
#######################################################
#                                                     #
#                        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   21 (  104),  selected   21 , name T0386TS245_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   21 , name T0386_D2.pdb
# PARAMETERS: T0386TS245_1-D2.T0386_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:    20       219 - 238         4.98     5.06
  LONGEST_CONTINUOUS_SEGMENT:    20       220 - 239         4.81     5.10
  LCS_AVERAGE:     24.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       229 - 237         1.86     9.84
  LCS_AVERAGE:      8.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       224 - 229         0.27     6.88
  LCS_AVERAGE:      5.58

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:   81
LCS_GDT     N     219     N     219      4    4   20     3    4    4    4    4    6    8   10   12   13   13   15   19   19   20   21   21   21   21   21 
LCS_GDT     P     220     P     220      4    4   20     3    4    4    4    6    6    8   10   12   14   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     E     221     E     221      4    5   20     4    4    5    5    6    8    9   10   13   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     K     222     K     222      4    5   20     4    4    5    5    7    8    9   11   13   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     I     223     I     223      4    5   20     4    4    5    5    7    8    9   11   13   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     R     224     R     224      6    8   20     6    6    6    6    7    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     L     225     L     225      6    8   20     6    6    6    6    6    9   13   14   14   14   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     L     226     L     226      6    8   20     6    6    6    6    6    9   13   14   14   14   15   18   19   19   20   21   21   21   21   21 
LCS_GDT     K     227     K     227      6    8   20     6    6    6    6    7    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     E     228     E     228      6    8   20     6    6    6    6    6    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     F     229     F     229      6    9   20     6    6    6    6    6    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     M     230     M     230      5    9   20     4    5    6    8    8    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     H     231     H     231      5    9   20     4    5    6    8    8    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     T     232     T     232      5    9   20     4    5    6    8    8    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     M     233     M     233      5    9   20     4    5    6    8    8    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     K     234     K     234      5    9   20     4    5    6    8    8    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     N     235     N     235      4    9   20     3    4    4    8    8    9   13   14   14   14   15   16   18   19   20   21   21   21   21   21 
LCS_GDT     T     236     T     236      4    9   20     3    5    6    8    8    9   13   14   14   14   15   17   18   19   20   21   21   21   21   21 
LCS_GDT     G     237     G     237      3    9   20     3    3    4    8    8    9   13   14   14   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     R     238     R     238      3    4   20     3    4    5    5    7    8    9   11   13   15   16   18   19   19   20   21   21   21   21   21 
LCS_GDT     N     239     N     239      0    4   20     0    0    4    4    5    8    9   10   13   15   16   18   19   19   20   21   21   21   21   21 
LCS_AVERAGE  LCS_A:  13.07  (   5.58    8.94   24.69 )

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      6      6      8      8      9     13     14     14     15     16     18     19     19     20     21     21     21     21     21 
GDT PERCENT_CA   7.41   7.41   7.41   9.88   9.88  11.11  16.05  17.28  17.28  18.52  19.75  22.22  23.46  23.46  24.69  25.93  25.93  25.93  25.93  25.93
GDT RMS_LOCAL    0.27   0.27   0.27   1.37   1.37   1.73   2.78   2.91   2.91   3.65   3.85   4.37   4.55   4.47   4.76   5.01   5.01   5.01   5.01   5.01
GDT RMS_ALL_CA   6.88   6.88   6.88   9.12   9.12   9.31   8.08   7.92   7.92   5.42   5.42   5.10   5.11   5.64   5.04   5.01   5.01   5.01   5.01   5.01

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         19.807
LGA    P     220      P     220         15.576
LGA    E     221      E     221         10.751
LGA    K     222      K     222         12.324
LGA    I     223      I     223          9.574
LGA    R     224      R     224          3.108
LGA    L     225      L     225          2.562
LGA    L     226      L     226          3.659
LGA    K     227      K     227          3.300
LGA    E     228      E     228          2.627
LGA    F     229      F     229          3.099
LGA    M     230      M     230          2.120
LGA    H     231      H     231          2.731
LGA    T     232      T     232          2.289
LGA    M     233      M     233          2.089
LGA    K     234      K     234          3.460
LGA    N     235      N     235          3.314
LGA    T     236      T     236          2.860
LGA    G     237      G     237          2.946
LGA    R     238      R     238          8.722
LGA    N     239      N     239         11.288

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   81    4.0     14    2.91    15.123    13.443     0.465

LGA_LOCAL      RMSD =  2.908  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.916  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  5.011  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.271556 * X  +   0.896981 * Y  +   0.348830 * Z  + -42.015053
  Y_new =  -0.902568 * X  +  -0.111525 * Y  +  -0.415853 * Z  +  68.817223
  Z_new =  -0.334109 * X  +  -0.427770 * Y  +   0.839871 * Z  + 104.267540 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.471082    2.670511  [ DEG:   -26.9910    153.0090 ]
  Theta =   0.340660    2.800932  [ DEG:    19.5184    160.4816 ]
  Phi   =  -1.863051    1.278541  [ DEG:  -106.7450     73.2550 ]
 
