
#######################################################
#                                                     #
#                        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   60 , name T0316TS393_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS393_1-D2.T0316_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:    41       230 - 274         5.00    10.01
  LCS_AVERAGE:     56.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       270 - 278         1.98    12.82
  LCS_AVERAGE:     11.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       221 - 225         0.81    19.48
  LONGEST_CONTINUOUS_SEGMENT:     5       267 - 271         0.98    17.50
  LONGEST_CONTINUOUS_SEGMENT:     5       270 - 274         0.89    13.60
  LONGEST_CONTINUOUS_SEGMENT:     5       273 - 277         0.94    11.77
  LONGEST_CONTINUOUS_SEGMENT:     5       274 - 278         0.81    12.44
  LCS_AVERAGE:      6.31

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:   60
LCS_GDT     G     220     G     220      4    7   11     3    3    6    6    7    7    7    7    8   12   12   13   17   19   21   22   24   25   34   35 
LCS_GDT     R     221     R     221      5    7   11     3    3    6    6    7    7    7    7    8   12   12   13   22   24   27   32   35   39   41   43 
LCS_GDT     M     222     M     222      5    7   11     4    4    6    6    7    7    7   14   16   19   20   22   25   29   34   37   40   42   46   46 
LCS_GDT     M     223     M     223      5    7   11     4    4    7    9    9   11   12   15   16   19   21   22   25   29   32   37   40   42   46   46 
LCS_GDT     T     224     T     224      5    7   11     4    4    6    6    7    8   11   15   16   19   21   24   25   29   32   37   40   42   46   47 
LCS_GDT     V     225     V     225      5    7   11     4    4    6    6    9   11   12   15   16   19   21   24   25   29   34   37   40   42   46   46 
LCS_GDT     D     226     D     226      3    7   11     1    3    5    6    7   11   12   15   16   19   21   24   25   29   34   37   40   42   46   46 
LCS_GDT     G     227     G     227      3    5   11     0    3    5    5    5    9   10   13   17   20   22   28   30   34   37   40   43   44   47   48 
LCS_GDT     R     228     R     228      3    5   21     1    3    5    5    5   10   10   15   18   21   24   28   31   35   39   42   45   45   47   48 
LCS_GDT     D     229     D     229      3    5   21     1    3    3    5    6    8   16   19   21   25   28   29   34   36   40   42   45   45   47   48 
LCS_GDT     M     230     M     230      4    5   41     1    3    4    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     231     G     231      4    5   41     2    3    4    6    8   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     E     232     E     232      4    5   41     3    3    4    6    8   11   16   22   24   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     H     233     H     233      4    6   41     3    3    4    5    5    7   12   13   19   21   24   28   35   36   40   42   45   45   47   48 
LCS_GDT     A     234     A     234      4    6   41     4    4    4    4    6    8   12   15   19   24   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     235     G     235      4    6   41     4    4    4    4    6    9   12   15   20   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     L     236     L     236      4    6   41     4    4    4    4    5    8   12   15   19   19   23   27   31   35   39   42   45   45   47   48 
LCS_GDT     M     237     M     237      4    6   41     4    4    4    4    6    9   12   15   19   24   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     Y     238     Y     238      3    6   41     3    3    5    6    8   11   16   22   24   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     Y     239     Y     239      3    6   41     3    3    5    6   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     T     240     T     240      3    6   41     3    3    5    6   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     I     241     I     241      3    6   41     3    3    5    6    8   10   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     242     G     242      4    6   41     3    4    5    6    8   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     Q     243     Q     243      4    6   41     3    4    5    6    8    9   12   14   16   22   26   32   35   38   40   42   45   45   47   48 
LCS_GDT     R     244     R     244      4    5   41     3    4    4    6    8    9   12   14   16   21   26   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     245     G     245      4    5   41     3    4    4    6    8    9   11   15   19   23   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     246     G     246      3    5   41     3    3    5    7    8    9   12   14   16   19   24   27   31   35   39   42   45   45   47   48 
