
#######################################################
#                                                     #
#                        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 T0316TS168_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS168_2-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:    24       228 - 251         4.78    12.50
  LCS_AVERAGE:     35.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       256 - 269         1.98    15.06
  LCS_AVERAGE:     14.39

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       220 - 224         0.83    14.20
  LONGEST_CONTINUOUS_SEGMENT:     5       222 - 226         0.84    17.46
  LONGEST_CONTINUOUS_SEGMENT:     5       260 - 264         0.65    16.04
  LONGEST_CONTINUOUS_SEGMENT:     5       263 - 267         0.98    15.11
  LONGEST_CONTINUOUS_SEGMENT:     5       264 - 268         0.81    17.91
  LCS_AVERAGE:      6.92

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      5    8   19     3    5    6    9   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     R     221     R     221      5    8   19     3    5    6    9   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     M     222     M     222      5    8   19     3    5    6    8   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     M     223     M     223      5    8   19     3    5    6    9   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     T     224     T     224      5    8   19     3    5    6    9   11   13   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     V     225     V     225      5    8   19     3    4    5    7    9   10   11   12   14   17   18   26   27   28   32   34   35   38   39   42 
LCS_GDT     D     226     D     226      5    8   19     3    4    5    6    9   10   11   12   14   17   19   22   24   28   32   33   35   38   39   42 
LCS_GDT     G     227     G     227      4    8   19     3    3    6    7   11   12   15   15   19   19   22   25   30   31   32   35   36   38   39   42 
LCS_GDT     R     228     R     228      4    8   24     3    4    6    7    9   11   14   16   19   21   22   26   31   31   32   35   36   38   39   42 
LCS_GDT     D     229     D     229      4    8   24     3    4    6    7    9   10   14   16   16   21   22   26   31   31   32   35   36   38   39   42 
LCS_GDT     M     230     M     230      4    7   24     3    4    6    8   10   11   14   17   19   21   22   27   31   32   34   37   37   38   39   42 
LCS_GDT     G     231     G     231      4    7   24     1    4    4    7    9   11   14   16   19   19   22   22   24   28   33   37   37   38   39   42 
LCS_GDT     E     232     E     232      4    7   24     0    4    5    8   10   10   14   17   21   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     H     233     H     233      4    7   24     3    4    5    9   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     A     234     A     234      4    7   24     3    4    5    7   10   12   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     G     235     G     235      4    7   24     3    4    5    8   10   11   15   21   25   26   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     L     236     L     236      4    6   24     3    4    5    7   10   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     M     237     M     237      4    7   24     3    4    5    7    8   11   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     Y     238     Y     238      4    7   24     4    4    5    9   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     Y     239     Y     239      4    7   24     4    4    5    9   11   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     T     240     T     240      4    7   24     4    4    5    9   10   12   15   20   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     I     241     I     241      4    7   24     4    4    5    5    8   11   15   16   23   25   28   30   31   32   34   37   37   38   39   41 
LCS_GDT     G     242     G     242      3    7   24     3    3    5    9   10   12   15   19   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     Q     243     Q     243      4    7   24     0    3    4    8   10   12   15   19   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     R     244     R     244      4    7   24     3    3    4    4    7   10   14   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     G     245     G     245      4    6   24     3    3    4    4    6    9   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     G     246     G     246      4    6   24     3    5    6    8   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     L     247     L     247      4    6   24     3    5    6    8   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     G     248     G     248      4    6   24     3    4    6    8   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     I     249     I     249      4    6   24     3    4    4    7    8   11   15   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     G     250     G     250      3    6   24     3    5    6    8   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     G     251     G     251      3    6   24     2    3    3    4   12   14   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     D     256     D     256      4   14   22     3    6   10   11   12   13   15   17   19   19   20   21   24   25   25   26   30   32   34   38 