# 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: T0386TS245_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS245_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   81   4.0   14   2.91  13.443     5.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS245_1-D2
PFRMAT TS
TARGET T0386
MODEL 1
PARENT 2g03A
ATOM    926  N   ASN   219       4.205  74.914  83.363  1.00  0.00
ATOM    927  CA  ASN   219       3.425  73.777  82.888  1.00  0.00
ATOM    928  C   ASN   219       3.704  72.842  84.045  1.00  0.00
ATOM    929  O   ASN   219       4.890  72.605  84.359  1.00  0.00
ATOM    930  CB  ASN   219       3.924  73.160  81.580  1.00  0.00
ATOM    931  N   PRO   220       2.701  72.248  84.593  1.00  0.00
ATOM    932  CA  PRO   220       2.827  71.245  85.626  1.00  0.00
ATOM    933  C   PRO   220       3.072  69.912  85.056  1.00  0.00
ATOM    934  O   PRO   220       3.395  69.103  85.952  1.00  0.00
ATOM    935  CB  PRO   220       1.534  71.239  86.443  1.00  0.00
ATOM    936  N   GLU   221       3.182  69.646  83.786  1.00  0.00
ATOM    937  CA  GLU   221       3.688  68.396  83.269  1.00  0.00
ATOM    938  C   GLU   221       5.202  68.343  83.313  1.00  0.00
ATOM    939  O   GLU   221       5.792  68.672  82.262  1.00  0.00
ATOM    940  CB  GLU   221       3.198  68.247  81.828  1.00  0.00
ATOM    941  N   LYS   222       5.801  68.257  84.465  1.00  0.00
ATOM    942  CA  LYS   222       7.206  68.514  84.735  1.00  0.00
ATOM    943  C   LYS   222       8.066  67.487  84.038  1.00  0.00
ATOM    944  O   LYS   222       8.664  67.912  83.026  1.00  0.00
ATOM    945  CB  LYS   222       7.437  68.455  86.247  1.00  0.00
ATOM    946  N   ILE   223       7.943  66.186  84.317  1.00  0.00
ATOM    947  CA  ILE   223       8.489  65.140  83.478  1.00  0.00
ATOM    948  C   ILE   223       8.038  64.694  82.122  1.00  0.00
ATOM    949  O   ILE   223       7.699  63.492  82.154  1.00  0.00
ATOM    950  CB  ILE   223       8.398  63.979  84.470  1.00  0.00
ATOM    951  N   ARG   224       7.772  65.428  81.201  1.00  0.00
ATOM    952  CA  ARG   224       7.042  65.133  79.980  1.00  0.00
ATOM    953  C   ARG   224       8.226  65.157  79.041  1.00  0.00
ATOM    954  O   ARG   224       8.981  66.149  79.131  1.00  0.00
ATOM    955  CB  ARG   224       6.021  66.195  79.565  1.00  0.00
ATOM    956  N   LEU   225       8.480  64.135  78.262  1.00  0.00
ATOM    957  CA  LEU   225       9.662  64.033  77.412  1.00  0.00
ATOM    958  C   LEU   225       9.722  65.169  76.403  1.00  0.00
ATOM    959  O   LEU   225      10.835  65.669  76.132  1.00  0.00
ATOM    960  CB  LEU   225       9.611  62.687  76.686  1.00  0.00
ATOM    961  N   LEU   226       8.597  65.552  75.818  1.00  0.00
ATOM    962  CA  LEU   226       8.550  66.598  74.798  1.00  0.00
ATOM    963  C   LEU   226       8.881  67.951  75.412  1.00  0.00
ATOM    964  O   LEU   226       9.707  68.684  74.824  1.00  0.00
ATOM    965  CB  LEU   226       7.148  66.626  74.187  1.00  0.00
ATOM    966  N   LYS   227       8.311  68.283  76.554  1.00  0.00
ATOM    967  CA  LYS   227       8.595  69.539  77.236  1.00  0.00
ATOM    968  C   LYS   227      10.047  69.612  77.681  1.00  0.00
ATOM    969  O   LYS   227      10.487  70.725  78.042  1.00  0.00
ATOM    970  CB  LYS   227       7.667  69.645  78.448  1.00  0.00
ATOM    971  N   GLU   228      10.708  68.458  77.892  1.00  0.00
ATOM    972  CA  GLU   228      12.000  68.462  78.570  1.00  0.00
ATOM    973  C   GLU   228      13.085  68.217  77.531  1.00  0.00
ATOM    974  O   GLU   228      12.516  69.314  77.723  1.00  0.00
ATOM    975  CB  GLU   228      12.030  67.361  79.632  1.00  0.00
