y     222     Y     222      6   11   12     3    5    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
LCS_GDT     K     223     K     223      6   11   12     3    4    6    9   11   11   12   12   12   12   12   13   13   13   14   14   15   15   15   15 
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   14   14   15   15   15   15 
LCS_GDT     T     301     T     301      4    6    7     4    4    4    5    5    6    6    6    6    6    6   13   13   13   14   14   15   15   15   15 
LCS_GDT     L     302     L     302      4    6    7     4    4    4    5    5    6    6    6    6    6    6    7    7   13   14   14   15   15   15   15 
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:   3.56  (   1.96    4.01    4.72 )

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     11     11     12     12     12     12     12     13     13     13     14     14     15     15     15     15 
GDT PERCENT_CA   1.72   2.15   2.58   3.86   4.72   4.72   5.15   5.15   5.15   5.15   5.15   5.58   5.58   5.58   6.01   6.01   6.44   6.44   6.44   6.44
GDT RMS_LOCAL    0.44   0.71   0.86   1.43   1.75   1.75   2.01   2.01   2.01   2.01   2.01   4.34   4.34   3.32   4.32   4.32   4.92   4.92   4.92   4.92
GDT RMS_ALL_CA  22.77   9.27   9.77   9.55   9.50   9.50   9.68   9.68   9.68   9.68   9.68   8.08   8.08   9.08   8.43   8.43   8.04   8.04   8.04   8.04

#      Molecule1      Molecule2       DISTANCE
LGA    K     212      K     212          2.382
LGA    E     213      E     213          2.110
LGA    F     214      F     214          2.539
LGA    P     215      P     215          0.815
LGA    P     216      P     216          3.413
LGA    C     217      C     217          1.140
LGA    A     218      A     218          2.050
LGA    I     219      I     219          1.035
LGA    D     220      D     220          1.622
LGA    V     221      V     221          1.906
LGA    Y     222      Y     222          1.535
LGA    K     223      K     223          2.111
LGA    T     298      T     298         22.987
LGA    K     299      K     299         19.227
LGA    L     300      L     300         14.174
LGA    T     301      T     301         13.830
LGA    L     302      L     302         10.654
LGA    N     303      N     303         15.331

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  233    4.0     12    2.01     4.292     4.397     0.568

LGA_LOCAL      RMSD =  2.011  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.682  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  7.635  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.362644 * X  +  -0.574366 * Y  +  -0.733889 * Z  +  63.509155
  Y_new =   0.371349 * X  +  -0.811336 * Y  +   0.451480 * Z  +  62.562828
  Z_new =  -0.854745 * X  +  -0.108803 * Y  +   0.507516 * Z  +  10.788859 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.211186    2.930407  [ DEG:   -12.1001    167.8999 ]
  Theta =   1.025060    2.116533  [ DEG:    58.7316    121.2684 ]
  Phi   =   2.344335   -0.797258  [ DEG:   134.3205    -45.6795 ]
 
