
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0356TS245_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   23 , name T0356_D3.pdb
# PARAMETERS: T0356TS245_1-D3.T0356_D3.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:    23       348 - 372         4.41     4.41
  LCS_AVERAGE:     19.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       366 - 372         1.98    10.51
  LCS_AVERAGE:      5.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       352 - 356         0.72     8.21
  LONGEST_CONTINUOUS_SEGMENT:     5       364 - 368         0.80     7.23
  LCS_AVERAGE:      3.62

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:  120
LCS_GDT     F     348     F     348      4    6   23     3    4    4    4    6    8    9   10   12   12   13   14   17   23   23   23   23   23   23   23 
LCS_GDT     P     349     P     349      4    6   23     3    4    5    8    9    9   10   11   15   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     E     350     E     350      4    6   23     3    5    6    7   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     I     351     I     351      4    6   23     3    5    6    7   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     V     352     V     352      5    6   23     3    5    5    6    7    9   10   13   15   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     D     353     D     353      5    6   23     4    5    5    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     F     354     F     354      5    6   23     4    5    5    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     Y     355     Y     355      5    6   23     4    5    5    7   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     L     356     L     356      5    6   23     4    5    5    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     E     359     E     359      3    4   23     0    3    3    4    4    6   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     G     360     G     360      4    5   23     3    5    6    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     C     361     C     361      4    5   23     3    5    6    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     S     362     S     362      4    5   23     3    4    6    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     Y     363     Y     363      4    6   23     3    5    6    8   10   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     R     364     R     364      5    6   23     3    5    5    5    7    8   10   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     L     365     L     365      5    6   23     3    5    5    5    7    9   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     A     366     A     366      5    7   23     3    5    5    5    7    9   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     V     367     V     367      5    7   23     3    5    5    5    7   11   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     V     368     V     368      5    7   23     3    5    5    5    7   10   15   16   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     T     369     T     369      4    7   23     3    4    4    5    7    8   12   15   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     I     370     I     370      4    7   23     3    4    4    5    8    8   12   13   18   19   20   21   22   23   23   23   23   23   23   23 
LCS_GDT     K     371     K     371      4    7   23     3    4    4    5    6    7   10   10   12   19   19   21   22   23   23   23   23   23   23   23 
LCS_GDT     K     372     K     372      3    7   23     3    3    4    6    8    8   10   11   12   19   19   21   22   23   23   23   23   23   23   23 
LCS_AVERAGE  LCS_A:   9.29  (   3.62    5.07   19.17 )

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      8     10     11     15     16     18     19     20     21     22     23     23     23     23     23     23     23 
GDT PERCENT_CA   3.33   4.17   5.00   6.67   8.33   9.17  12.50  13.33  15.00  15.83  16.67  17.50  18.33  19.17  19.17  19.17  19.17  19.17  19.17  19.17
GDT RMS_LOCAL    0.37   0.72   0.91   1.54   1.89   2.22   2.81   2.94   3.38   3.51   3.72   4.00   4.19   4.41   4.41   4.41   4.41   4.41   4.41   4.41
GDT RMS_ALL_CA   8.52   8.21   6.56   5.65   5.24   5.27   5.49   5.53   4.93   4.99   4.73   4.51   4.45   4.41   4.41   4.41   4.41   4.41   4.41   4.41

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348          9.708
LGA    P     349      P     349          9.124
LGA    E     350      E     350          2.604
LGA    I     351      I     351          1.151
LGA    V     352      V     352          6.769
LGA    D     353      D     353          3.652
LGA    F     354      F     354          3.245
LGA    Y     355      Y     355          2.948
LGA    L     356      L     356          2.871
LGA    E     359      E     359          3.487
LGA    G     360      G     360          3.292
LGA    C     361      C     361          2.544
LGA    S     362      S     362          3.094
LGA    Y     363      Y     363          2.580
LGA    R     364      R     364          3.964
LGA    L     365      L     365          2.723
LGA    A     366      A     366          2.960
LGA    V     367      V     367          2.426
LGA    V     368      V     368          3.826
LGA    T     369      T     369          7.375
LGA    I     370      I     370          8.001
LGA    K     371      K     371         12.384
LGA    K     372      K     372         11.437

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  120    4.0     16    2.94    10.833     9.982     0.526

LGA_LOCAL      RMSD =  2.943  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.797  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  4.409  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.178167 * X  +   0.380400 * Y  +   0.907498 * Z  +  17.693264
  Y_new =  -0.982422 * X  +  -0.016555 * Y  +  -0.185937 * Z  + 110.525848
  Z_new =  -0.055706 * X  +  -0.924674 * Y  +   0.376663 * Z  +  95.725716 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.183973    1.957620  [ DEG:   -67.8367    112.1633 ]
  Theta =   0.055735    3.085857  [ DEG:     3.1934    176.8066 ]
  Phi   =  -1.750201    1.391392  [ DEG:  -100.2791     79.7209 ]
 
