
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0372TS464_4_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   64 , name T0372_D2.pdb
# PARAMETERS: T0372TS464_4_1-D2.T0372_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:    31       173 - 203         5.00    20.91
  LCS_AVERAGE:     14.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       186 - 201         1.79    23.77
  LONGEST_CONTINUOUS_SEGMENT:    16       187 - 202         1.57    24.34
  LCS_AVERAGE:      6.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       187 - 200         0.52    24.71
  LCS_AVERAGE:      4.72

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:  172
LCS_GDT     R     142     R     142      8   13   22     4    7    8   11   12   13   13   15   16   16   17   17   19   20   23   23   26   28   28   29 
LCS_GDT     N     143     N     143     10   13   25     6    7   10   11   12   13   13   15   16   17   18   23   24   26   27   27   27   28   29   31 
LCS_GDT     H     144     H     144     10   13   25     6    7   10   11   12   13   13   15   16   17   19   23   24   26   27   28   32   33   34   39 
LCS_GDT     I     145     I     145     10   13   25     6    7   10   11   12   13   13   15   16   17   19   23   24   26   27   28   32   34   37   39 
LCS_GDT     N     146     N     146     10   13   25     6    7   10   11   12   13   13   15   16   17   19   23   24   26   27   28   31   33   34   38 
LCS_GDT     R     147     R     147     10   13   25     6    7   10   11   12   13   13   15   16   17   19   23   24   26   27   28   32   33   34   39 
LCS_GDT     F     148     F     148     10   13   25     6    7   10   11   12   13   13   15   16   17   19   23   24   26   27   30   33   34   37   39 
LCS_GDT     R     149     R     149     10   13   25     4    7   10   11   12   13   13   15   16   17   19   23   24   26   27   30   33   34   37   39 
LCS_GDT     N     150     N     150     10   13   25     4    6   10   11   12   13   13   15   16   17   19   23   24   26   27   28   33   34   37   39 
LCS_GDT     T     151     T     151     10   13   25     4    6   10   11   12   13   13   15   16   16   19   23   24   26   27   28   32   34   37   39 
LCS_GDT     Y     152     Y     152     10   13   25     4    6   10   11   12   13   13   15   16   16   17   19   24   26   27   30   33   34   37   39 
LCS_GDT     P     153     P     153      7   13   25     3    4    8   10   12   13   13   15   16   17   19   23   24   26   27   30   33   34   37   39 
LCS_GDT     D     154     D     154      3   13   25     3    3    7   10   11   13   13   14   15   17   20   23   24   26   27   30   33   34   37   39 
LCS_GDT     A     173     A     173      8    9   31     7    8   13   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     E     174     E     174      8    9   31     7    8    8    8    8   13   17   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     W     175     W     175      8    9   31     7    8    8    8    8   11   17   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     C     176     C     176      8    9   31     7    8    9   13   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     K     177     K     177      8    9   31     7    8    8    9   12   15   18   20   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     V     178     V     178      8    9   31     7    8    8    8    8   11   13   18   23   24   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     N     179     N     179      8    9   31     7    8    8    8   14   15   18   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     N     180     N     180      8    9   31     5    8    8    8    9   12   16   18   23   24   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     C     181     C     181      4    4   31     3    4    4    5    6    6    7   10   12   15   18   23   24   26   32   35   36   37   37   39 
LCS_GDT     D     182     D     182      5    5   31     3    5    5    5    7    8    8   10   10   16   19   23   24   26   32   32   34   36   37   39 
LCS_GDT     Q     183     Q     183      5    5   31     3    5    6    7    8   10   13   14   16   19   22   24   25   29   32   35   36   37   37   39 
LCS_GDT     Q     184     Q     184      5    5   31     3    5    6    7    9   11   15   18   23   24   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     E     185     E     185      5    5   31     3    5    5    5    9   11   15   18   23   24   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     G     186     G     186      5   16   31     0    5    5    6    9   15   18   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     T     187     T     187     14   16   31     4   14   14   15   15   17   18   21   23   26   26   29   31   32   33   35   36   37   37   39 
