
#######################################################
#                                                     #
#                        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 (   92),  selected   23 , name T0356TS383_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   23 , name T0356_D3.pdb
# PARAMETERS: T0356TS383_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: T0356TS383_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_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 T0356TS383_1-D3
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    645  N   PHE   348      48.519  71.348  55.529  1.00  0.00
ATOM    646  CA  PHE   348      48.938  70.180  56.287  1.00  0.00
ATOM    647  C   PHE   348      49.536  69.086  55.410  1.00  0.00
ATOM    648  O   PHE   348      50.559  68.497  55.760  1.00  0.00
ATOM    649  N   PRO   349      48.914  68.816  54.267  1.00  0.00
ATOM    650  CA  PRO   349      49.429  67.773  53.384  1.00  0.00
ATOM    651  C   PRO   349      50.898  68.002  53.051  1.00  0.00
ATOM    652  O   PRO   349      51.686  67.061  52.989  1.00  0.00
ATOM    653  N   GLU   350      51.262  69.258  52.850  1.00  0.00
ATOM    654  CA  GLU   350      52.637  69.608  52.529  1.00  0.00
ATOM    655  C   GLU   350      53.493  69.720  53.787  1.00  0.00
ATOM    656  O   GLU   350      54.547  69.098  53.902  1.00  0.00
ATOM    657  N   ILE   351      53.020  70.526  54.728  1.00  0.00
ATOM    658  CA  ILE   351      53.714  70.772  55.981  1.00  0.00
ATOM    659  C   ILE   351      53.807  69.569  56.914  1.00  0.00
ATOM    660  O   ILE   351      54.826  69.378  57.575  1.00  0.00
ATOM    661  N   VAL   352      52.745  68.768  56.970  1.00  0.00
ATOM    662  CA  VAL   352      52.708  67.596  57.845  1.00  0.00
ATOM    663  C   VAL   352      53.058  68.007  59.277  1.00  0.00
ATOM    664  O   VAL   352      54.081  67.592  59.825  1.00  0.00
ATOM    665  N   ASP   353      52.196  68.823  59.907  1.00  0.00
ATOM    666  CA  ASP   353      52.416  69.301  61.279  1.00  0.00
ATOM    667  C   ASP   353      52.555  68.166  62.274  1.00  0.00
ATOM    668  O   ASP   353      51.871  67.153  62.157  1.00  0.00
ATOM    669  N   PHE   354      53.435  68.342  63.254  1.00  0.00
ATOM    670  CA  PHE   354      53.643  67.339  64.290  1.00  0.00
ATOM    671  C   PHE   354      52.634  67.558  65.417  1.00  0.00
ATOM    672  O   PHE   354      52.478  68.673  65.912  1.00  0.00
ATOM    673  N   TYR   355      51.950  66.491  65.818  1.00  0.00
ATOM    674  CA  TYR   355      50.959  66.566  66.887  1.00  0.00
ATOM    675  C   TYR   355      51.442  65.656  68.008  1.00  0.00
ATOM    676  O   TYR   355      51.935  64.566  67.749  1.00  0.00
ATOM    677  N   LEU   356      51.311  66.111  69.250  1.00  0.00
ATOM    678  CA  LEU   356      51.755  65.334  70.397  1.00  0.00
ATOM    679  C   LEU   356      50.619  64.494  70.957  1.00  0.00
ATOM    680  O   LEU   356      49.507  64.986  71.145  1.00  0.00
ATOM    681  N   GLU   359      50.897  63.220  71.205  1.00  0.00
ATOM    682  CA  GLU   359      49.901  62.322  71.777  1.00  0.00
ATOM    683  C   GLU   359      50.209  62.282  73.268  1.00  0.00
ATOM    684  O   GLU   359      49.321  62.426  74.108  1.00  0.00
ATOM    685  N   GLY   360      51.490  62.111  73.575  1.00  0.00
ATOM    686  CA  GLY   360      51.947  62.053  74.951  1.00  0.00
