
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS168_4-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:    22       262 - 283         4.82    12.75
  LCS_AVERAGE:     31.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       224 - 231         1.95    18.36
  LONGEST_CONTINUOUS_SEGMENT:     8       225 - 232         1.91    19.10
  LONGEST_CONTINUOUS_SEGMENT:     8       240 - 247         1.97    15.92
  LONGEST_CONTINUOUS_SEGMENT:     8       241 - 248         1.96    16.68
  LONGEST_CONTINUOUS_SEGMENT:     8       242 - 249         1.55    18.72
  LONGEST_CONTINUOUS_SEGMENT:     8       243 - 250         1.91    20.32
  LONGEST_CONTINUOUS_SEGMENT:     8       256 - 263         1.88    16.74
  LONGEST_CONTINUOUS_SEGMENT:     8       260 - 267         1.90    12.23
  LONGEST_CONTINUOUS_SEGMENT:     8       265 - 272         1.87    13.20
  LONGEST_CONTINUOUS_SEGMENT:     8       268 - 275         1.95    12.32
  LCS_AVERAGE:     11.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       242 - 247         0.97    18.17
  LCS_AVERAGE:      7.25

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      3    3   11     3    3    3    3    4    7    8    8    8    8   11   12   18   21   24   28   30   32   35   38 
LCS_GDT     R     221     R     221      4    5   12     3    3    5    5    6    6    7   10   11   14   17   20   23   30   32   33   34   36   37   40 
LCS_GDT     M     222     M     222      4    6   13     3    3    4    5    6    6    7   10   11   14   20   24   28   30   32   33   34   36   38   40 
LCS_GDT     M     223     M     223      4    6   14     0    3    4    5    5    6    7   11   15   17   20   24   28   30   32   33   34   36   38   40 
LCS_GDT     T     224     T     224      4    8   14     2    3    4    5    7    8   10   12   13   16   16   17   28   30   32   33   34   36   38   40 
LCS_GDT     V     225     V     225      5    8   14     1    5    6    6    9   11   12   12   14   16   16   23   28   30   32   33   34   36   38   40 
LCS_GDT     D     226     D     226      5    8   14     3    5    6    6    9   11   12   12   15   17   20   24   28   30   32   33   34   36   38   40 
LCS_GDT     G     227     G     227      5    8   14     3    5    6    6    9   11   12   12   15   17   20   24   28   30   32   33   34   36   38   40 
LCS_GDT     R     228     R     228      5    8   14     3    6    8    9   10   12   12   13   14   16   17   20   24   25   31   33   34   36   36   38 
LCS_GDT     D     229     D     229      5    8   14     3    4    6    6    9   11   12   12   14   16   17   19   20   23   26   29   30   33   35   37 
LCS_GDT     M     230     M     230      4    8   14     3    3    5    6    7    8   12   12   14   16   16   17   20   21   26   28   30   33   35   39 
LCS_GDT     G     231     G     231      4    8   15     3    3    5    6    9   11   12   12   14   16   17   21   22   23   28   30   32   34   34   39 
LCS_GDT     E     232     E     232      3    8   15     3    3    5    6    9   11   12   17   21   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     H     233     H     233      3    6   15     3    4    4    8   11   14   17   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     A     234     A     234      4    6   15     3    4    5    8   11   15   17   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     G     235     G     235      4    6   15     3    4    5    8   10   15   17   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     L     236     L     236      4    6   15     3    3    4    5    7    8   13   14   16   24   26   27   30   31   31   32   32   34   38   40 