LCS_GDT     L     247     L     247      3    4   41     3    3    4    4    8    8   10   13   18   19   24   29   33   38   40   42   45   45   47   48 
LCS_GDT     G     248     G     248      3    4   41     3    3    4    5    5    9   10   11   15   21   26   30   34   38   40   42   45   45   47   48 
LCS_GDT     I     249     I     249      3    4   41     3    3    3    4    4    6   10   12   19   21   26   31   35   38   40   42   45   45   47   48 
LCS_GDT     G     250     G     250      3    6   41     3    4    5    6   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     251     G     251      3    6   41     3    4    5    6   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     D     256     D     256      0    7   41     1    1    5    9   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     N     257     N     257      3    7   41     2    3    4    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     A     258     A     258      3    8   41     3    3    4    6   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     P     259     P     259      3    8   41     3    4    5    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     W     260     W     260      3    8   41     3    3    4    6    8   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     F     261     F     261      3    8   41     3    3    5    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     V     262     V     262      3    8   41     3    3    5    7    9   14   17   20   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     V     263     V     263      3    8   41     0    3    4    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     264     G     264      4    8   41     3    4    5    7    9   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     K     265     K     265      4    8   41     3    4    5    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     D     266     D     266      4    8   41     3    4    5    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     L     267     L     267      5    7   41     3    4    5    6    8    9   12   17   22   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     S     268     S     268      5    5   41     3    4    5    6    6    9   10   11   14   17   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     K     269     K     269      5    7   41     3    4    5    7    8   13   16   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     N     270     N     270      5    9   41     3    4    5    8   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     I     271     I     271      5    9   41     3    4    5    7   10   13   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     L     272     L     272      5    9   41     3    4    5    7   10   14   17   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     Y     273     Y     273      5    9   41     3    4    7    9    9   12   16   22   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     V     274     V     274      5    9   41     3    4    7    9    9   12   16   23   25   28   29   33   35   38   40   42   45   45   47   48 
LCS_GDT     G     275     G     275      5    9   36     3    4    7    9    9   11   12   15   17   19   25   30   35   37   39   42   45   45   47   48 
LCS_GDT     Q     276     Q     276      5    9   36     3    4    7    9    9   10   12   15   17   22   26   30   35   37   39   42   45   45   47   48 
LCS_GDT     G     277     G     277      5    9   29     3    4    7    9    9   11   12   15   16   19   21   24   25   29   36   38   42   43   46   48 
LCS_GDT     F     278     F     278      5    9   19     3    4    7    9    9   11   12   15   16   19   20   24   25   29   31   34   39   40   43   46 
LCS_GDT     Y     279     Y     279      3    8   19     3    3    5    9    9   11   12   15   16   19   20   24   25   29   31   34   39   40   41   45 
LCS_GDT     H     280     H     280      3    8   19     3    3    4    5    7   11   12   15   16   19   21   24   25   29   34   37   40   42   46   46 
LCS_GDT     D     281     D     281      3    7   19     3    3    4    5    6   11   12   15   16   19   21   24   25   29   34   37   40   42   46   46 
LCS_GDT     S     282     S     282      3    7   19     3    3    4    5    8    9   12   14   16   19   22   26   30   34   37   41   43   45   47   48 
LCS_GDT     L     283     L     283      3    6   19     3    3    3    4    8   11   12   15   16   19   22   24   30   34   37   41   43   45   46   48 
LCS_AVERAGE  LCS_A:  24.62  (   6.31   11.28   56.28 )

