
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS168_3-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:    23       246 - 272         4.95    13.13
  LONGEST_CONTINUOUS_SEGMENT:    23       247 - 273         4.88    12.89
  LCS_AVERAGE:     34.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       225 - 232         1.91    14.45
  LONGEST_CONTINUOUS_SEGMENT:     8       226 - 233         1.91    17.21
  LONGEST_CONTINUOUS_SEGMENT:     8       261 - 268         1.97    13.90
  LONGEST_CONTINUOUS_SEGMENT:     8       274 - 281         1.93    14.50
  LCS_AVERAGE:     11.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       225 - 229         0.76    14.42
  LONGEST_CONTINUOUS_SEGMENT:     5       264 - 268         0.84    16.67
  LONGEST_CONTINUOUS_SEGMENT:     5       275 - 279         0.65    14.54
  LCS_AVERAGE:      6.67

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   10     0    3    4    6    6    7    7    7    8   10   11   13   14   14   15   20   22   24   26   29 
LCS_GDT     R     221     R     221      4    6   10     3    4    4    6    6    7    7    8    9   10   12   15   17   18   20   23   23   27   29   33 
LCS_GDT     M     222     M     222      4    6   17     3    4    4    5    6    7    7    8   10   14   14   15   17   19   20   24   26   27   29   33 
LCS_GDT     M     223     M     223      4    6   17     3    4    4    7    8    8   10   11   13   14   20   20   24   27   27   30   30   30   31   33 
LCS_GDT     T     224     T     224      4    6   17     3    4    4    6    8    9   12   14   17   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     V     225     V     225      5    8   17     3    5    6    7    9    9   11   14   17   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     D     226     D     226      5    8   17     3    5    6    7    9    9   11   14   17   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     G     227     G     227      5    8   17     3    5    6    7    9    9   12   14   17   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     R     228     R     228      5    8   17     3    5    6    7    9    9   11   14   17   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     D     229     D     229      5    8   17     3    5    5    7    8    9   11   14   15   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     M     230     M     230      4    8   17     3    5    5    6    8    9    9   14   15   19   20   21   24   27   27   30   30   32   34   35 
LCS_GDT     G     231     G     231      4    8   20     3    5    6    7    9    9   15   17   17   19   22   23   25   27   29   31   32   34   35   37 
LCS_GDT     E     232     E     232      4    8   20     3    5    6    7    9   12   15   17   17   19   22   23   25   27   29   31   32   34   35   37 
LCS_GDT     H     233     H     233      4    8   20     4    5    6    7    9   12   15   17   17   18   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     A     234     A     234      4    7   20     4    5    6    7    9   12   15   17   17   18   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     G     235     G     235      4    7   20     4    5    5    7    9   12   15   17   17   18   19   23   25   27   29   31   32   34   35   37 
LCS_GDT     L     236     L     236      4    7   20     4    5    6    6    8   10   15   17   17   18   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     M     237     M     237      4    6   20     3    4    5    7    8   12   15   17   17   19   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     Y     238     Y     238      4    6   20     3    3    5    7    8   11   12   16   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     Y     239     Y     239      4    5   20     3    3    5    7    8   11   12   16   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     T     240     T     240      4    5   20     3    3    4    5    6    8   11   13   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     I     241     I     241      4    5   20     3    4    4    5    6    8   10   10   13   15   20   22   25   27   29   31   32   34   35   37 
LCS_GDT     G     242     G     242      4    5   20     3    4    4    5    6    8   10   10   11   13   16   19   20   27   29   31   32   34   35   37 
LCS_GDT     Q     243     Q     243      4    5   20     3    4    4    4    5    6    8   10   10   13   16   18   20   21   23   27   32   34   34   37 
LCS_GDT     R     244     R     244      4    5   20     3    4    4    7    8    9   10   11   12   13   16   18   20   24   26   29   32   34   34   37 
LCS_GDT     G     245     G     245      3    5   20     3    3    4    4    4    7   10   11   12   13   16   18   20   24   29   31   32   34   35   37 
LCS_GDT     G     246     G     246      3    5   23     3    3    4    7    8    9   10   11   12   13   17   18   22   26   29   31   32   34   35   37 