LCS_GDT     N     257     N     257      4   14   22     3    6   10   11   12   13   15   17   19   19   20   21   24   25   25   26   30   32   34   38 
LCS_GDT     A     258     A     258      4   14   22     3    3    5    9   12   13   15   17   19   19   20   21   24   25   25   26   30   32   34   37 
LCS_GDT     P     259     P     259      4   14   22     3    4    5    7    9   12   14   16   19   19   20   21   24   25   25   27   30   32   34   38 
LCS_GDT     W     260     W     260      5   14   22     3    6   10   11   12   13   15   17   19   19   20   21   24   25   25   27   30   32   38   39 
LCS_GDT     F     261     F     261      5   14   22     3    6   10   11   12   13   15   17   19   19   20   21   24   25   27   28   29   34   38   39 
LCS_GDT     V     262     V     262      5   14   22     3    5    9   11   12   13   15   17   19   19   22   23   26   30   31   34   35   38   39   42 
LCS_GDT     V     263     V     263      5   14   22     3    6   10   11   12   14   16   21   22   25   27   29   31   32   34   37   37   38   39   42 
LCS_GDT     G     264     G     264      5   14   22     3    5   10   11   12   13   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     K     265     K     265      5   14   22     3    4   10   11   12   13   15   17   19   22   27   30   31   32   34   37   37   38   39   42 
LCS_GDT     D     266     D     266      5   14   22     3    6   10   11   12   13   15   17   19   19   20   21   24   30   32   35   36   37   38   41 
LCS_GDT     L     267     L     267      5   14   22     3    6   10   11   12   13   15   17   19   19   20   21   24   25   25   26   33   35   35   35 
LCS_GDT     S     268     S     268      5   14   22     3    4    6    9   12   13   15   16   19   19   20   21   24   25   25   26   33   35   35   35 
LCS_GDT     K     269     K     269      3   14   22     3    4   10   11   12   13   15   17   19   19   20   21   24   25   25   26   27   29   32   34 
LCS_GDT     N     270     N     270      3    9   22     0    3    3    8    9   12   14   17   19   19   20   21   24   25   25   26   33   35   35   35 
LCS_GDT     I     271     I     271      4    9   22     0    5    6    8    9   12   14   17   19   19   20   21   24   28   31   35   36   37   38   41 
LCS_GDT     L     272     L     272      4    9   22     3    5    6    8   10   13   14   17   19   24   28   30   31   32   34   37   37   38   39   42 
LCS_GDT     Y     273     Y     273      4    7   22     3    5    6    9   11   13   16   21   25   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     V     274     V     274      4    7   22     3    5    6    6    7    9   14   16   19   19   22   24   28   31   33   37   37   38   39   42 
LCS_GDT     G     275     G     275      4    7   22     3    3    6    7    7    9   10   16   16   16   19   21   22   25   27   30   31   36   38   39 
LCS_GDT     Q     276     Q     276      4    6   21     3    3    4    7    7    9   10   12   13   18   19   22   23   25   27   28   31   34   38   39 
LCS_GDT     G     277     G     277      4    6   15     3    3    4    7    7   10   13   16   16   18   22   22   24   25   27   28   30   34   37   39 
LCS_GDT     F     278     F     278      3    6   15     3    4    4    5    9   11   12   14   19   19   22   22   24   25   27   28   32   35   38   39 
LCS_GDT     Y     279     Y     279      3    6   15     3    3    4    5    9   11   12   14   19   19   22   22   24   25   28   32   34   36   38   39 
LCS_GDT     H     280     H     280      4    6   15     3    3    4    5    9   11   12   14   19   19   22   25   28   31   33   37   37   38   38   42 
LCS_GDT     D     281     D     281      4    6   15     3    4    4    5    6    8   12   21   24   28   29   29   31   32   34   37   37   38   39   42 
LCS_GDT     S     282     S     282      4    6   15     3    4    4    4    5    6   10   16   20   28   29   30   31   32   34   37   37   38   39   42 
LCS_GDT     L     283     L     283      4    6   15     3    4    4    4    5    8   16   21   24   28   29   29   31   32   34   37   37   38   39   42 
LCS_AVERAGE  LCS_A:  19.08  (   6.92   14.39   35.94 )