LCS_GDT     M     237     M     237      4    6   15     0    3    4    7   11   15   17   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     Y     238     Y     238      3    6   15     3    3    4    6   11   14   16   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     Y     239     Y     239      3    6   21     3    3    4    6   11   14   16   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     T     240     T     240      3    8   21     3    3    4    7   11   15   17   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     I     241     I     241      3    8   21     3    4    5    8   11   15   17   20   22   25   28   28   30   31   31   32   33   34   38   40 
LCS_GDT     G     242     G     242      6    8   21     3    5    6    7   11   15   17   20   22   25   28   28   30   31   31   32   32   34   38   40 
LCS_GDT     Q     243     Q     243      6    8   21     3    5    6    6    9   11   15   18   22   25   28   28   30   31   31   32   33   35   37   40 
LCS_GDT     R     244     R     244      6    8   21     3    5    6    6    9   11   16   19   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     G     245     G     245      6    8   21     3    5    8    9   10   12   12   14   15   19   22   25   28   30   32   33   34   36   38   40 
LCS_GDT     G     246     G     246      6    8   21     3    5    6    9   10   12   13   15   16   18   21   24   28   30   32   33   34   36   37   40 
LCS_GDT     L     247     L     247      6    8   21     3    6    8    9   10   12   13   15   16   18   21   24   28   30   32   33   34   36   36   39 
LCS_GDT     G     248     G     248      4    8   21     3    3    4    7    9   11   13   15   16   18   21   24   28   30   32   33   34   36   36   40 
LCS_GDT     I     249     I     249      4    8   21     3    3    6    6    9   11   13   15   16   18   21   23   27   30   32   33   34   36   38   40 
LCS_GDT     G     250     G     250      3    8   21     3    4    5    7    7   11   13   15   16   18   21   23   26   27   29   32   34   36   38   40 
LCS_GDT     G     251     G     251      3    4   21     0    1    4    5    8    9   11   12   15   19   22   24   27   28   29   31   32   34   38   40 
LCS_GDT     D     256     D     256      4    8   21     3    3    6    6    9   11   15   18   21   24   28   28   30   31   31   32   32   33   36   39 
LCS_GDT     N     257     N     257      5    8   21     3    4    6    7    9   11   13   15   16   18   24   28   30   31   31   32   32   33   36   39 
LCS_GDT     A     258     A     258      5    8   21     3    4    6    7    9   11   13   15   16   18   19   23   26   27   31   32   32   33   35   38 
LCS_GDT     P     259     P     259      5    8   21     3    4    6    7    9   11   13   15   16   18   24   28   30   31   31   32   32   33   38   40 
LCS_GDT     W     260     W     260      5    8   21     3    4    6    7   11   15   17   19   22   25   28   28   30   31   31   32   34   36   38   40 
LCS_GDT     F     261     F     261      5    8   21     3    4    6    8   11   15   17   19   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     V     262     V     262      4    8   22     3    4    6    8   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     V     263     V     263      5    8   22     3    4    6    7    9   14   16   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     G     264     G     264      5    8   22     3    4    6    8   10   14   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     K     265     K     265      5    8   22     3    4    6    7   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     D     266     D     266      5    8   22     3    4    6    7   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     L     267     L     267      5    8   22     3    4    5    7    9   14   16   17   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     S     268     S     268      4    8   22     3    4    5    6   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     K     269     K     269      4    8   22     3    4    4    7   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     N     