LCS_GDT     L     247     L     247      4    5   23     3    4    4    6    8    9   10   11   12   13   17   19   25   27   29   31   32   34   35   37 
LCS_GDT     G     248     G     248      4    5   23     3    4    4    7    8    9   11   16   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     I     249     I     249      4    5   23     3    4    4    7    8   10   12   16   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     G     250     G     250      4    5   23     1    4    4    6    8    9   10   11   12   19   20   23   25   26   29   31   32   34   35   37 
LCS_GDT     G     251     G     251      3    5   23     0    3    3    4    5    9   11   16   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     D     256     D     256      4    6   23     1    5    6    7    9   12   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     N     257     N     257      4    6   23     4    5    6    7    9   12   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     A     258     A     258      4    6   23     4    5    6    7    9   12   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     P     259     P     259      4    6   23     4    5    6    7    9   12   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     W     260     W     260      3    7   23     3    3    4    6    8   10   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     F     261     F     261      3    8   23     3    3    4    6    8   10   14   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     V     262     V     262      3    8   23     3    4    5    6    8   12   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     V     263     V     263      3    8   23     3    4    4    6    9   12   15   17   18   20   21   23   25   27   29   31   32   34   35   37 
LCS_GDT     G     264     G     264      5    8   23     3    5    6    7    9   12   15   17   18   20   22   23   25   27   29   31   32   34   35   37 
LCS_GDT     K     265     K     265      5    8   23     3    4    6    7    9   11   13   15   18   20   22   23   25   27   29   31   32   34   35   37 
LCS_GDT     D     266     D     266      5    8   23     3    4    6    7    9   10   13   14   17   20   22   23   25   27   29   30   32   34   35   37 
LCS_GDT     L     267     L     267      5    8   23     3    4    6    6    9   10   13   14   17   19   22   23   24   27   27   30   30   33   35   36 
LCS_GDT     S     268     S     268      5    8   23     3    4    6    7    9    9   10   12   15   16   20   21   23   26   27   30   30   32   35   36 
LCS_GDT     K     269     K     269      3    7   23     3    3    4    6    6   10   11   15   18   20   21   23   25   26   29   30   32   33   35   37 
LCS_GDT     N     270     N     270      3    6   23     3    3    4    7    9   10   12   15   18   20   21   23   25   26   29   30   32   34   35   37 
LCS_GDT     I     271     I     271      3    6   23     3    3    4    7    9   10   12   16   18   20   21   23   25   26   29   31   32   34   35   37 
LCS_GDT     L     272     L     272      4    6   23     3    4    5    7    9   11   13   16   18   20   22   23   25   27   29   31   32   34   35   37 
LCS_GDT     Y     273     Y     273      4    7   23     4    4    5    7    9   12   15   17   17   19   22   23   25   27   29   31   32   34   35   37 
LCS_GDT     V     274     V     274      4    8   21     3    4    5    7    8   11   13   14   17   19   22   23   24   27   27   30   31   32   35   37 
LCS_GDT     G     275     G     275      5    8   21     3    5    5    7    8   11   13   14   17   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     Q     276     Q     276      5    8   21     3    5    5    7    8   11   13   14   16   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     G     277     G     277      5    8   21     3    5    5    7    8   11   13   14   16   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     F     278     F     278      5    8   21     3    5    5    7    8   11   13   14   16   17   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     Y     279     Y     279      5    8   21     3    5    5    7    8   11   13   14   16   19   22   23   24   27   27   30   30   30   31   33 
LCS_GDT     H     280     H     280      3    8   21     3    3    4    4    5    6   11   13   15   16   20   23   24   27   27   30   30   30   32   34 
LCS_GDT     D     281     D     281      3    8   21     3    4    6    7    8   11   13   14   17   19   22   23   24   27   27   30   30   31   33   35 
LCS_GDT     S     282     S     282      3    4   21     3    4    6    6    7   11   13   14   17   19   22   23   24   27   27   30   31   32   35   37 
LCS_GDT     L     283     L     283      3    4   21     3    3    5    6    9    9   11   14   15   16   21   23   24   27   27   30   31   32   35   37 
