
#######################################################
#                                                     #
#                        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   14 (  113),  selected   14 , name T0356TS249_1_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   14 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_1_3-D1.T0356_D1.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:    14       314 - 327         3.89     3.89
  LCS_AVERAGE:     11.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       314 - 324         1.94     4.96
  LONGEST_CONTINUOUS_SEGMENT:    11       315 - 325         1.99     4.41
  LCS_AVERAGE:      8.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       316 - 321         0.99     5.38
  LONGEST_CONTINUOUS_SEGMENT:     6       317 - 322         0.90     4.98
  LCS_AVERAGE:      3.97

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:  124
LCS_GDT     D     314     D     314      4   11   14     3    4    4    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     A     315     A     315      4   11   14     3    4    4    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     I     316     I     316      6   11   14     3    5    6    8    9   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     Y     317     Y     317      6   11   14     3    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     H     318     H     318      6   11   14     3    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     S     319     S     319      6   11   14     3    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     T     320     T     320      6   11   14     4    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     Y     321     Y     321      6   11   14     4    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     T     322     T     322      6   11   14     4    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     G     323     G     323      4   11   14     3    4    5    8    9   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     R     324     R     324      4   11   14     4    5    7    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     P     325     P     325      4   11   14     3    3    4    8   10   11   12   12   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     P     326     P     326      4    5   14     2    3    4    4    4    6    7   11   13   13   13   13   13   13   13   13   13   13   13   14 
LCS_GDT     D     327     D     327      3    4   14     0    3    3    3    4    4    4    5    5    5    5    6    6    6    6    7    8    8   13   14 
LCS_AVERAGE  LCS_A:   7.80  (   3.97    8.12   11.29 )

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      7      8     10     11     12     12     13     13     13     13     13     13     13     13     13     13     13     14 
GDT PERCENT_CA   3.23   4.03   5.65   6.45   8.06   8.87   9.68   9.68  10.48  10.48  10.48  10.48  10.48  10.48  10.48  10.48  10.48  10.48  10.48  11.29
GDT RMS_LOCAL    0.33   0.44   1.11   1.20   1.72   1.90   2.08   2.08   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   3.89
GDT RMS_ALL_CA   5.01   5.21   4.64   5.33   4.18   4.31   4.37   4.37   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.89

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          2.492
LGA    A     315      A     315          2.727
LGA    I     316      I     316          3.145
LGA    Y     317      Y     317          1.944
LGA    H     318      H     318          1.499
LGA    S     319      S     319          1.206
LGA    T     320      T     320          1.319
LGA    Y     321      Y     321          1.034
LGA    T     322      T     322          1.227
LGA    G     323      G     323          2.880
LGA    R     324      R     324          1.143
LGA    P     325      P     325          2.622
LGA    P     326      P     326          7.611
LGA    D     327      D     327         12.546

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  124    4.0     12    2.08     7.661     8.394     0.551

LGA_LOCAL      RMSD =  2.078  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.368  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  3.888  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.679588 * X  +   0.505801 * Y  +   0.531343 * Z  + -30.025581
  Y_new =   0.512907 * X  +   0.190236 * Y  +  -0.837100 * Z  +  82.813034
  Z_new =  -0.524487 * X  +   0.841413 * Y  +  -0.130147 * Z  +  95.915657 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.724257   -1.417336  [ DEG:    98.7926    -81.2074 ]
  Theta =   0.552112    2.589481  [ DEG:    31.6337    148.3663 ]
  Phi   =   0.646523   -2.495070  [ DEG:    37.0430   -142.9570 ]
 
