
#######################################################
#                                                     #
#                        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   34 (   34),  selected   34 , name T0372TS464_5_2
# Molecule2: number of CA atoms  298 ( 2427),  selected   34 , name T0372.pdb
# PARAMETERS: T0372TS464_5_2.T0372.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:    16       193 - 208         2.27    29.17
  LCS_AVERAGE:      4.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        98 - 110         1.37    29.23
  LCS_AVERAGE:      3.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        99 - 108         0.95    28.95
  LCS_AVERAGE:      2.75

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:  298
LCS_GDT     S      98     S      98      9   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     N      99     N      99     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     M     100     M     100     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     R     101     R     101     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     A     102     A     102     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     D     103     D     103     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     L     104     L     104     10   13   13     7    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     105     E     105     10   13   13     5    7   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     106     A     106     10   13   13     5    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     107     I     107     10   13   13     5    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     108     L     108     10   13   13     5    6   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     P     109     P     109      7   13   13     1    3   10   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     110     E     110      4   13   13     0    3    8   12   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     S     128     S     128      5    5    5     5    5    5    5    5    6    7    7    7    7    7    9   10   10   11   11   12   13   17   17 
LCS_GDT     D     129     D     129      5    5    5     5    5    5    5    5    6    7    7    7    7    7    9   10   10   11   11   12   13   13   14 
LCS_GDT     L     130     L     130      5    5    5     5    5    5    5    5    6    7    7    7    7    7    8   10   10   11   11   12   13   13   14 
LCS_GDT     A     131     A     131      5    5    5     5    5    5    5    5    6    7    7    7    7    7    9   10   10   11   11   12   15   17   17 
LCS_GDT     T     132     T     132      5    5   15     5    5    5    5    5    6    7    7    7    7    7    8   10   10   11   11   12   13   15   16 
LCS_GDT     A     193     A     193      9   11   16     8    9    9    9   11   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     L     194     L     194      9   11   16     8    9    9    9   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     I     195     I     195      9   11   16     8    9    9    9   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     Y     196     Y     196      9   11   16     8    9    9    9   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     A     197     A     197      9   12   16     8    9    9    9   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     L     198     L     198      9   12   16     8    9    9    9   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     H     199     H     199      9   12   16     8    9    9    9   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     N     200     N     200      9   12   16     8    9    9    9   11   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     F     201     F     201      9   12   16     6    9    9    9   11   14   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     E     202     E     202      8   12   16     6    7    8    8   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     A     203     A     203      8   12   16     6    7    8    8   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     L     204     L     204      8   12   16     6    7    8    8   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     G     205     G     205      8   12   16     6    7    8    8   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     L     206     L     206      8   12   16     3    7    8    8   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     T     207     T     207      8   12   16     3    6    8    8   12   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_GDT     G     208     G     208      5   12   16     3    3    5    8   10   15   16   16   16   16   16   16   16   16   16   16   16   16   17   17 
LCS_AVERAGE  LCS_A:   3.69  (   2.75    3.77    4.54 )

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      8      9     10     12     13     15     16     16     16     16     16     16     16     16     16     16     16     16     17     17 
GDT PERCENT_CA   2.68   3.02   3.36   4.03   4.36   5.03   5.37   5.37   5.37   5.37   5.37   5.37   5.37   5.37   5.37   5.37   5.37   5.37   5.70   5.70
GDT RMS_LOCAL    0.33   0.43   0.95   1.26   1.37   2.18   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   5.01   5.01
GDT RMS_ALL_CA  29.90  29.82  28.95  28.81  29.23  29.08  29.17  29.17  29.17  29.17  29.17  29.17  29.17  29.17  29.17  29.17  29.17  29.17  28.97  28.97

#      Molecule1      Molecule2       DISTANCE
LGA    S      98      S      98         37.252
LGA    N      99      N      99         40.773
LGA    M     100      M     100         37.005
LGA    R     101      R     101         39.706
LGA    A     102      A     102         46.131
LGA    D     103      D     103         44.790
LGA    L     104      L     104         42.598
LGA    E     105      E     105         48.796
LGA    A     106      A     106         50.481
LGA    I     107      I     107         46.279
LGA    L     108      L     108         46.372
LGA    P     109      P     109         50.678
LGA    E     110      E     110         48.600
LGA    S     128      S     128         24.340
LGA    D     129      D     129         22.681
LGA    L     130      L     130         22.058
LGA    A     131      A     131         23.802
LGA    T     132      T     132         24.285
LGA    A     193      A     193          2.950
LGA    L     194      L     194          1.355
LGA    I     195      I     195          1.407
LGA    Y     196      Y     196          1.287
LGA    A     197      A     197          1.762
LGA    L     198      L     198          1.912
LGA    H     199      H     199          2.366
LGA    N     200      N     200          2.845
LGA    F     201      F     201          3.212
LGA    E     202      E     202          2.367
LGA    A     203      A     203          1.741
LGA    L     204      L     204          2.705
LGA    G     205      G     205          2.887
LGA    L     206      L     206          1.906
LGA    T     207      T     207          1.352
LGA    G     208      G     208          2.822