LCS_AVERAGE  LCS_A:  17.32  (   6.67   11.00   34.31 )

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      4      5      6      7      9     12     15     17     18     20     22     23     25     27     29     31     32     34     35     37 
GDT PERCENT_CA   6.67   8.33  10.00  11.67  15.00  20.00  25.00  28.33  30.00  33.33  36.67  38.33  41.67  45.00  48.33  51.67  53.33  56.67  58.33  61.67
GDT RMS_LOCAL    0.32   0.54   0.86   1.07   1.59   2.18   2.48   2.68   3.29   3.50   3.89   3.94   4.32   4.53   5.06   5.60   5.73   5.99   6.13   6.46
GDT RMS_ALL_CA  14.65  16.84  12.29  12.44  11.83  11.71  11.78  11.83  12.76  12.66  14.06  12.54  12.82  13.92  13.00  12.32  12.74  12.46  12.52  11.97

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         17.557
LGA    R     221      R     221         16.942
LGA    M     222      M     222         13.315
LGA    M     223      M     223         13.026
LGA    T     224      T     224         12.159
LGA    V     225      V     225         15.762
LGA    D     226      D     226         21.629
LGA    G     227      G     227         19.049
LGA    R     228      R     228         18.034
LGA    D     229      D     229         14.571
LGA    M     230      M     230          7.184
LGA    G     231      G     231          3.421
LGA    E     232      E     232          2.240
LGA    H     233      H     233          2.242
LGA    A     234      A     234          0.823
LGA    G     235      G     235          2.411
LGA    L     236      L     236          3.557
LGA    M     237      M     237          3.396
LGA    Y     238      Y     238          6.670
LGA    Y     239      Y     239          6.248
LGA    T     240      T     240          8.527
LGA    I     241      I     241          9.749
LGA    G     242      G     242         11.123
LGA    Q     243      Q     243         14.382
LGA    R     244      R     244         14.634
LGA    G     245      G     245         12.418
LGA    G     246      G     246         12.710
LGA    L     247      L     247         10.849
LGA    G     248      G     248          8.091
LGA    I     249      I     249          8.638
LGA    G     250      G     250         12.040
LGA    G     251      G     251          8.805
LGA    D     256      D     256          0.544
LGA    N     257      N     257          2.272
LGA    A     258      A     258          1.984
LGA    P     259      P     259          2.467
LGA    W     260      W     260          3.170
LGA    F     261      F     261          3.841
LGA    V     262      V     262          2.874
LGA    V     263      V     263          1.965
LGA    G     264      G     264          3.017
LGA    K     265      K     265          9.777
LGA    D     266      D     266         12.964
LGA    L     267      L     267         18.317
LGA    S     268      S     268         20.177
LGA    K     269      K     269         16.324
LGA    N     270      N     270         15.377
LGA    I     271      I     271         11.050
LGA    L     272      L     272          8.092
LGA    Y     273      Y     273          2.926
LGA    V     274      V     274          8.423
LGA    G     275      G     275         12.995
LGA    Q     276      Q     276         18.042
LGA    G     277      G     277         20.775
LGA    F     278      F     278         19.012
LGA    Y     279      Y     279         18.105
LGA    H     280      H     280         14.659
LGA    D     281      D     281         14.063
LGA    S     282      S     282          8.859
LGA    L     283      L     283          7.350

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   60    4.0     17    2.68    25.000    21.690     0.611

LGA_LOCAL      RMSD =  2.684  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.833  Number of atoms =   60 
Std_ALL_ATOMS  RMSD = 11.359  (standard rmsd on all 60 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.959829 * X  +   0.241664 * Y  +  -0.142574 * Z  +  38.060677
  Y_new =  -0.271927 * X  +  -0.926432 * Y  +   0.260346 * Z  +  16.319067
  Z_new =  -0.069169 * X  +   0.288657 * Y  +   0.954931 * Z  + -21.009871 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.293548   -2.848044  [ DEG:    16.8191   -163.1809 ]
  Theta =   0.069224    3.072368  [ DEG:     3.9663    176.0337 ]
  Phi   =  -2.865519    0.276074  [ DEG:  -164.1821     15.8179 ]
 
# 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_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_3-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   17   2.68  21.690    11.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_3-D2
PFRMAT TS
TARGET T0316
MODEL 3
PARENT N/A
ATOM    220  CA  GLY   220      33.596  24.669  -7.889  1.00 25.00           C
ATOM    221  CA  ARG   221      37.241  23.447  -7.827  1.00 25.00           C