270     N     270      4    8   22     3    4    5    7   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     I     271     I     271      5    8   22     3    6    8    9   10   14   16   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     L     272     L     272      5    8   22     3    6    8    9   11   15   17   20   22   25   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     Y     273     Y     273      5    8   22     3    6    8    9   10   14   16   18   22   23   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     V     274     V     274      5    8   22     3    5    8    9   11   14   16   20   22   23   28   28   29   31   32   33   34   36   38   40 
LCS_GDT     G     275     G     275      5    8   22     3    6    8    9   10   14   16   17   19   20   23   25   28   30   32   33   34   36   38   40 
LCS_GDT     Q     276     Q     276      4    6   22     3    4    4    5    9   11   14   17   18   19   20   24   28   30   32   33   34   36   38   40 
LCS_GDT     G     277     G     277      4    6   22     2    4    4    5    6    9    9   11   13   18   20   24   28   30   32   33   34   36   36   40 
LCS_GDT     F     278     F     278      4    6   22     3    3    4    5    7    9   12   15   15   18   20   24   28   30   32   33   34   36   38   40 
LCS_GDT     Y     279     Y     279      4    6   22     3    3    4    7    9   10   10   14   15   18   21   24   28   30   32   33   34   36   38   40 
LCS_GDT     H     280     H     280      4    6   22     3    3    4    5    5    7    8   13   15   18   21   24   26   28   31   33   34   36   38   40 
LCS_GDT     D     281     D     281      4    6   22     3    3    4    7    9   10   10   14   15   18   21   24   26   28   31   31   31   34   38   40 
LCS_GDT     S     282     S     282      3    6   22     3    3    4    7    9   10   10   14   16   18   21   24   26   28   31   31   31   34   38   40 
LCS_GDT     L     283     L     283      3    3   22     3    3    3    6    9    9   10   14   14   18   21   23   26   28   31   31   32   34   38   40 
LCS_AVERAGE  LCS_A:  17.06  (   7.25   11.97   31.97 )

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      3      6      8      9     11     15     17     20     22     25     28     28     30     31     32     33     34     36     38     40 
GDT PERCENT_CA   5.00  10.00  13.33  15.00  18.33  25.00  28.33  33.33  36.67  41.67  46.67  46.67  50.00  51.67  53.33  55.00  56.67  60.00  63.33  66.67
GDT RMS_LOCAL    0.04   0.76   0.95   1.12   1.84   2.23   2.39   2.85   3.04   3.31   3.66   3.66   4.19   4.28   5.13   5.23   5.35   5.70   7.10   7.29
GDT RMS_ALL_CA  19.05  12.05  12.05  12.01  12.58  12.66  12.51  12.27  12.34  12.53  12.49  12.49  12.58  12.50  11.68  11.70  11.64  11.38   9.92   9.87

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         20.141
LGA    R     221      R     221         20.467
LGA    M     222      M     222         16.944
LGA    M     223      M     223         14.978
LGA    T     224      T     224         14.749
LGA    V     225      V     225         18.207
LGA    D     226      D     226         23.034
LGA    G     227      G     227         21.522
LGA    R     228      R     228         22.472
LGA    D     229      D     229         17.640
LGA    M     230      M     230         12.664
LGA    G     231      G     231          9.839
LGA    E     232      E     232          5.374
LGA    H     233      H     233          3.015
LGA    A     234      A     234          3.131
LGA    G     235      G     235          3.714
LGA    L     236      L     236          5.834
LGA    M     237      M     237          3.337
LGA    Y     238      Y     238          3.177
LGA    Y     239      Y     239          3.934
LGA    T     240      T     240          2.469
LGA    I     241      I     241          3.071
LGA    G     242      G     242          2.010