# 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: T0356TS245_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS245_1-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  120   4.0   16   2.94   9.982     4.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS245_1-D3
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    806  N   PHE   348      48.496  71.298  55.463  1.00  0.00
ATOM    807  CA  PHE   348      48.938  70.180  56.287  1.00  0.00
ATOM    808  C   PHE   348      49.503  69.055  55.437  1.00  0.00
ATOM    809  O   PHE   348      50.347  68.300  55.967  1.00  0.00
ATOM    810  CB  PHE   348      47.738  69.678  57.093  1.00  0.00
ATOM    811  N   PRO   349      49.047  68.868  54.264  1.00  0.00
ATOM    812  CA  PRO   349      49.429  67.773  53.384  1.00  0.00
ATOM    813  C   PRO   349      50.875  68.021  52.985  1.00  0.00
ATOM    814  O   PRO   349      51.595  67.007  52.860  1.00  0.00
ATOM    815  CB  PRO   349      48.538  67.745  52.141  1.00  0.00
ATOM    816  N   GLU   350      51.305  69.180  52.845  1.00  0.00
ATOM    817  CA  GLU   350      52.637  69.608  52.529  1.00  0.00
ATOM    818  C   GLU   350      53.367  69.876  53.790  1.00  0.00
ATOM    819  O   GLU   350      54.243  68.999  53.630  1.00  0.00
ATOM    820  CB  GLU   350      52.576  70.877  51.676  1.00  0.00
ATOM    821  N   ILE   351      53.279  70.444  54.674  1.00  0.00
ATOM    822  CA  ILE   351      53.714  70.772  55.981  1.00  0.00
ATOM    823  C   ILE   351      53.215  69.746  56.891  1.00  0.00
ATOM    824  O   ILE   351      53.063  70.359  57.969  1.00  0.00
ATOM    825  CB  ILE   351      53.167  72.144  56.384  1.00  0.00
ATOM    826  N   VAL   352      53.060  68.457  56.781  1.00  0.00
ATOM    827  CA  VAL   352      52.708  67.596  57.845  1.00  0.00
ATOM    828  C   VAL   352      52.720  67.945  59.262  1.00  0.00
ATOM    829  O   VAL   352      53.772  67.363  59.605  1.00  0.00
ATOM    830  CB  VAL   352      53.661  66.427  57.583  1.00  0.00
ATOM    831  N   ASP   353      52.162  68.746  59.957  1.00  0.00
ATOM    832  CA  ASP   353      52.416  69.301  61.279  1.00  0.00
ATOM    833  C   ASP   353      52.548  68.203  62.319  1.00  0.00
ATOM    834  O   ASP   353      51.909  67.144  62.139  1.00  0.00
ATOM    835  CB  ASP   353      51.255  70.231  61.640  1.00  0.00
ATOM    836  N   PHE   354      53.373  68.369  63.299  1.00  0.00
ATOM    837  CA  PHE   354      53.643  67.339  64.290  1.00  0.00
ATOM    838  C   PHE   354      52.666  67.523  65.438  1.00  0.00
ATOM    839  O   PHE   354      52.610  68.644  65.988  1.00  0.00
ATOM    840  CB  PHE   354      55.081  67.469  64.798  1.00  0.00
ATOM    841  N   TYR   355      51.929  66.517  65.805  1.00  0.00
ATOM    842  CA  TYR   355      50.959  66.566  66.887  1.00  0.00
ATOM    843  C   TYR   355      51.443  65.645  67.994  1.00  0.00
ATOM    844  O   TYR   355      52.588  65.251  67.686  1.00  0.00
ATOM    845  CB  TYR   355      49.590  66.106  66.381  1.00  0.00
ATOM    846  N   LEU   356      51.020  65.699  69.219  1.00  0.00
ATOM    847  CA  LEU   356      51.755  65.334  70.397  1.00  0.00
ATOM    848  C   LEU   356      50.677  64.497  71.012  1.00  0.00
ATOM    849  O   LEU   356      50.406  65.287  71.942  1.00  0.00
ATOM    850  CB  LEU   356      52.116  66.492  71.329  1.00  0.00
ATOM    851  N   GLU   359      50.453  63.445  71.053  1.00  0.00
ATOM    852  CA  GLU   359      49.901  62.322  71.777  1.00  0.00
ATOM    853  C   GLU   359      50.288  62.065  73.207  1.00  0.00
ATOM    854  O   GLU   359      49.248  62.029  73.899  1.00  0.00
ATOM    855  CB  GLU   359      50.283  61.125  70.905  1.00  0.00
ATOM    856  N   GLY   360      51.368  62.073  73.671  1.00  0.00
ATOM    857  CA  GLY   360      51.947  62.053  74.951  1.00  0.00
ATOM    858  C   GLY   360      53.349  61.743  75.038  1.00  0.00
ATOM    859  O   GLY   360      53.335  62.672  74.202  1.00  0.00
ATOM    861  N   CYS   361      54.191  61.422  75.483  1.00  0.00