ATOM    687  C   GLY   360      53.304  61.383  74.967  1.00  0.00
ATOM    688  O   GLY   360      53.559  60.521  74.133  1.00  0.00
ATOM    689  N   CYS   361      54.172  61.763  75.901  1.00  0.00
ATOM    690  CA  CYS   361      55.491  61.162  75.958  1.00  0.00
ATOM    691  C   CYS   361      56.243  61.387  74.654  1.00  0.00
ATOM    692  O   CYS   361      56.339  62.524  74.185  1.00  0.00
ATOM    693  N   SER   362      56.766  60.312  74.064  1.00  0.00
ATOM    694  CA  SER   362      57.500  60.416  72.805  1.00  0.00
ATOM    695  C   SER   362      56.684  59.897  71.625  1.00  0.00
ATOM    696  O   SER   362      57.243  59.493  70.603  1.00  0.00
ATOM    697  N   TYR   363      55.364  59.895  71.770  1.00  0.00
ATOM    698  CA  TYR   363      54.491  59.439  70.697  1.00  0.00
ATOM    699  C   TYR   363      53.872  60.654  70.028  1.00  0.00
ATOM    700  O   TYR   363      53.406  61.571  70.704  1.00  0.00
ATOM    701  N   ARG   364      53.875  60.665  68.701  1.00  0.00
ATOM    702  CA  ARG   364      53.307  61.780  67.966  1.00  0.00
ATOM    703  C   ARG   364      52.432  61.312  66.829  1.00  0.00
ATOM    704  O   ARG   364      52.357  60.123  66.521  1.00  0.00
ATOM    705  N   LEU   365      51.773  62.274  66.205  1.00  0.00
ATOM    706  CA  LEU   365      50.910  62.012  65.076  1.00  0.00
ATOM    707  C   LEU   365      51.261  63.051  64.026  1.00  0.00
ATOM    708  O   LEU   365      51.362  64.239  64.334  1.00  0.00
ATOM    709  N   ALA   366      51.488  62.600  62.798  1.00  0.00
ATOM    710  CA  ALA   366      51.800  63.515  61.713  1.00  0.00
ATOM    711  C   ALA   366      50.448  63.836  61.094  1.00  0.00
ATOM    712  O   ALA   366      49.782  62.950  60.566  1.00  0.00
ATOM    713  N   VAL   367      50.046  65.100  61.175  1.00  0.00
ATOM    714  CA  VAL   367      48.750  65.501  60.662  1.00  0.00
ATOM    715  C   VAL   367      48.637  65.837  59.190  1.00  0.00
ATOM    716  O   VAL   367      48.292  66.966  58.851  1.00  0.00
ATOM    717  N   VAL   368      48.899  64.863  58.323  1.00  0.00
ATOM    718  CA  VAL   368      48.817  65.072  56.878  1.00  0.00
ATOM    719  C   VAL   368      47.674  64.268  56.254  1.00  0.00
ATOM    720  O   VAL   368      47.721  63.909  55.080  1.00  0.00
ATOM    721  N   THR   369      46.644  64.002  57.052  1.00  0.00
ATOM    722  CA  THR   369      45.479  63.241  56.609  1.00  0.00
ATOM    723  C   THR   369      44.244  64.110  56.461  1.00  0.00
ATOM    724  O   THR   369      43.415  64.179  57.368  1.00  0.00
ATOM    725  N   ILE   370      44.112  64.757  55.310  1.00  0.00
ATOM    726  CA  ILE   370      42.976  65.626  55.068  1.00  0.00
ATOM    727  C   ILE   370      41.708  64.856  54.742  1.00  0.00
ATOM    728  O   ILE   370      41.697  63.990  53.870  1.00  0.00
ATOM    729  N   LYS   371      40.637  65.186  55.454  1.00  0.00
ATOM    730  CA  LYS   371      39.347  64.544  55.250  1.00  0.00
ATOM    731  C   LYS   371      38.293  65.643  55.339  1.00  0.00
ATOM    732  O   LYS   371      38.128  66.266  56.385  1.00  0.00
ATOM    733  N   LYS   372      37.601  65.903  54.235  1.00  0.00
ATOM    734  CA  LYS   372      36.568  66.928  54.232  1.00  0.00
ATOM    735  C   LYS   372      35.241  66.325  54.632  1.00  0.00
ATOM    736  O   LYS   372      34.991  65.145  54.402  1.00  0.00
TER
END