LCS_GDT     G     188     G     188     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     N     189     N     189     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     E     190     E     190     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     R     191     R     191     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     R     192     R     192     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     A     193     A     193     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     L     194     L     194     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     I     195     I     195     14   16   31     7   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     Y     196     Y     196     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     A     197     A     197     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     L     198     L     198     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     H     199     H     199     14   16   31     9   14   14   15   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     N     200     N     200     14   16   31     7   14   14   15   15   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     F     201     F     201      7   16   31     5    6    7   10   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     E     202     E     202      7   16   31     5    6    7   12   15   16   19   20   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     A     203     A     203      7    9   31     5    6    7    7    9   12   15   19   20   23   26   29   31   32   33   35   36   37   37   39 
LCS_GDT     L     204     L     204      7    9   26     5    6    7    7    8    9   11   13   14   18   20   24   25   29   33   35   36   37   37   39 
LCS_GDT     G     205     G     205      7    9   26     5    6    7    7    8   10   12   13   17   22   24   25   31   32   33   35   36   37   37   39 
LCS_GDT     L     206     L     206      7    9   26     3    6    7    7    9   12   19   20   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     T     207     T     207      7    9   26     3    5    7    9   16   17   19   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     G     208     G     208      5    9   26     3    4    5    7    8   15   18   21   23   26   27   29   31   32   33   35   36   37   37   39 
LCS_GDT     I     242     I     242      3    5   12     3    3    3    4    9    9   13   15   16   16   17   17   19   20   23   23   23   23   23   23 
LCS_GDT     D     243     D     243      4    5   12     3    4    4    4    5    6    8    8    9   12   12   17   19   20   23   23   24   34   37   39 
LCS_GDT     G     244     G     244      4    5   12     3    4    4    4    9    9   12   15   16   16   17   19   22   25   27   30   33   34   37   39 
LCS_GDT     A     245     A     245      4    5   12     3    4    4    4   10   12   13   15   16   16   17   18   22   24   27   30   33   34   37   39 
LCS_GDT     Y     246     Y     246      4    5   12     0    4    4    4    5    6    8    8   16   16   17   17   19   23   25   28   32   34   37   38 
LCS_GDT     E     268     E     268      3    7   12     3    3    3    4    6   11   12   12   14   15   16   17   17   18   21   21   21   23   24   25 
LCS_GDT     D     269     D     269      3    7   12     3    3    4    4    5    6    7    7    9   10   15   15   16   18   21   21   21   25   26   26 
LCS_GDT     L     270     L     270      5    7   12     4    4    5    5    6    6    7    7    9   10   11   11   13   15   16   17   19   25   26   26 
LCS_GDT     G     271     G     271      5    7   12     4    4    5    5    6    6    7    7    8    8    9   11   12   13   16   17   21   23   26   26 
LCS_GDT     I     272     I     272      5    7   12     4    4    5    5    6    6    7    7    8    8    9   11   12   15   21   22   26   28   30   30 
LCS_GDT     E     273     E     273      5    7   12     4    4    5    5    6    6    7    7    8    8   11   14   15   18   21   23   26   29   30   34 
LCS_GDT     G     274     G     274      5    7   12     0    4    5    5    6    6    7    7    7   12   16   18   21   23   24   27   32   34   37   38 
LCS_GDT     I     287     I     287      3    3    6     3    3    4    5    9   10   13   14   16   18   19   20   22   25   27   30   33   36   37   39 