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      6     10     11     12     14     16     21     25     28     29     30     31     32     34     37     37     38     39     42 
GDT PERCENT_CA   6.67  10.00  16.67  18.33  20.00  23.33  26.67  35.00  41.67  46.67  48.33  50.00  51.67  53.33  56.67  61.67  61.67  63.33  65.00  70.00
GDT RMS_LOCAL    0.38   0.59   1.07   1.16   1.41   2.00   2.30   2.85   3.32   3.65   3.70   3.99   3.98   4.11   4.42   5.03   5.03   5.20   5.40   6.00
GDT RMS_ALL_CA  21.91  15.10  15.02  15.06  15.08  12.03  11.94  11.84  11.71  11.60  11.62  11.74  11.60  11.59  11.55  11.38  11.38  11.37  11.77  11.70

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220          0.728
LGA    R     221      R     221          1.230
LGA    M     222      M     222          1.939
LGA    M     223      M     223          2.513
LGA    T     224      T     224          3.798
LGA    V     225      V     225         11.028
LGA    D     226      D     226         12.910
LGA    G     227      G     227         11.016
LGA    R     228      R     228         10.212
LGA    D     229      D     229          9.087
LGA    M     230      M     230          6.800
LGA    G     231      G     231          9.325
LGA    E     232      E     232          4.988
LGA    H     233      H     233          2.018
LGA    A     234      A     234          3.902
LGA    G     235      G     235          4.439
LGA    L     236      L     236          2.485
LGA    M     237      M     237          3.986
LGA    Y     238      Y     238          1.807
LGA    Y     239      Y     239          2.806
LGA    T     240      T     240          5.404
LGA    I     241      I     241          8.792
LGA    G     242      G     242          7.211
LGA    Q     243      Q     243          7.501
LGA    R     244      R     244          5.411
LGA    G     245      G     245          3.486
LGA    G     246      G     246          1.162
LGA    L     247      L     247          1.433
LGA    G     248      G     248          2.623
LGA    I     249      I     249          3.975
LGA    G     250      G     250          2.764
LGA    G     251      G     251          2.559
LGA    D     256      D     256         24.547
LGA    N     257      N     257         27.441
LGA    A     258      A     258         25.088
LGA    P     259      P     259         19.534
LGA    W     260      W     260         15.673
LGA    F     261      F     261         14.020
LGA    V     262      V     262          8.581
LGA    V     263      V     263          3.706
LGA    G     264      G     264          3.719
LGA    K     265      K     265         10.369
LGA    D     266      D     266         16.696
LGA    L     267      L     267         22.523
LGA    S     268      S     268         26.156
LGA    K     269      K     269         24.189
LGA    N     270      N     270         19.443
LGA    I     271      I     271         13.257
LGA    L     272      L     272          7.797
LGA    Y     273      Y     273          3.321
LGA    V     274      V     274          7.988
LGA    G     275      G     275         12.766
LGA    Q     276      Q     276         15.288
LGA    G     277      G     277         16.632
LGA    F     278      F     278         17.065
LGA    Y     279      Y     279         14.700
LGA    H     280      H     280         10.281
LGA    D     281      D     281          7.906
LGA    S     282      S     282          9.189
LGA    L     283      L     283          7.953

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   60    4.0     21    2.85    31.250    27.713     0.713

LGA_LOCAL      RMSD =  2.846  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.838  Number of atoms =   60 
Std_ALL_ATOMS  RMSD = 10.616  (standard rmsd on all 60 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.397906 * X  +  -0.908914 * Y  +   0.124684 * Z  +  29.846184
  Y_new =   0.792139 * X  +  -0.408938 * Y  +  -0.453084 * Z  +  21.345123
  Z_new =   0.462802 * X  +  -0.081518 * Y  +   0.882706 * Z  + -18.238495 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.092089    3.049504  [ DEG:    -5.2763    174.7237 ]
  Theta =  -0.481153   -2.660439  [ DEG:   -27.5681   -152.4319 ]
  Phi   =   2.036297   -1.105296  [ DEG:   116.6712    -63.3288 ]
 