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      4      7      9     10     14     17     23     25     28     29     33     35     38     40     42     45     45     47     48 
GDT PERCENT_CA   6.67   6.67  11.67  15.00  16.67  23.33  28.33  38.33  41.67  46.67  48.33  55.00  58.33  63.33  66.67  70.00  75.00  75.00  78.33  80.00
GDT RMS_LOCAL    0.22   0.22   1.05   1.36   1.91   2.22   2.49   3.07   3.21   3.48   3.63   4.08   4.35   4.66   4.83   5.12   5.40   5.40   5.87   6.07
GDT RMS_ALL_CA  19.72  19.72  12.36  12.14  10.03  10.17   9.93   9.78   9.72   9.92   9.95  10.07  10.10   9.96  10.03   9.69   9.75   9.75   9.44   9.32

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         20.820
LGA    R     221      R     221         16.561
LGA    M     222      M     222         13.519
LGA    M     223      M     223         11.804
LGA    T     224      T     224         11.494
LGA    V     225      V     225         14.351
LGA    D     226      D     226         16.196
LGA    G     227      G     227         10.282
LGA    R     228      R     228          7.787
LGA    D     229      D     229          6.074
LGA    M     230      M     230          3.160
LGA    G     231      G     231          3.464
LGA    E     232      E     232          6.263
LGA    H     233      H     233          9.883
LGA    A     234      A     234          9.524
LGA    G     235      G     235          8.352
LGA    L     236      L     236         10.746
LGA    M     237      M     237          9.030
LGA    Y     238      Y     238          5.770
LGA    Y     239      Y     239          3.870
LGA    T     240      T     240          3.495
LGA    I     241      I     241          3.993
LGA    G     242      G     242          3.502
LGA    Q     243      Q     243          7.648
LGA    R     244      R     244          7.523
LGA    G     245      G     245          6.631
LGA    G     246      G     246          9.214
LGA    L     247      L     247          8.044
LGA    G     248      G     248          7.780
LGA    I     249      I     249          6.074
LGA    G     250      G     250          2.783
LGA    G     251      G     251          2.550
LGA    D     256      D     256          1.452
LGA    N     257      N     257          2.567
LGA    A     258      A     258          3.595
LGA    P     259      P     259          1.093
LGA    W     260      W     260          3.365
LGA    F     261      F     261          3.450
LGA    V     262      V     262          4.286
LGA    V     263      V     263          2.802
LGA    G     264      G     264          3.925
LGA    K     265      K     265          2.753
LGA    D     266      D     266          3.223
LGA    L     267      L     267          5.303
LGA    S     268      S     268          6.738
LGA    K     269      K     269          3.836
LGA    N     270      N     270          1.816
LGA    I     271      I     271          3.697
LGA    L     272      L     272          1.473
LGA    Y     273      Y     273          4.304
LGA    V     274      V     274          3.568
LGA    G     275      G     275          8.084
LGA    Q     276      Q     276          7.843
LGA    G     277      G     277         14.986
LGA    F     278      F     278         20.366
LGA    Y     279      Y     279         24.037
LGA    H     280      H     280         19.850
LGA    D     281      D     281         19.050
LGA    S     282      S     282         14.528
LGA    L     283      L     283         14.311

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   60    4.0     23    3.07    32.500    27.461     0.725

LGA_LOCAL      RMSD =  3.074  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.678  Number of atoms =   60 
Std_ALL_ATOMS  RMSD =  8.674  (standard rmsd on all 60 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.370222 * X  +   0.801218 * Y  +  -0.470090 * Z  +  36.310131
  Y_new =   0.851366 * X  +   0.495102 * Y  +   0.173351 * Z  +  21.065632
  Z_new =   0.371635 * X  +  -0.336040 * Y  +  -0.865427 * Z  + -14.862232 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.771218    0.370374  [ DEG:  -158.7791     21.2209 ]
  Theta =  -0.380769   -2.760824  [ DEG:   -21.8165   -158.1835 ]
  Phi   =   1.980986   -1.160607  [ DEG:   113.5021    -66.4979 ]
 
# 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: T0316TS393_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_1-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   64   60   4.0   23   3.07  27.461     8.67
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_1-D2
PFRMAT TS
TARGET T0316
MODEL 1
PARENT N/A
ATOM    220  CA  GLY   220      26.254  30.948 -20.159  1.00 25.00           C
ATOM    221  CA  ARG   221      29.358  29.261 -18.851  1.00 25.00           C
ATOM    222  CA  MET   222      30.999  28.170 -15.604  1.00 25.00           C