ATOM    862  CA  CYS   361      55.491  61.162  75.958  1.00  0.00
ATOM    863  C   CYS   361      56.147  60.881  74.726  1.00  0.00
ATOM    864  O   CYS   361      55.193  61.295  74.034  1.00  0.00
ATOM    865  CB  CYS   361      55.579  59.951  76.890  1.00  0.00
ATOM    866  N   SER   362      57.216  60.470  74.232  1.00  0.00
ATOM    867  CA  SER   362      57.500  60.416  72.805  1.00  0.00
ATOM    868  C   SER   362      56.634  60.043  71.627  1.00  0.00
ATOM    869  O   SER   362      57.304  59.734  70.618  1.00  0.00
ATOM    870  CB  SER   362      58.707  59.480  72.887  1.00  0.00
ATOM    871  N   TYR   363      55.447  59.925  71.680  1.00  0.00
ATOM    872  CA  TYR   363      54.491  59.439  70.697  1.00  0.00
ATOM    873  C   TYR   363      53.881  60.656  70.026  1.00  0.00
ATOM    874  O   TYR   363      53.539  61.659  70.691  1.00  0.00
ATOM    875  CB  TYR   363      53.399  58.614  71.381  1.00  0.00
ATOM    876  N   ARG   364      53.808  60.607  68.668  1.00  0.00
ATOM    877  CA  ARG   364      53.307  61.780  67.966  1.00  0.00
ATOM    878  C   ARG   364      52.547  61.339  66.731  1.00  0.00
ATOM    879  O   ARG   364      52.552  60.158  66.322  1.00  0.00
ATOM    880  CB  ARG   364      54.485  62.671  67.567  1.00  0.00
ATOM    881  N   LEU   365      51.794  62.284  66.195  1.00  0.00
ATOM    882  CA  LEU   365      50.910  62.012  65.076  1.00  0.00
ATOM    883  C   LEU   365      51.362  63.043  64.060  1.00  0.00
ATOM    884  O   LEU   365      51.635  64.199  64.447  1.00  0.00
ATOM    885  CB  LEU   365      49.435  62.226  65.420  1.00  0.00
ATOM    886  N   ALA   366      51.422  62.684  62.827  1.00  0.00
ATOM    887  CA  ALA   366      51.800  63.515  61.713  1.00  0.00
ATOM    888  C   ALA   366      50.469  63.896  61.127  1.00  0.00
ATOM    889  O   ALA   366      49.718  62.924  60.896  1.00  0.00
ATOM    890  CB  ALA   366      52.636  62.764  60.675  1.00  0.00
ATOM    891  N   VAL   367      50.094  65.073  61.040  1.00  0.00
ATOM    892  CA  VAL   367      48.750  65.501  60.662  1.00  0.00
ATOM    893  C   VAL   367      48.413  65.640  59.194  1.00  0.00
ATOM    894  O   VAL   367      47.263  66.044  58.915  1.00  0.00
ATOM    895  CB  VAL   367      48.570  66.846  61.371  1.00  0.00
ATOM    896  N   VAL   368      49.278  65.133  58.252  1.00  0.00
ATOM    897  CA  VAL   368      48.817  65.072  56.878  1.00  0.00
ATOM    898  C   VAL   368      47.542  64.477  56.342  1.00  0.00
ATOM    899  O   VAL   368      47.330  64.669  55.125  1.00  0.00
ATOM    900  CB  VAL   368      50.026  64.369  56.256  1.00  0.00
ATOM    901  N   THR   369      46.714  63.811  57.116  1.00  0.00
ATOM    902  CA  THR   369      45.479  63.241  56.609  1.00  0.00
ATOM    903  C   THR   369      44.443  64.341  56.471  1.00  0.00
ATOM    904  O   THR   369      44.227  65.050  57.478  1.00  0.00
ATOM    905  CB  THR   369      44.981  62.168  57.579  1.00  0.00
ATOM    906  N   ILE   370      43.907  64.554  55.359  1.00  0.00
ATOM    907  CA  ILE   370      42.976  65.626  55.068  1.00  0.00
ATOM    908  C   ILE   370      41.685  64.931  54.715  1.00  0.00
ATOM    909  O   ILE   370      41.908  64.100  53.810  1.00  0.00
ATOM    910  CB  ILE   370      43.453  66.478  53.890  1.00  0.00
ATOM    911  N   LYS   371      40.662  65.042  55.225  1.00  0.00
ATOM    912  CA  LYS   371      39.347  64.544  55.250  1.00  0.00
ATOM    913  C   LYS   371      38.396  65.623  55.055  1.00  0.00
ATOM    914  O   LYS   371      38.752  66.068  56.168  1.00  0.00
ATOM    915  CB  LYS   371      39.104  63.867  56.601  1.00  0.00
ATOM    916  N   LYS   372      37.616  66.032  54.505  1.00  0.00
ATOM    917  CA  LYS   372      36.568  66.928  54.232  1.00  0.00
ATOM    918  C   LYS   372      35.899  66.559  52.999  1.00  0.00
ATOM    919  O   LYS   372      36.944  66.890  52.399  1.00  0.00
ATOM    920  CB  LYS   372      37.146  68.340  54.113  1.00  0.00
TER
END