LCS_GDT     L     288     L     288      3    3    6     3    3    4    5    9   10   13   14   16   18   19   26   30   30   33   34   36   37   37   39 
LCS_GDT     E     289     E     289      3    3    6     3    3    3    3    3    3    4   14   15   18   19   21   30   30   33   34   36   37   37   39 
LCS_AVERAGE  LCS_A:   8.38  (   4.72    6.12   14.31 )

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      9     14     14     15     16     17     19     21     23     26     27     29     31     32     33     35     36     37     37     39 
GDT PERCENT_CA   5.23   8.14   8.14   8.72   9.30   9.88  11.05  12.21  13.37  15.12  15.70  16.86  18.02  18.60  19.19  20.35  20.93  21.51  21.51  22.67
GDT RMS_LOCAL    0.33   0.52   0.52   0.79   1.74   1.47   2.26   2.26   2.56   3.10   3.57   3.70   4.01   4.22   4.38   4.92   5.46   5.66   5.66   6.07
GDT RMS_ALL_CA  24.31  24.71  24.71  24.52  23.04  23.75  23.22  22.49  22.33  22.29  21.37  21.39  21.70  21.90  22.02  21.70  21.50  21.26  21.26  20.89

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142         38.481
LGA    N     143      N     143         42.783
LGA    H     144      H     144         37.727
LGA    I     145      I     145         35.616
LGA    N     146      N     146         42.429
LGA    R     147      R     147         43.660
LGA    F     148      F     148         37.750
LGA    R     149      R     149         39.956
LGA    N     150      N     150         45.650
LGA    T     151      T     151         42.635
LGA    Y     152      Y     152         37.257
LGA    P     153      P     153         36.687
LGA    D     154      D     154         29.885
LGA    A     173      A     173          1.505
LGA    E     174      E     174          3.620
LGA    W     175      W     175          3.504
LGA    C     176      C     176          2.106
LGA    K     177      K     177          5.793
LGA    V     178      V     178          6.893
LGA    N     179      N     179          3.751
LGA    N     180      N     180          8.129
LGA    C     181      C     181         13.270
LGA    D     182      D     182         16.353
LGA    Q     183      Q     183         14.558
LGA    Q     184      Q     184          9.838
LGA    E     185      E     185          8.989
LGA    G     186      G     186          4.749
LGA    T     187      T     187          2.939
LGA    G     188      G     188          1.942
LGA    N     189      N     189          1.061
LGA    E     190      E     190          1.126
LGA    R     191      R     191          0.877
LGA    R     192      R     192          0.629
LGA    A     193      A     193          1.059
LGA    L     194      L     194          0.988
LGA    I     195      I     195          1.207
LGA    Y     196      Y     196          0.984
LGA    A     197      A     197          1.524
LGA    L     198      L     198          2.088
LGA    H     199      H     199          1.795
LGA    N     200      N     200          2.815
LGA    F     201      F     201          2.924
LGA    E     202      E     202          6.560
LGA    A     203      A     203          9.821
LGA    L     204      L     204         11.291
LGA    G     205      G     205         11.615
LGA    L     206      L     206          7.427
LGA    T     207      T     207          5.555
LGA    G     208      G     208          3.736
LGA    I     242      I     242         38.386
LGA    D     243      D     243         37.266
LGA    G     244      G     244         32.824
LGA    A     245      A     245         26.400
LGA    Y     246      Y     246         24.491
LGA    E     268      E     268         22.215
LGA    D     269      D     269         24.756
LGA    L     270      L     270         25.857
LGA    G     271      G     271         29.119
LGA    I     272      I     272         24.972
LGA    E     273      E     273         24.626
LGA    G     274      G     274         18.818
LGA    I     287      I     287         21.217
LGA    L     288      L     288         17.706
LGA    E     289      E     289         17.560

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64  172    4.0     21    2.26    12.355    10.782     0.891

LGA_LOCAL      RMSD =  2.257  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 22.491  Number of atoms =   64 
Std_ALL_ATOMS  RMSD = 13.391  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.891421 * X  +  -0.452933 * Y  +   0.014831 * Z  + 162.306473
  Y_new =  -0.183296 * X  +   0.390290 * Y  +   0.902262 * Z  +  32.062798
  Z_new =  -0.414453 * X  +   0.801577 * Y  +  -0.430934 * Z  +  42.948486 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.064076   -1.077517  [ DEG:   118.2628    -61.7372 ]