ATOM    976  N   PHE   229      13.411  67.905  76.594  1.00  0.00
ATOM    977  CA  PHE   229      13.694  67.858  75.195  1.00  0.00
ATOM    978  C   PHE   229      15.177  68.087  74.806  1.00  0.00
ATOM    979  O   PHE   229      14.934  69.237  75.230  1.00  0.00
ATOM    980  CB  PHE   229      12.810  68.927  74.552  1.00  0.00
ATOM    981  N   MET   230      14.588  66.446  75.738  1.00  0.00
ATOM    982  CA  MET   230      14.450  67.867  75.996  1.00  0.00
ATOM    983  C   MET   230      13.243  68.470  75.287  1.00  0.00
ATOM    984  O   MET   230      14.482  68.406  75.438  1.00  0.00
ATOM    985  CB  MET   230      15.734  68.551  75.522  1.00  0.00
ATOM    986  N   HIS   231      12.795  69.193  74.757  1.00  0.00
ATOM    987  CA  HIS   231      12.345  70.321  73.950  1.00  0.00
ATOM    988  C   HIS   231      12.696  71.634  74.640  1.00  0.00
ATOM    989  O   HIS   231      12.993  72.669  74.002  1.00  0.00
ATOM    990  CB  HIS   231      10.831  70.217  73.757  1.00  0.00
ATOM    991  N   THR   232      12.635  71.594  75.974  1.00  0.00
ATOM    992  CA  THR   232      12.919  72.786  76.772  1.00  0.00
ATOM    993  C   THR   232      14.407  73.106  76.733  1.00  0.00
ATOM    994  O   THR   232      14.763  74.284  76.520  1.00  0.00
ATOM    995  CB  THR   232      12.474  72.529  78.214  1.00  0.00
ATOM    996  N   MET   233      15.239  72.146  76.908  1.00  0.00
ATOM    997  CA  MET   233      16.682  72.354  76.873  1.00  0.00
ATOM    998  C   MET   233      17.152  72.728  75.476  1.00  0.00
ATOM    999  O   MET   233      18.057  73.583  75.363  1.00  0.00
ATOM   1000  CB  MET   233      17.361  71.062  77.328  1.00  0.00
ATOM   1001  N   LYS   234      16.582  72.155  74.451  1.00  0.00
ATOM   1002  CA  LYS   234      16.962  72.473  73.079  1.00  0.00
ATOM   1003  C   LYS   234      16.715  73.955  72.828  1.00  0.00
ATOM   1004  O   LYS   234      17.555  74.644  72.209  1.00  0.00
ATOM   1005  CB  LYS   234      16.128  71.631  72.111  1.00  0.00
ATOM   1006  N   ASN   235      15.592  74.467  73.343  1.00  0.00
ATOM   1007  CA  ASN   235      15.263  75.882  73.219  1.00  0.00
ATOM   1008  C   ASN   235      16.205  76.743  74.044  1.00  0.00
ATOM   1009  O   ASN   235      16.611  77.818  73.552  1.00  0.00
ATOM   1010  CB  ASN   235      13.821  76.079  73.690  1.00  0.00
ATOM   1011  N   THR   236      16.590  76.310  75.186  1.00  0.00
ATOM   1012  CA  THR   236      17.538  77.008  76.042  1.00  0.00
ATOM   1013  C   THR   236      18.956  77.062  75.498  1.00  0.00
ATOM   1014  O   THR   236      19.543  78.164  75.443  1.00  0.00
ATOM   1015  CB  THR   236      17.520  76.286  77.391  1.00  0.00
ATOM   1016  N   GLY   237      19.430  75.653  74.502  1.00  0.00
ATOM   1017  CA  GLY   237      20.537  76.237  73.779  1.00  0.00
ATOM   1018  C   GLY   237      20.410  77.688  73.406  1.00  0.00
ATOM   1019  O   GLY   237      21.426  77.626  72.681  1.00  0.00
ATOM   1021  N   ARG   238      18.974  79.925  73.716  1.00  0.00
ATOM   1022  CA  ARG   238      18.957  81.310  73.268  1.00  0.00
ATOM   1023  C   ARG   238      19.989  82.384  73.041  1.00  0.00
ATOM   1024  O   ARG   238      20.012  83.634  73.000  1.00  0.00
ATOM   1025  CB  ARG   238      17.943  81.768  74.319  1.00  0.00
ATOM   1026  N   ASN   239      21.322  81.486  73.170  1.00  0.00
ATOM   1027  CA  ASN   239      22.715  81.650  73.268  1.00  0.00
ATOM   1028  C   ASN   239      23.268  82.029  71.981  1.00  0.00
ATOM   1029  O   ASN   239      22.967  80.885  71.577  1.00  0.00
ATOM   1030  CB  ASN   239      23.333  80.333  73.738  1.00  0.00
TER
END