LGA    Q     243      Q     243          6.972
LGA    R     244      R     244          7.654
LGA    G     245      G     245         12.720
LGA    G     246      G     246         16.512
LGA    L     247      L     247         22.078
LGA    G     248      G     248         22.087
LGA    I     249      I     249         17.139
LGA    G     250      G     250         18.710
LGA    G     251      G     251         13.788
LGA    D     256      D     256          8.422
LGA    N     257      N     257         14.401
LGA    A     258      A     258         14.696
LGA    P     259      P     259         12.453
LGA    W     260      W     260          6.381
LGA    F     261      F     261          6.376
LGA    V     262      V     262          3.611
LGA    V     263      V     263          3.390
LGA    G     264      G     264          2.839
LGA    K     265      K     265          1.877
LGA    D     266      D     266          1.800
LGA    L     267      L     267          4.291
LGA    S     268      S     268          2.280
LGA    K     269      K     269          2.037
LGA    N     270      N     270          1.878
LGA    I     271      I     271          3.724
LGA    L     272      L     272          0.845
LGA    Y     273      Y     273          4.355
LGA    V     274      V     274          3.098
LGA    G     275      G     275          7.030
LGA    Q     276      Q     276         10.760
LGA    G     277      G     277         15.258
LGA    F     278      F     278         13.754
LGA    Y     279      Y     279         16.328
LGA    H     280      H     280         16.952
LGA    D     281      D     281         18.228
LGA    S     282      S     282         16.116
LGA    L     283      L     283         10.473

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   60    4.0     20    2.85    28.333    25.595     0.679

LGA_LOCAL      RMSD =  2.846  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.344  Number of atoms =   60 
Std_ALL_ATOMS  RMSD =  9.623  (standard rmsd on all 60 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.639199 * X  +  -0.699935 * Y  +  -0.318615 * Z  +  31.023628
  Y_new =   0.336048 * X  +  -0.118442 * Y  +   0.934368 * Z  +  15.671639
  Z_new =  -0.691734 * X  +  -0.704317 * Y  +   0.159504 * Z  + -13.741122 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.348087    1.793506  [ DEG:   -77.2397    102.7603 ]
  Theta =   0.763887    2.377705  [ DEG:    43.7675    136.2325 ]
  Phi   =   0.484022   -2.657571  [ DEG:    27.7324   -152.2676 ]
 
# 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_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_4-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   20   2.85  25.595     9.62
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_4-D2
PFRMAT TS
TARGET T0316
MODEL 4
PARENT N/A
ATOM    220  CA  GLY   220      34.756  14.308  -5.227  1.00 25.00           C
ATOM    221  CA  ARG   221      35.790  10.981  -6.745  1.00 25.00           C
ATOM    222  CA  MET   222      35.974  10.457 -10.484  1.00 25.00           C
ATOM    223  CA  MET   223      36.906  14.044 -10.948  1.00 25.00           C
ATOM    224  CA  THR   224      38.227  17.313 -12.293  1.00 25.00           C
ATOM    225  CA  VAL   225      38.191  17.706  -8.509  1.00 25.00           C
ATOM    226  CA  ASP   226      34.942  18.998  -6.956  1.00 25.00           C
ATOM    227  CA  GLY   227      31.809  20.253  -8.801  1.00 25.00           C
ATOM    228  CA  ARG   228      33.153  23.725  -9.576  1.00 25.00           C
ATOM    229  CA  ASP   229      34.163  24.323 -13.195  1.00 25.00           C
ATOM    230  CA  MET   230      36.014  22.170 -15.720  1.00 25.00           C
ATOM    231  CA  GLY   231      39.165  23.218 -17.615  1.00 25.00           C
ATOM    232  CA  GLU   232      40.641  21.424 -20.590  1.00 25.00           C
ATOM    233  CA  HIS   233      43.392  24.031 -20.757  1.00 25.00           C