  Theta =   0.427341    2.714251  [ DEG:    24.4849    155.5152 ]
  Phi   =  -2.938797    0.202796  [ DEG:  -168.3807     11.6193 ]
 
# 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_4_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   64  172   4.0   21   2.26  10.782    13.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM     48  CA  ARG   142      57.572  43.095  17.648  1.00  0.00
ATOM     49  CA  ASN   143      58.727  45.854  15.363  1.00  0.00
ATOM     50  CA  HIS   144      56.672  48.378  17.328  1.00  0.00
ATOM     51  CA  ILE   145      58.788  47.530  20.390  1.00  0.00
ATOM     52  CA  ASN   146      61.851  48.546  18.338  1.00  0.00
ATOM     53  CA  ARG   147      60.254  51.828  17.240  1.00  0.00
ATOM     54  CA  PHE   148      59.021  52.612  20.750  1.00  0.00
ATOM     55  CA  ARG   149      62.536  53.504  21.892  1.00  0.00
ATOM     56  CA  ASN   150      61.975  56.637  19.815  1.00  0.00
ATOM     57  CA  THR   151      58.415  57.153  21.000  1.00  0.00
ATOM     58  CA  TYR   152      58.632  56.891  24.750  1.00  0.00
ATOM     59  CA  PRO   153      61.158  56.256  27.567  1.00  0.00
ATOM     60  CA  ASP   154      58.650  54.061  29.379  1.00  0.00
ATOM     61  CA  ALA   173      48.906  27.821  22.235  1.00  0.00
ATOM     62  CA  GLU   174      46.793  30.143  24.286  1.00  0.00
ATOM     63  CA  TRP   175      44.275  30.487  21.504  1.00  0.00
ATOM     64  CA  CYS   176      44.127  26.644  21.392  1.00  0.00
ATOM     65  CA  LYS   177      43.035  26.475  25.044  1.00  0.00
ATOM     66  CA  VAL   178      40.372  29.167  24.483  1.00  0.00
ATOM     67  CA  ASN   179      38.984  27.181  21.624  1.00  0.00
ATOM     68  CA  ASN   180      39.093  23.993  23.700  1.00  0.00
ATOM     69  CA  CYS   181      37.370  25.543  26.714  1.00  0.00
ATOM     70  CA  ASP   182      34.771  27.372  24.752  1.00  0.00
ATOM     71  CA  GLN   183      34.206  24.442  22.363  1.00  0.00
ATOM     72  CA  GLN   184      34.269  26.870  19.443  1.00  0.00
ATOM     73  CA  GLU   185      37.020  26.551  16.885  1.00  0.00
ATOM     74  CA  GLY   186      38.646  29.187  14.715  1.00  0.00
ATOM     75  CA  THR   187      39.789  29.728  11.142  1.00  0.00
ATOM     76  CA  GLY   188      43.336  30.277  10.149  1.00  0.00
ATOM     77  CA  ASN   189      42.431  33.786   9.372  1.00  0.00
ATOM     78  CA  GLU   190      41.057  34.911  12.720  1.00  0.00
ATOM     79  CA  ARG   191      43.907  33.445  14.789  1.00  0.00
ATOM     80  CA  ARG   192      46.181  35.281  12.414  1.00  0.00
ATOM     81  CA  ALA   193      44.115  38.433  12.954  1.00  0.00
ATOM     82  CA  LEU   194      44.327  37.955  16.727  1.00  0.00
ATOM     83  CA  ILE   195      48.001  37.062  16.431  1.00  0.00
ATOM     84  CA  TYR   196      48.846  40.680  15.680  1.00  0.00
ATOM     85  CA  ALA   197      46.651  42.086  18.454  1.00  0.00
ATOM     86  CA  LEU   198      48.136  39.827  21.142  1.00  0.00
ATOM     87  CA  HIS   199      51.582  40.948  19.972  1.00  0.00
ATOM     88  CA  ASN   200      50.716  44.634  20.314  1.00  0.00
ATOM     89  CA  PHE   201      51.883  46.906  23.001  1.00  0.00
ATOM     90  CA  GLU   202      52.935  44.298  25.602  1.00  0.00
ATOM     91  CA  ALA   203      56.544  45.397  25.235  1.00  0.00
ATOM     92  CA  LEU   204      55.344  48.829  26.281  1.00  0.00
ATOM     93  CA  GLY   205      53.393  48.240  29.467  1.00  0.00
ATOM     94  CA  LEU   206      50.003  48.249  27.750  1.00  0.00
ATOM     95  CA  THR   207      47.697  45.394  28.772  1.00  0.00
ATOM     96  CA  GLY   208      46.324  44.033  25.515  1.00  0.00
ATOM     97  CA  ILE   242      55.122  60.663  25.601  1.00  0.00
ATOM     98  CA  ASP   243      55.764  57.577  27.795  1.00  0.00
ATOM     99  CA  GLY   244      54.460  54.909  25.271  1.00  0.00
ATOM    100  CA  ALA   245      51.580  53.996  27.589  1.00  0.00
ATOM    101  CA  TYR   246      48.021  55.160  26.821  1.00  0.00
ATOM    102  CA  GLU   268      46.991  33.338  26.863  1.00  0.00
ATOM    103  CA  ASP   269      50.483  33.757  25.488  1.00  0.00
ATOM    104  CA  LEU   270      50.730  37.490  26.215  1.00  0.00
ATOM    105  CA  GLY   271      48.736  37.740  29.445  1.00  0.00
ATOM    106  CA  ILE   272      46.394  40.191  27.752  1.00  0.00
ATOM    107  CA  GLU   273      42.873  40.310  29.185  1.00  0.00
ATOM    108  CA  GLY   274      39.402  40.984  27.744  1.00  0.00
ATOM    109  CA  ILE   287      41.424  51.096   8.108  1.00  0.00
ATOM    110  CA  LEU   288      39.850  49.764   4.924  1.00  0.00
ATOM    111  CA  GLU   289      40.230  46.004   4.255  1.00  0.00
TER
END
