
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0289TS550_2-D2
# Molecule2: number of CA atoms   74 (  581),  selected   21 , name T0289_D2.pdb
# PARAMETERS: T0289TS550_2-D2.T0289_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:    11       227 - 237         4.50    19.61
  LCS_AVERAGE:     14.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       229 - 235         1.71    17.47
  LCS_AVERAGE:      8.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       225 - 228         0.99    18.90
  LONGEST_CONTINUOUS_SEGMENT:     4       227 - 230         0.73    20.31
  LONGEST_CONTINUOUS_SEGMENT:     4       229 - 232         0.56    16.47
  LONGEST_CONTINUOUS_SEGMENT:     4       230 - 233         0.90    17.37
  LONGEST_CONTINUOUS_SEGMENT:     4       231 - 234         0.34    17.58
  LONGEST_CONTINUOUS_SEGMENT:     4       256 - 259         0.70    26.97
  LONGEST_CONTINUOUS_SEGMENT:     4       257 - 260         0.94    21.88
  LCS_AVERAGE:      5.02

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:   74
LCS_GDT     I     224     I     224      3    6    9     0    3    3    3    5    6    7    8    8    8    9   10   10   11   11   11   13   13   13   15 
LCS_GDT     M     225     M     225      4    6    9     2    3    3    5    5    6    7    8    9    9    9   10   10   11   11   11   13   13   13   15 
LCS_GDT     E     226     E     226      4    6   10     0    3    3    5    5    6    7    7    9    9    9   10   10   11   11   11   13   15   16   17 
LCS_GDT     K     227     K     227      4    6   11     3    3    4    5    5    6    7    7    7    8   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     V     228     V     228      4    6   11     3    3    4    5    5    6    7    7    7    8   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     D     229     D     229      4    7   11     3    4    5    6    6    7    7    7    7    8   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     Y     230     Y     230      4    7   11     3    4    5    6    6    7    7    7    7    8   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     P     231     P     231      4    7   11     4    4    5    6    6    7    7    7    7    8   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     R     232     R     232      4    7   11     4    4    5    6    6    7    7    7    7    8   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     N     233     N     233      4    7   11     4    4    5    6    6    7    7    7    9    9   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     E     234     E     234      4    7   11     4    4    5    6    6    7    8    8    9    9   10   11   11   12   13   13   14   15   16   17 
LCS_GDT     S     235     S     235      3    7   11     3    3    4    5    6    7    8    8    9    9   10   10   11   12   13   13   14   15   16   17 
LCS_GDT     G     236     G     236      3    5   11     3    3    4    4    5    5    8    8    9    9   10   10   11   11   12   13   14   15   16   17 
LCS_GDT     D     237     D     237      3    5   11     3    3    4    4    5    5    8    8    9    9    9   10   11   11   12   12   14   15   16   17 
LCS_GDT     H     255     H     255      3    6   10     3    3    3    4    5    6    7    8    9    9    9   11   11   12   13   13   14   15   16   17 
LCS_GDT     P     256     P     256      4    6   10     3    4    4    4    5    6    7    8    9    9    9   11   11   12   13   13   14   15   16   17 
LCS_GDT     G     257     G     257      4    6   10     3    4    4    5    5    6    7    8    9    9    9   11   11   12   13   13   14   15   16   17 
LCS_GDT     D     258     D     258      4    6   10     3    4    4    5    5    6    8    8    9    9    9   10   11   12   13   13   14   15   16   17 
LCS_GDT     P     259     P     259      4    6   10     3    4    4    5    5    6    8    8    9    9    9   10   11   11   12   12   14   15   16   17 
LCS_GDT     V     260     V     260      4    6   10     3    3    4    5    5    6    8    8    9    9    9   10   11   11   12   12   13   14   14   15 
LCS_GDT     F     261     F     261      3    3   10     3    3    3    3    4    4    8    8    9    9    9   10   11   11   12   12   13   15   16   17 
LCS_AVERAGE  LCS_A:   9.12  (   5.02    8.24   14.09 )

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      5      6      6      7      8      8      9      9     10     11     11     12     13     13     14     15     16     17 
GDT PERCENT_CA   5.41   5.41   6.76   8.11   8.11   9.46  10.81  10.81  12.16  12.16  13.51  14.86  14.86  16.22  17.57  17.57  18.92  20.27  21.62  22.97
GDT RMS_LOCAL    0.34   0.34   1.01   1.29   1.29   1.71   2.89   2.89   3.10   3.10   4.07   4.47   4.47   5.06   5.38   5.38   5.87   6.26   6.72   7.02
GDT RMS_ALL_CA  17.58  17.58  17.46  15.89  15.89  17.47  16.18  16.18  15.91  15.91  18.10   9.72   9.72   9.42   9.02   9.02   8.84   8.77   8.53   8.49