# 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_5_1-D1                             
REMARK     2: T0289_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289TS239_5_1-D1.T0289_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  233   4.0   12   2.01   4.397     7.64
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS239_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0289
PARENT 2bco_A
ATOM    979  N   LYS   212      40.173  25.075  -7.987  1.00  9.99
ATOM    980  CA  LYS   212      39.173  24.625  -7.015  1.00  9.99
ATOM    981  C   LYS   212      39.579  23.295  -6.370  1.00  9.99
ATOM    982  O   LYS   212      39.172  22.226  -6.830  1.00  9.99
ATOM    983  CB  LYS   212      37.914  24.500  -7.862  1.00  9.99
ATOM    984  N   GLU   213      40.382  23.362  -5.311  1.00  9.99
ATOM    985  CA  GLU   213      40.837  22.154  -4.631  1.00  9.99
ATOM    986  C   GLU   213      40.277  22.044  -3.216  1.00  9.99
ATOM    987  O   GLU   213      39.727  23.004  -2.678  1.00  9.99
ATOM    988  CB  GLU   213      42.371  22.116  -4.595  1.00  9.99
ATOM    989  N   PHE   214      40.424  20.862  -2.622  1.00  9.99
ATOM    990  CA  PHE   214      39.929  20.589  -1.273  1.00  9.99
ATOM    991  C   PHE   214      40.990  19.890  -0.423  1.00  9.99
ATOM    992  O   PHE   214      40.664  19.096   0.459  1.00  9.99
ATOM    993  CB  PHE   214      38.681  19.702  -1.355  1.00  9.99
ATOM    994  N   PRO   215      42.255  20.196  -0.687  1.00  9.99
ATOM    995  CA  PRO   215      43.360  19.582   0.032  1.00  9.99
ATOM    996  C   PRO   215      43.623  20.230   1.395  1.00  9.99
ATOM    997  O   PRO   215      44.215  19.608   2.280  1.00  9.99
ATOM    998  CB  PRO   215      44.626  19.644  -0.829  1.00  9.99
ATOM    999  N   PRO   216      43.182  21.474   1.561  1.00  9.99
ATOM   1000  CA  PRO   216      43.365  22.213   2.814  1.00  9.99
ATOM   1001  C   PRO   216      42.492  21.683   3.947  1.00  9.99
ATOM   1002  O   PRO   216      41.520  20.963   3.722  1.00  9.99
ATOM   1003  CB  PRO   216      43.050  23.694   2.598  1.00  9.99
ATOM   1004  N   CYS   217      42.840  22.059   5.173  1.00  9.99
ATOM   1005  CA  CYS   217      42.087  21.626   6.343  1.00  9.99
ATOM   1006  C   CYS   217      40.902  22.544   6.639  1.00  9.99
ATOM   1007  O   CYS   217      40.863  23.696   6.191  1.00  9.99
ATOM   1008  CB  CYS   217      42.989  21.584   7.578  1.00  9.99
ATOM   1009  N   ALA   218      39.917  22.037   7.399  1.00  9.99
ATOM   1010  CA  ALA   218      38.754  22.863   7.733  1.00  9.99
ATOM   1011  C   ALA   218      39.119  23.901   8.788  1.00  9.99
ATOM   1012  O   ALA   218      39.820  23.589   9.756  1.00  9.99
ATOM   1013  CB  ALA   218      37.746  21.849   8.263  1.00  9.99
ATOM   1014  N   ILE   219      38.668  25.136   8.589  1.00  9.99
ATOM   1015  CA  ILE   219      38.927  26.183   9.567  1.00  9.99
ATOM   1016  C   ILE   219      38.106  25.818  10.802  1.00  9.99
ATOM   1017  O   ILE   219      37.120  25.085  10.702  1.00  9.99
ATOM   1018  CB  ILE   219      38.486  27.548   9.026  1.00  9.99
ATOM   1019  N   ASP   220      38.513  26.301  11.966  1.00  9.99
ATOM   1020  CA  ASP   220      37.767  26.011  13.178  1.00  9.99
ATOM   1021  C   ASP   220      36.444  26.790  13.125  1.00  9.99
ATOM   1022  O   ASP   220      36.422  27.958  12.727  1.00  9.99
ATOM   1023  CB  ASP   220      38.581  26.416  14.421  1.00  9.99
ATOM   1024  N   VAL   221      35.349  26.133  13.498  1.00  9.99
ATOM   1025  CA  VAL   221      34.036  26.768  13.480  1.00  9.99
ATOM   1026  C   VAL   221      33.635  27.092  14.920  1.00  9.99
ATOM   1027  O   VAL   221      33.682  26.227  15.800  1.00  9.99
ATOM   1028  CB  VAL   221      32.992  25.828  12.860  1.00  9.99
ATOM   1029  N   TYR   222      33.247  28.342  15.158  1.00  9.99
ATOM   1030  CA  TYR   222      32.840  28.783  16.488  1.00  9.99
ATOM   1031  C   TYR   222      31.390  29.239  16.451  1.00  9.99
ATOM   1032  O   TYR   222      30.874  29.581  15.398  1.00  9.99
ATOM   1033  CB  TYR   222      33.703  29.960  16.960  1.00  9.99
ATOM   1034  N   LYS   223      30.737  29.220  17.605  1.00  9.99
ATOM   1035  CA  LYS   223      29.359  29.684  17.726  1.00  9.99
ATOM   1036  C   LYS   223      29.366  30.568  18.962  1.00  9.99
ATOM   1037  O   LYS   223      30.277  30.476  19.784  1.00  9.99
ATOM   1038  CB  LYS   223      28.374  28.517  17.919  1.00  9.99
ATOM   1370  N   THR   298      22.958  22.972   1.797  1.00  9.99
ATOM   1371  CA  THR   298      23.925  23.954   1.338  1.00  9.99
ATOM   1372  C   THR   298      24.219  25.075   2.321  1.00  9.99
ATOM   1373  O   THR   298      24.906  26.038   1.978  1.00  9.99
ATOM   1374  CB  THR   298      23.419  24.533   0.005  1.00  9.99
ATOM   1375  N   LYS   299      23.704  24.950   3.539  1.00  9.99
ATOM   1376  CA  LYS   299      23.901  25.951   4.581  1.00  9.99
ATOM   1377  C   LYS   299      24.680  25.344   5.752  1.00  9.99
ATOM   1378  O   LYS   299      24.367  24.241   6.213  1.00  9.99
ATOM   1379  CB  LYS   299      22.534  26.456   5.070  1.00  9.99
ATOM   1380  N   LEU   300      25.694  26.056   6.235  1.00  9.99
ATOM   1381  CA  LEU   300      26.473  25.539   7.352  1.00  9.99
ATOM   1382  C   LEU   300      25.735  25.848   8.649  1.00  9.99
ATOM   1383  O   LEU   300      25.588  27.015   9.022  1.00  9.99
ATOM   1384  CB  LEU   300      27.881  26.158   7.392  1.00  9.99
ATOM   1385  N   THR   301      25.266  24.802   9.324  1.00  9.99
ATOM   1386  CA  THR   301      24.541  24.962  10.581  1.00  9.99
ATOM   1387  C   THR   301      25.238  24.169  11.676  1.00  9.99
ATOM   1388  O   THR   301      26.107  23.347  11.394  1.00  9.99
ATOM   1389  CB  THR   301      23.067  24.459  10.471  1.00  9.99
ATOM   1390  N   LEU   302      24.877  24.421  12.926  1.00  9.99
ATOM   1391  CA  LEU   302      25.488  23.681  14.024  1.00  9.99
ATOM   1392  C   LEU   302      24.486  22.962  14.929  1.00  9.99
ATOM   1393  O   LEU   302      23.303  23.312  14.985  1.00  9.99
ATOM   1394  CB  LEU   302      26.387  24.587  14.866  1.00  9.99
ATOM   1395  N   ASN   303      24.994  21.957  15.642  1.00  9.99
ATOM   1396  CA  ASN   303      24.212  21.114  16.547  1.00  9.99
ATOM   1397  C   ASN   303      23.368  20.107  15.767  1.00  9.99
ATOM   1398  O   ASN   303      23.799  18.939  15.682  1.00  9.99
ATOM   1399  CB  ASN   303      23.303  21.963  17.444  1.00  9.99
TER
END