ATOM    223  CA  MET   223      33.094  25.671 -17.635  1.00 25.00           C
ATOM    224  CA  THR   224      36.465  23.930 -17.899  1.00 25.00           C
ATOM    225  CA  VAL   225      39.072  24.986 -20.496  1.00 25.00           C
ATOM    226  CA  ASP   226      42.126  22.746 -20.853  1.00 25.00           C
ATOM    227  CA  GLY   227      42.458  19.905 -23.381  1.00 25.00           C
ATOM    228  CA  ARG   228      41.634  16.465 -24.659  1.00 25.00           C
ATOM    229  CA  ASP   229      38.104  17.273 -23.568  1.00 25.00           C
ATOM    230  CA  MET   230      38.084  20.030 -26.234  1.00 25.00           C
ATOM    231  CA  GLY   231      38.166  22.176 -29.294  1.00 25.00           C
ATOM    232  CA  GLU   232      41.908  21.542 -29.402  1.00 25.00           C
ATOM    233  CA  HIS   233      45.068  20.099 -27.881  1.00 25.00           C
ATOM    234  CA  ALA   234      46.147  22.891 -25.516  1.00 25.00           C
ATOM    235  CA  GLY   235      46.521  25.748 -23.051  1.00 25.00           C
ATOM    236  CA  LEU   236      48.177  27.104 -19.913  1.00 25.00           C
ATOM    237  CA  MET   237      45.241  25.577 -18.092  1.00 25.00           C
ATOM    238  CA  TYR   238      41.904  24.596 -16.619  1.00 25.00           C
ATOM    239  CA  TYR   239      38.999  23.226 -14.640  1.00 25.00           C
ATOM    240  CA  THR   240      35.381  23.791 -13.550  1.00 25.00           C
ATOM    241  CA  ILE   241      31.930  22.595 -14.657  1.00 25.00           C
ATOM    242  CA  GLY   242      30.828  19.130 -13.489  1.00 25.00           C
ATOM    243  CA  GLN   243      32.451  17.770 -16.676  1.00 25.00           C
ATOM    244  CA  ARG   244      32.841  21.074 -18.547  1.00 25.00           C
ATOM    245  CA  GLY   245      30.253  21.620 -21.314  1.00 25.00           C
ATOM    246  CA  GLY   246      29.153  23.673 -24.370  1.00 25.00           C
ATOM    247  CA  LEU   247      30.493  26.900 -22.851  1.00 25.00           C
ATOM    248  CA  GLY   248      29.663  29.958 -24.943  1.00 25.00           C
ATOM    249  CA  ILE   249      30.851  33.221 -23.341  1.00 25.00           C
ATOM    250  CA  GLY   250      33.976  31.498 -24.584  1.00 25.00           C
ATOM    251  CA  GLY   251      34.101  28.353 -26.713  1.00 25.00           C
ATOM    252  CA  GLN   252      31.362  27.176 -29.085  1.00 25.00           C
ATOM    253  CA  HIS   253      30.042  27.977 -32.576  1.00 25.00           C
ATOM    254  CA  GLY   254      29.727  24.593 -34.227  1.00 25.00           C
ATOM    255  CA  GLY   255      26.404  22.883 -33.843  1.00 25.00           C
ATOM    256  CA  ASP   256      24.506  26.134 -34.019  1.00 25.00           C
ATOM    257  CA  ASN   257      25.509  26.944 -30.464  1.00 25.00           C
ATOM    258  CA  ALA   258      26.498  27.194 -26.821  1.00 25.00           C
ATOM    259  CA  PRO   259      25.457  26.864 -23.148  1.00 25.00           C
ATOM    260  CA  TRP   260      25.177  23.593 -21.305  1.00 25.00           C
ATOM    261  CA  PHE   261      25.790  20.076 -20.118  1.00 25.00           C
ATOM    262  CA  VAL   262      28.345  17.640 -18.803  1.00 25.00           C
ATOM    263  CA  VAL   263      29.821  14.530 -17.172  1.00 25.00           C
ATOM    264  CA  GLY   264      31.478  14.003 -13.786  1.00 25.00           C
ATOM    265  CA  LYS   265      34.964  14.164 -15.211  1.00 25.00           C
ATOM    266  CA  ASP   266      37.494  11.936 -16.842  1.00 25.00           C
ATOM    267  CA  LEU   267      39.490  14.796 -18.283  1.00 25.00           C
ATOM    268  CA  SER   268      42.376  15.487 -20.685  1.00 25.00           C
ATOM    269  CA  LYS   269      45.361  17.551 -19.740  1.00 25.00           C
ATOM    270  CA  ASN   270      44.415  16.961 -16.096  1.00 25.00           C
ATOM    271  CA  ILE   271      41.567  19.279 -16.950  1.00 25.00           C
ATOM    272  CA  LEU   272      39.170  19.686 -19.817  1.00 25.00           C
ATOM    273  CA  TYR   273      36.172  21.363 -21.417  1.00 25.00           C
ATOM    274  CA  VAL   274      33.540  22.341 -24.009  1.00 25.00           C
ATOM    275  CA  GLY   275      34.438  23.296 -27.625  1.00 25.00           C
ATOM    276  CA  GLN   276      31.593  21.757 -29.574  1.00 25.00           C
ATOM    277  CA  GLY   277      33.441  21.111 -32.802  1.00 25.00           C
ATOM    278  CA  PHE   278      36.198  18.502 -33.143  1.00 25.00           C
ATOM    279  CA  TYR   279      39.487  16.803 -33.946  1.00 25.00           C
ATOM    280  CA  HIS   280      41.043  16.859 -30.503  1.00 25.00           C
ATOM    281  CA  ASP   281      40.886  13.451 -28.755  1.00 25.00           C
ATOM    282  CA  SER   282      38.150  10.780 -28.527  1.00 25.00           C
ATOM    283  CA  LEU   283      36.365  12.808 -25.812  1.00 25.00           C
TER
END