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224         29.629
LGA    M     225      M     225         26.453
LGA    E     226      E     226         25.729
LGA    K     227      K     227         25.162
LGA    V     228      V     228         23.780
LGA    D     229      D     229         23.908
LGA    Y     230      Y     230         20.981
LGA    P     231      P     231         14.743
LGA    R     232      R     232         11.479
LGA    N     233      N     233          4.378
LGA    E     234      E     234          3.582
LGA    S     235      S     235          2.561
LGA    G     236      G     236          1.612
LGA    D     237      D     237          2.193
LGA    H     255      H     255         17.136
LGA    P     256      P     256         13.216
LGA    G     257      G     257          9.057
LGA    D     258      D     258          3.872
LGA    P     259      P     259          3.245
LGA    V     260      V     260          3.075
LGA    F     261      F     261          3.262

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   74    4.0      8    2.89    10.473    10.132     0.267

LGA_LOCAL      RMSD =  2.892  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.097  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  8.164  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.441513 * X  +  -0.713611 * Y  +   0.543899 * Z  +  16.471235
  Y_new =   0.894200 * X  +  -0.299970 * Y  +   0.332303 * Z  +   5.314507
  Z_new =  -0.073982 * X  +   0.633070 * Y  +   0.770551 * Z  + -13.261353 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.687762   -2.453830  [ DEG:    39.4059   -140.5941 ]
  Theta =   0.074049    3.067543  [ DEG:     4.2427    175.7573 ]
  Phi   =   2.029433   -1.112160  [ DEG:   116.2779    -63.7221 ]
 