ATOM    222  CA  MET   222      36.206  21.129 -10.672  1.00 25.00           C
ATOM    223  CA  MET   223      34.047  22.244 -13.599  1.00 25.00           C
ATOM    224  CA  THR   224      30.834  21.646 -15.515  1.00 25.00           C
ATOM    225  CA  VAL   225      28.636  24.744 -15.232  1.00 25.00           C
ATOM    226  CA  ASP   226      27.136  28.133 -15.869  1.00 25.00           C
ATOM    227  CA  GLY   227      28.055  27.480 -19.444  1.00 25.00           C
ATOM    228  CA  ARG   228      29.985  30.282 -21.130  1.00 25.00           C
ATOM    229  CA  ASP   229      33.152  30.913 -23.222  1.00 25.00           C
ATOM    230  CA  MET   230      34.400  27.537 -24.398  1.00 25.00           C
ATOM    231  CA  GLY   231      37.878  26.412 -25.487  1.00 25.00           C
ATOM    232  CA  GLU   232      40.161  24.468 -23.151  1.00 25.00           C
ATOM    233  CA  HIS   233      42.856  25.005 -20.520  1.00 25.00           C
ATOM    234  CA  ALA   234      43.008  27.898 -18.140  1.00 25.00           C
ATOM    235  CA  GLY   235      44.105  26.643 -14.714  1.00 25.00           C
ATOM    236  CA  LEU   236      43.873  23.108 -13.210  1.00 25.00           C
ATOM    237  CA  MET   237      40.899  20.874 -12.655  1.00 25.00           C
ATOM    238  CA  TYR   238      38.100  20.423 -15.162  1.00 25.00           C
ATOM    239  CA  TYR   239      34.887  18.741 -16.296  1.00 25.00           C
ATOM    240  CA  THR   240      32.771  18.552 -19.424  1.00 25.00           C
ATOM    241  CA  ILE   241      30.876  18.855 -22.627  1.00 25.00           C
ATOM    242  CA  GLY   242      29.036  20.526 -25.467  1.00 25.00           C
ATOM    243  CA  GLN   243      31.411  20.666 -28.435  1.00 25.00           C
ATOM    244  CA  ARG   244      28.531  19.542 -30.690  1.00 25.00           C
ATOM    245  CA  GLY   245      25.618  21.715 -29.434  1.00 25.00           C
ATOM    246  CA  GLY   246      28.423  24.193 -28.762  1.00 25.00           C
ATOM    247  CA  LEU   247      31.698  25.104 -27.053  1.00 25.00           C
ATOM    248  CA  GLY   248      34.544  26.033 -29.391  1.00 25.00           C
ATOM    249  CA  ILE   249      36.236  22.604 -29.344  1.00 25.00           C
ATOM    250  CA  GLY   250      36.090  19.761 -31.821  1.00 25.00           C
ATOM    251  CA  GLY   251      32.725  19.692 -33.570  1.00 25.00           C
ATOM    252  CA  GLN   252      31.841  23.288 -32.679  1.00 25.00           C
ATOM    253  CA  HIS   253      30.583  26.906 -32.969  1.00 25.00           C
ATOM    254  CA  GLY   254      29.094  26.236 -36.363  1.00 25.00           C
ATOM    255  CA  GLY   255      26.452  23.620 -35.584  1.00 25.00           C
ATOM    256  CA  ASP   256      25.616  26.064 -32.740  1.00 25.00           C
ATOM    257  CA  ASN   257      23.755  26.718 -29.489  1.00 25.00           C
ATOM    258  CA  ALA   258      23.284  24.955 -26.125  1.00 25.00           C
ATOM    259  CA  PRO   259      25.547  24.295 -23.139  1.00 25.00           C
ATOM    260  CA  TRP   260      27.845  27.020 -24.505  1.00 25.00           C
ATOM    261  CA  PHE   261      29.796  24.224 -22.914  1.00 25.00           C
ATOM    262  CA  VAL   262      29.330  21.809 -20.040  1.00 25.00           C
ATOM    263  CA  VAL   263      28.762  18.300 -18.604  1.00 25.00           C
ATOM    264  CA  GLY   264      30.466  15.104 -17.674  1.00 25.00           C
ATOM    265  CA  LYS   265      28.665  13.066 -20.322  1.00 25.00           C
ATOM    266  CA  ASP   266      29.523  10.989 -23.376  1.00 25.00           C
ATOM    267  CA  LEU   267      30.500  10.824 -27.061  1.00 25.00           C
ATOM    268  CA  SER   268      29.308   7.240 -26.728  1.00 25.00           C
ATOM    269  CA  LYS   269      31.280   6.589 -23.546  1.00 25.00           C
ATOM    270  CA  ASN   270      34.989   6.252 -22.913  1.00 25.00           C
ATOM    271  CA  ILE   271      34.932   9.458 -24.911  1.00 25.00           C
ATOM    272  CA  LEU   272      35.360  11.739 -21.935  1.00 25.00           C
ATOM    273  CA  TYR   273      34.721  14.710 -19.619  1.00 25.00           C
ATOM    274  CA  VAL   274      34.316  14.623 -15.827  1.00 25.00           C
ATOM    275  CA  GLY   275      34.563  16.509 -12.515  1.00 25.00           C
ATOM    276  CA  GLN   276      35.938  12.957 -12.154  1.00 25.00           C
ATOM    277  CA  GLY   277      34.857  10.424  -9.513  1.00 25.00           C
ATOM    278  CA  PHE   278      32.295   7.705 -10.350  1.00 25.00           C
ATOM    279  CA  TYR   279      30.619   7.727  -6.893  1.00 25.00           C
ATOM    280  CA  HIS   280      27.363   8.308  -8.780  1.00 25.00           C
ATOM    281  CA  ASP   281      27.307  11.538  -6.785  1.00 25.00           C
ATOM    282  CA  SER   282      28.659  12.687 -10.179  1.00 25.00           C
ATOM    283  CA  LEU   283      27.711  16.306  -9.358  1.00 25.00           C
TER
END