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  298    4.0     16    2.27     4.446     4.454     0.674

LGA_LOCAL      RMSD =  2.273  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 29.169  Number of atoms =   34 
Std_ALL_ATOMS  RMSD = 15.949  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.119226 * X  +   0.158097 * Y  +  -0.980199 * Z  +  62.380852
  Y_new =   0.222964 * X  +   0.957763 * Y  +   0.181598 * Z  + -56.647324
  Z_new =   0.967508 * X  +  -0.240201 * Y  +   0.078941 * Z  + -69.576439 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.253272    1.888321  [ DEG:   -71.8072    108.1928 ]
  Theta =  -1.315182   -1.826411  [ DEG:   -75.3544   -104.6456 ]
  Phi   =   1.079750   -2.061842  [ DEG:    61.8651   -118.1349 ]
 
# 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: T0372TS464_5_2                                
REMARK     2: T0372.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_5_2.T0372.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  298   4.0   16   2.27   4.454    15.95
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  SER    98      45.381  30.201  25.271  1.00  0.00
ATOM      2  CA  ASN    99      48.988  30.269  24.198  1.00  0.00
ATOM      3  CA  MET   100      48.608  33.872  23.045  1.00  0.00
ATOM      4  CA  ARG   101      47.751  34.802  26.647  1.00  0.00
ATOM      5  CA  ALA   102      51.134  33.326  27.649  1.00  0.00
ATOM      6  CA  ASP   103      52.988  35.269  24.946  1.00  0.00
ATOM      7  CA  LEU   104      51.154  38.498  25.748  1.00  0.00
ATOM      8  CA  GLU   105      53.173  38.972  28.931  1.00  0.00
ATOM      9  CA  ALA   106      55.976  39.882  26.531  1.00  0.00
ATOM     10  CA  ILE   107      53.768  41.963  24.263  1.00  0.00
ATOM     11  CA  LEU   108      51.918  44.253  26.608  1.00  0.00
ATOM     12  CA  PRO   109      51.552  45.057  30.340  1.00  0.00
ATOM     13  CA  GLU   110      47.796  45.414  29.939  1.00  0.00
ATOM     14  CA  SER   128      39.912  48.508  10.954  1.00  0.00
ATOM     15  CA  ASP   129      40.553  47.109  14.444  1.00  0.00
ATOM     16  CA  LEU   130      43.725  49.105  15.165  1.00  0.00
ATOM     17  CA  ALA   131      42.401  52.172  13.315  1.00  0.00
ATOM     18  CA  THR   132      39.034  51.987  14.994  1.00  0.00
ATOM     19  CA  ALA   193      46.797  36.665  13.643  1.00  0.00
ATOM     20  CA  LEU   194      45.564  37.119  17.228  1.00  0.00
ATOM     21  CA  ILE   195      49.109  37.415  18.583  1.00  0.00
ATOM     22  CA  TYR   196      50.159  39.645  15.688  1.00  0.00
ATOM     23  CA  ALA   197      47.042  41.769  16.210  1.00  0.00
ATOM     24  CA  LEU   198      47.963  42.343  19.896  1.00  0.00
ATOM     25  CA  HIS   199      51.434  43.491  18.833  1.00  0.00
ATOM     26  CA  ASN   200      49.859  46.042  16.507  1.00  0.00
ATOM     27  CA  PHE   201      47.428  47.122  19.221  1.00  0.00
ATOM     28  CA  GLU   202      49.983  47.600  21.844  1.00  0.00
ATOM     29  CA  ALA   203      52.259  49.376  19.387  1.00  0.00
ATOM     30  CA  LEU   204      49.502  51.948  19.075  1.00  0.00
ATOM     31  CA  GLY   205      48.688  52.926  22.636  1.00  0.00
ATOM     32  CA  LEU   206      45.674  50.627  22.900  1.00  0.00
ATOM     33  CA  THR   207      45.538  48.550  26.090  1.00  0.00
ATOM     34  CA  GLY   208      44.724  45.035  24.934  1.00  0.00
TER
END