ATOM    234  CA  ALA   234      43.091  27.814 -21.076  1.00 25.00           C
ATOM    235  CA  GLY   235      41.822  27.561 -17.461  1.00 25.00           C
ATOM    236  CA  LEU   236      44.338  26.464 -14.882  1.00 25.00           C
ATOM    237  CA  MET   237      40.944  25.497 -13.475  1.00 25.00           C
ATOM    238  CA  TYR   238      38.622  23.673 -11.019  1.00 25.00           C
ATOM    239  CA  TYR   239      36.033  20.928 -11.498  1.00 25.00           C
ATOM    240  CA  THR   240      32.584  19.939 -12.832  1.00 25.00           C
ATOM    241  CA  ILE   241      29.742  20.709 -15.241  1.00 25.00           C
ATOM    242  CA  GLY   242      26.407  19.030 -14.450  1.00 25.00           C
ATOM    243  CA  GLN   243      27.231  18.144 -18.012  1.00 25.00           C
ATOM    244  CA  ARG   244      26.692  19.513 -21.497  1.00 25.00           C
ATOM    245  CA  GLY   245      27.166  16.166 -23.307  1.00 25.00           C
ATOM    246  CA  GLY   246      29.531  13.445 -22.316  1.00 25.00           C
ATOM    247  CA  LEU   247      28.610   9.819 -21.667  1.00 25.00           C
ATOM    248  CA  GLY   248      25.777  10.723 -24.020  1.00 25.00           C
ATOM    249  CA  ILE   249      26.709  12.817 -27.069  1.00 25.00           C
ATOM    250  CA  GLY   250      30.097  11.144 -26.772  1.00 25.00           C
ATOM    251  CA  GLY   251      33.578  12.566 -26.234  1.00 25.00           C
ATOM    252  CA  GLN   252      31.891  15.204 -28.348  1.00 25.00           C
ATOM    253  CA  HIS   253      33.776  14.940 -31.611  1.00 25.00           C
ATOM    254  CA  GLY   254      31.635  17.333 -33.591  1.00 25.00           C
ATOM    255  CA  GLY   255      30.822  21.062 -33.433  1.00 25.00           C
ATOM    256  CA  ASP   256      33.087  24.032 -34.214  1.00 25.00           C
ATOM    257  CA  ASN   257      36.284  22.253 -33.120  1.00 25.00           C
ATOM    258  CA  ALA   258      36.930  22.377 -29.351  1.00 25.00           C
ATOM    259  CA  PRO   259      34.429  19.579 -28.656  1.00 25.00           C
ATOM    260  CA  TRP   260      30.874  20.476 -27.556  1.00 25.00           C
ATOM    261  CA  PHE   261      30.798  18.525 -24.247  1.00 25.00           C
ATOM    262  CA  VAL   262      30.906  18.007 -20.474  1.00 25.00           C
ATOM    263  CA  VAL   263      32.942  18.953 -17.412  1.00 25.00           C
ATOM    264  CA  GLY   264      34.667  16.743 -14.810  1.00 25.00           C
ATOM    265  CA  LYS   265      37.117  13.957 -15.527  1.00 25.00           C
ATOM    266  CA  ASP   266      40.284  11.942 -16.119  1.00 25.00           C
ATOM    267  CA  LEU   267      43.880  10.919 -15.395  1.00 25.00           C
ATOM    268  CA  SER   268      45.083  14.532 -15.126  1.00 25.00           C
ATOM    269  CA  LYS   269      43.711  15.045 -18.608  1.00 25.00           C
ATOM    270  CA  ASN   270      43.128  18.448 -17.125  1.00 25.00           C
ATOM    271  CA  ILE   271      39.653  17.134 -16.498  1.00 25.00           C
ATOM    272  CA  LEU   272      37.283  18.640 -19.030  1.00 25.00           C
ATOM    273  CA  TYR   273      35.174  21.538 -20.239  1.00 25.00           C
ATOM    274  CA  VAL   274      31.524  22.299 -21.128  1.00 25.00           C
ATOM    275  CA  GLY   275      29.013  25.049 -20.576  1.00 25.00           C
ATOM    276  CA  GLN   276      29.944  28.104 -18.588  1.00 25.00           C
ATOM    277  CA  GLY   277      31.094  30.090 -15.601  1.00 25.00           C
ATOM    278  CA  PHE   278      28.058  32.282 -16.294  1.00 25.00           C
ATOM    279  CA  TYR   279      24.750  32.609 -18.149  1.00 25.00           C
ATOM    280  CA  HIS   280      23.329  31.371 -14.886  1.00 25.00           C
ATOM    281  CA  ASP   281      20.480  28.996 -15.412  1.00 25.00           C
ATOM    282  CA  SER   282      22.749  26.589 -13.483  1.00 25.00           C
ATOM    283  CA  LEU   283      21.059  23.600 -15.180  1.00 25.00           C
TER
END