# 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: T0289TS550_2-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289TS550_2-D2.T0289_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   74   4.0    8   2.89  10.132     8.16
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS550_2-D2
PFRMAT TS
TARGET T0289
MODEL 2
PARENT 2bco_B
ATOM    223  N   ILE   224      18.594  54.004  33.116  1.00  0.00
ATOM    223  CA  ILE   224      18.318  53.896  34.538  1.00  0.00
ATOM    223  C   ILE   224      18.182  52.419  34.933  1.00  0.00
ATOM    223  O   ILE   224      17.099  51.842  34.830  1.00  0.00
ATOM    224  N   MET   225      19.285  51.837  35.379  1.00  0.00
ATOM    224  CA  MET   225      19.294  50.433  35.783  1.00  0.00
ATOM    224  C   MET   225      18.385  50.116  36.977  1.00  0.00
ATOM    224  O   MET   225      18.809  50.208  38.131  1.00  0.00
ATOM    225  N   GLU   226      17.542  51.095  37.528  1.00  0.00
ATOM    225  CA  GLU   226      16.150  51.493  37.718  1.00  0.00
ATOM    225  C   GLU   226      16.047  53.009  37.611  1.00  0.00
ATOM    225  O   GLU   226      16.912  53.752  38.074  1.00  0.00
ATOM    226  N   LYS   227      14.984  53.449  36.960  1.00  0.00
ATOM    226  CA  LYS   227      14.607  54.859  37.016  1.00  0.00
ATOM    226  C   LYS   227      13.263  55.031  37.683  1.00  0.00
ATOM    226  O   LYS   227      12.621  56.056  37.520  1.00  0.00
ATOM    227  N   VAL   228      12.849  54.048  38.466  1.00  0.00
ATOM    227  CA  VAL   228      11.628  54.171  39.264  1.00  0.00
ATOM    227  C   VAL   228      11.921  54.949  40.542  1.00  0.00
ATOM    227  O   VAL   228      12.837  54.602  41.296  1.00  0.00
ATOM    228  N   ASP   229      11.147  56.010  40.790  1.00  0.00
ATOM    228  CA  ASP   229      11.322  56.848  41.977  1.00  0.00
ATOM    228  C   ASP   229      11.238  56.038  43.262  1.00  0.00
ATOM    228  O   ASP   229      12.015  56.266  44.193  1.00  0.00
ATOM    229  N   TYR   230      10.314  55.084  43.287  1.00  0.00
ATOM    229  CA  TYR   230      10.137  54.209  44.446  1.00  0.00
ATOM    229  C   TYR   230      10.961  52.925  44.422  1.00  0.00
ATOM    229  O   TYR   230      10.812  52.074  45.300  1.00  0.00
ATOM    230  N   PRO   231      11.831  52.817  43.429  1.00  0.00
ATOM    230  CA  PRO   231      12.762  51.704  43.281  1.00  0.00
ATOM    230  C   PRO   231      12.050  50.359  43.156  1.00  0.00
ATOM    230  O   PRO   231      12.643  49.318  43.414  1.00  0.00
ATOM    231  N   ARG   232      10.786  50.363  42.739  1.00  0.00
ATOM    231  CA  ARG   232      10.023  49.112  42.684  1.00  0.00
ATOM    231  C   ARG   232       9.948  48.598  41.259  1.00  0.00
ATOM    231  O   ARG   232       9.504  49.298  40.355  1.00  0.00
ATOM    232  N   ASN   233      10.411  47.372  41.037  1.00  0.00
ATOM    232  CA  ASN   233      10.423  46.789  39.704  1.00  0.00
ATOM    232  C   ASN   233       9.014  46.631  39.121  1.00  0.00
ATOM    232  O   ASN   233       8.090  46.196  39.805  1.00  0.00
ATOM    233  N   GLU   234       8.890  47.004  37.857  1.00  0.00
ATOM    233  CA  GLU   234       7.713  46.712  37.041  1.00  0.00
ATOM    233  C   GLU   234       8.111  45.908  35.820  1.00  0.00
ATOM    233  O   GLU   234       9.231  46.007  35.333  1.00  0.00
ATOM    234  N   SER   235       7.163  45.134  35.304  1.00  0.00
ATOM    234  CA  SER   235       7.408  44.297  34.147  1.00  0.00
ATOM    234  C   SER   235       7.990  45.134  33.010  1.00  0.00
ATOM    234  O   SER   235       7.480  46.214  32.698  1.00  0.00
ATOM    235  N   GLY   236       9.095  44.660  32.433  1.00  0.00
ATOM    235  CA  GLY   236       9.807  45.374  31.388  1.00  0.00
ATOM    235  C   GLY   236      11.060  46.098  31.861  1.00  0.00
ATOM    235  O   GLY   236      11.947  46.446  31.073  1.00  0.00
ATOM    236  N   ASP   237      11.138  46.352  33.162  1.00  0.00
ATOM    236  CA  ASP   237      12.296  47.038  33.721  1.00  0.00
ATOM    236  C   ASP   237      13.510  46.100  33.718  1.00  0.00
ATOM    236  O   ASP   237      13.357  44.875  33.675  1.00  0.00
ATOM    254  N   HIS   255      27.635  47.883  38.717  1.00  0.00
ATOM    254  CA  HIS   255      28.938  48.038  38.095  1.00  0.00
ATOM    254  C   HIS   255      29.402  46.737  37.433  1.00  0.00
ATOM    254  O   HIS   255      29.136  45.652  37.946  1.00  0.00
ATOM    255  N   PRO   256      30.086  46.870  36.308  1.00  0.00
ATOM    255  CA  PRO   256      30.571  45.725  35.538  1.00  0.00
ATOM    255  C   PRO   256      31.711  44.920  36.158  1.00  0.00
ATOM    255  O   PRO   256      32.795  45.451  36.384  1.00  0.00
ATOM    256  N   GLY   257      32.787  44.953  36.508  1.00  0.00
ATOM    256  CA  GLY   257      33.612  44.633  37.667  1.00  0.00
ATOM    256  C   GLY   257      33.835  43.146  37.861  1.00  0.00
ATOM    256  O   GLY   257      34.591  42.741  38.744  1.00  0.00
ATOM    257  N   ASP   258      33.172  42.335  37.047  1.00  0.00
ATOM    257  CA  ASP   258      33.324  40.878  37.100  1.00  0.00
ATOM    257  C   ASP   258      34.007  40.345  35.837  1.00  0.00
ATOM    257  O   ASP   258      33.864  39.169  35.500  1.00  0.00
ATOM    258  N   PRO   259      34.724  41.242  35.166  1.00  0.00
ATOM    258  CA  PRO   259      35.431  41.023  33.884  1.00  0.00
ATOM    258  C   PRO   259      34.571  41.391  32.683  1.00  0.00
ATOM    258  O   PRO   259      35.086  41.630  31.598  1.00  0.00
ATOM    259  N   VAL   260      33.185  41.443  33.061  1.00  0.00
ATOM    259  CA  VAL   260      32.450  41.717  31.840  1.00  0.00
ATOM    259  C   VAL   260      30.954  41.495  31.992  1.00  0.00
ATOM    259  O   VAL   260      30.233  41.325  31.004  1.00  0.00
ATOM    260  N   PHE   261      30.483  41.499  33.231  1.00  0.00
ATOM    260  CA  PHE   261      29.067  41.281  33.507  1.00  0.00
ATOM    260  C   PHE   261      28.495  42.299  34.497  1.00  0.00
ATOM    260  O   PHE   261      29.088  42.567  35.546  1.00  0.00
TER
END