# 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: T0316TS168_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_2-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   21   2.85  27.713    10.62
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_2-D2
PFRMAT TS
TARGET T0316
MODEL 2
PARENT N/A
ATOM    220  CA  GLY   220      45.575  21.872 -21.036  1.00 25.00           C
ATOM    221  CA  ARG   221      42.630  21.587 -23.403  1.00 25.00           C
ATOM    222  CA  MET   222      39.354  20.336 -21.913  1.00 25.00           C
ATOM    223  CA  MET   223      37.408  20.190 -25.128  1.00 25.00           C
ATOM    224  CA  THR   224      34.900  19.746 -27.878  1.00 25.00           C
ATOM    225  CA  VAL   225      36.898  21.800 -30.368  1.00 25.00           C
ATOM    226  CA  ASP   226      34.278  24.616 -30.317  1.00 25.00           C
ATOM    227  CA  GLY   227      31.739  22.956 -28.050  1.00 25.00           C
ATOM    228  CA  ARG   228      29.740  21.676 -25.065  1.00 25.00           C
ATOM    229  CA  ASP   229      32.568  20.226 -22.979  1.00 25.00           C
ATOM    230  CA  MET   230      35.047  22.899 -21.889  1.00 25.00           C
ATOM    231  CA  GLY   231      36.768  23.566 -18.625  1.00 25.00           C
ATOM    232  CA  GLU   232      38.421  26.109 -20.929  1.00 25.00           C
ATOM    233  CA  HIS   233      41.284  24.431 -18.978  1.00 25.00           C
ATOM    234  CA  ALA   234      44.106  24.329 -16.494  1.00 25.00           C
ATOM    235  CA  GLY   235      45.011  20.683 -16.041  1.00 25.00           C
ATOM    236  CA  LEU   236      42.436  20.577 -13.248  1.00 25.00           C
ATOM    237  CA  MET   237      39.589  22.680 -14.573  1.00 25.00           C
ATOM    238  CA  TYR   238      38.695  26.288 -14.213  1.00 25.00           C
ATOM    239  CA  TYR   239      35.005  26.638 -14.927  1.00 25.00           C
ATOM    240  CA  THR   240      31.875  24.858 -16.154  1.00 25.00           C
ATOM    241  CA  ILE   241      28.593  26.781 -16.571  1.00 25.00           C
ATOM    242  CA  GLY   242      26.514  25.461 -19.525  1.00 25.00           C
ATOM    243  CA  GLN   243      28.145  28.699 -20.678  1.00 25.00           C
ATOM    244  CA  ARG   244      30.105  25.870 -22.303  1.00 25.00           C
ATOM    245  CA  GLY   245      33.103  26.667 -20.111  1.00 25.00           C
ATOM    246  CA  GLY   246      32.219  29.616 -17.842  1.00 25.00           C
ATOM    247  CA  LEU   247      35.463  30.284 -19.652  1.00 25.00           C
ATOM    248  CA  GLY   248      34.731  30.542 -23.365  1.00 25.00           C
ATOM    249  CA  ILE   249      31.044  30.483 -24.317  1.00 25.00           C
ATOM    250  CA  GLY   250      31.163  27.277 -26.428  1.00 25.00           C
ATOM    251  CA  GLY   251      34.585  25.873 -25.718  1.00 25.00           C
ATOM    252  CA  GLN   252      38.359  25.562 -26.012  1.00 25.00           C
ATOM    253  CA  HIS   253      41.203  24.198 -28.203  1.00 25.00           C
ATOM    254  CA  GLY   254      44.727  23.883 -29.598  1.00 25.00           C
ATOM    255  CA  GLY   255      45.678  24.777 -26.000  1.00 25.00           C
ATOM    256  CA  ASP   256      48.467  22.212 -26.344  1.00 25.00           C
ATOM    257  CA  ASN   257      48.753  18.602 -25.142  1.00 25.00           C
ATOM    258  CA  ALA   258      45.795  16.659 -23.868  1.00 25.00           C
ATOM    259  CA  PRO   259      42.136  16.929 -24.787  1.00 25.00           C
ATOM    260  CA  TRP   260      41.414  16.534 -21.043  1.00 25.00           C
ATOM    261  CA  PHE   261      39.923  14.787 -18.091  1.00 25.00           C
ATOM    262  CA  VAL   262      36.394  14.018 -16.922  1.00 25.00           C
ATOM    263  CA  VAL   263      33.478  16.415 -16.559  1.00 25.00           C
ATOM    264  CA  GLY   264      30.138  15.270 -15.115  1.00 25.00           C
ATOM    265  CA  LYS   265      26.686  15.914 -16.543  1.00 25.00           C
ATOM    266  CA  ASP   266      23.912  16.479 -19.077  1.00 25.00           C
ATOM    267  CA  LEU   267      21.204  14.083 -20.170  1.00 25.00           C
ATOM    268  CA  SER   268      20.615  16.342 -23.140  1.00 25.00           C
ATOM    269  CA  LYS   269      22.059  19.774 -22.534  1.00 25.00           C
ATOM    270  CA  ASN   270      25.560  20.622 -21.263  1.00 25.00           C
ATOM    271  CA  ILE   271      28.797  21.891 -19.690  1.00 25.00           C
ATOM    272  CA  LEU   272      30.146  18.330 -19.391  1.00 25.00           C
ATOM    273  CA  TYR   273      32.136  15.448 -20.933  1.00 25.00           C
ATOM    274  CA  VAL   274      33.444  12.000 -19.952  1.00 25.00           C
ATOM    275  CA  GLY   275      34.193   8.336 -19.135  1.00 25.00           C
ATOM    276  CA  GLN   276      30.946   6.863 -20.566  1.00 25.00           C
ATOM    277  CA  GLY   277      28.332   5.284 -18.290  1.00 25.00           C
ATOM    278  CA  PHE   278      26.474   4.410 -21.484  1.00 25.00           C
ATOM    279  CA  TYR   279      24.938   4.089 -24.972  1.00 25.00           C
ATOM    280  CA  HIS   280      26.372   7.266 -26.429  1.00 25.00           C
ATOM    281  CA  ASP   281      23.532   9.310 -27.912  1.00 25.00           C
ATOM    282  CA  SER   282      22.186  12.612 -26.515  1.00 25.00           C
ATOM    283  CA  LEU   283      25.014  12.700 -23.933  1.00 25.00           C
TER
END