# 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: T0356TS249_1_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_1_3-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  124   4.0   12   2.08   8.394     3.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1tqy_B
ATOM    417  N   ASP   314      74.148  77.001  95.904  1.00  9.99
ATOM    418  CA  ASP   314      74.689  75.931  96.682  1.00  9.99
ATOM    419  CB  ASP   314      73.875  75.687  97.965  1.00  9.99
ATOM    420  CG  ASP   314      74.013  76.921  98.842  1.00  9.99
ATOM    421  OD1 ASP   314      74.818  77.814  98.467  1.00  9.99
ATOM    422  OD2 ASP   314      73.323  76.987  99.893  1.00  9.99
ATOM    423  C   ASP   314      74.725  74.612  95.963  1.00  9.99
ATOM    424  O   ASP   314      75.728  73.904  96.056  1.00  9.99
ATOM    425  N   ALA   315      73.671  74.228  95.209  1.00  9.99
ATOM    426  CA  ALA   315      73.698  72.840  94.811  1.00  9.99
ATOM    427  CB  ALA   315      72.514  72.033  95.373  1.00  9.99
ATOM    428  C   ALA   315      73.706  72.604  93.321  1.00  9.99
ATOM    429  O   ALA   315      72.916  73.166  92.567  1.00  9.99
ATOM    430  N   ILE   316      74.660  71.741  92.900  1.00  9.99
ATOM    431  CA  ILE   316      74.998  71.240  91.589  1.00  9.99
ATOM    432  CB  ILE   316      76.459  70.857  91.543  1.00  9.99
ATOM    433  CG2 ILE   316      76.684  69.763  92.589  1.00  9.99
ATOM    434  CG1 ILE   316      76.969  70.537  90.125  1.00  9.99
ATOM    435  CD1 ILE   316      76.487  69.214  89.528  1.00  9.99
ATOM    436  C   ILE   316      74.117  70.143  91.003  1.00  9.99
ATOM    437  O   ILE   316      73.917  70.123  89.791  1.00  9.99
ATOM    438  N   TYR   317      73.580  69.174  91.785  1.00  9.99
ATOM    439  CA  TYR   317      72.958  68.056  91.095  1.00  9.99
ATOM    440  CB  TYR   317      73.383  66.684  91.646  1.00  9.99
ATOM    441  CG  TYR   317      74.852  66.542  91.445  1.00  9.99
ATOM    442  CD1 TYR   317      75.733  66.978  92.406  1.00  9.99
ATOM    443  CD2 TYR   317      75.351  65.976  90.295  1.00  9.99
ATOM    444  CE1 TYR   317      77.090  66.851  92.228  1.00  9.99
ATOM    445  CE2 TYR   317      76.707  65.847  90.108  1.00  9.99
ATOM    446  CZ  TYR   317      77.579  66.283  91.076  1.00  9.99
ATOM    447  OH  TYR   317      78.971  66.151  90.885  1.00  9.99
ATOM    448  C   TYR   317      71.457  68.097  91.173  1.00  9.99
ATOM    449  O   TYR   317      70.864  68.025  92.248  1.00  9.99
ATOM    450  N   HIS   318      70.797  68.125  89.995  1.00  9.99
ATOM    451  CA  HIS   318      69.369  68.280  89.951  1.00  9.99
ATOM    452  ND1 HIS   318      66.829  70.451  89.956  1.00  9.99
ATOM    453  CG  HIS   318      67.407  69.501  89.147  1.00  9.99
ATOM    454  CB  HIS   318      68.882  69.358  88.979  1.00  9.99
ATOM    455  NE2 HIS   318      65.178  69.190  89.175  1.00  9.99
ATOM    456  CD2 HIS   318      66.383  68.742  88.671  1.00  9.99
ATOM    457  CE1 HIS   318      65.494  70.217  89.938  1.00  9.99
ATOM    458  C   HIS   318      68.687  67.032  89.486  1.00  9.99
ATOM    459  O   HIS   318      68.325  66.191  90.295  1.00  9.99
ATOM    460  N   SER   319      68.504  66.879  88.159  1.00  9.99
ATOM    461  CA  SER   319      67.809  65.770  87.552  1.00  9.99
ATOM    462  CB  SER   319      68.584  64.441  87.638  1.00  9.99
ATOM    463  OG  SER   319      68.615  63.964  88.975  1.00  9.99
ATOM    464  C   SER   319      66.399  65.527  88.054  1.00  9.99
ATOM    465  O   SER   319      66.166  64.765  88.994  1.00  9.99
ATOM    466  N   THR   320      65.417  66.231  87.435  1.00  9.99
ATOM    467  CA  THR   320      64.007  66.159  87.741  1.00  9.99
ATOM    468  CB  THR   320      63.173  67.030  86.823  1.00  9.99
ATOM    469  OG1 THR   320      63.451  66.745  85.460  1.00  9.99
ATOM    470  CG2 THR   320      63.438  68.508  87.085  1.00  9.99
ATOM    471  C   THR   320      63.349  64.814  87.618  1.00  9.99
ATOM    472  O   THR   320      63.312  64.093  88.607  1.00  9.99
ATOM    473  N   TYR   321      62.906  64.360  86.408  1.00  9.99
ATOM    474  CA  TYR   321      61.924  63.312  86.569  1.00  9.99
ATOM    475  CB  TYR   321      60.524  63.797  87.021  1.00  9.99
ATOM    476  CG  TYR   321      60.595  64.226  88.439  1.00  9.99
ATOM    477  CD1 TYR   321      60.549  63.287  89.441  1.00  9.99
ATOM    478  CD2 TYR   321      60.751  65.554  88.761  1.00  9.99
ATOM    479  CE1 TYR   321      60.638  63.673  90.754  1.00  9.99
ATOM    480  CE2 TYR   321      60.841  65.945  90.071  1.00  9.99
ATOM    481  CZ  TYR   321      60.783  65.004  91.067  1.00  9.99
ATOM    482  OH  TYR   321      60.877  65.406  92.415  1.00  9.99
ATOM    483  C   TYR   321      61.584  62.423  85.434  1.00  9.99
ATOM    484  O   TYR   321      62.292  62.277  84.443  1.00  9.99
ATOM    485  N   THR   322      60.426  61.747  85.654  1.00  9.99
ATOM    486  CA  THR   322      59.795  60.863  84.717  1.00  9.99
ATOM    487  CB  THR   322      59.620  59.462  85.226  1.00  9.99
ATOM    488  OG1 THR   322      60.873  58.922  85.618  1.00  9.99
ATOM    489  CG2 THR   322      59.039  58.612  84.086  1.00  9.99
ATOM    490  C   THR   322      58.435  61.432  84.430  1.00  9.99
ATOM    491  O   THR   322      57.823  62.041  85.301  1.00  9.99
ATOM    492  N   GLY   323      57.912  61.276  83.196  1.00  9.99
ATOM    493  CA  GLY   323      56.622  61.865  82.953  1.00  9.99
ATOM    494  C   GLY   323      55.746  60.885  82.239  1.00  9.99
ATOM    495  O   GLY   323      56.156  60.230  81.281  1.00  9.99
ATOM    496  N   ARG   324      54.486  60.772  82.694  1.00  9.99
ATOM    497  CA  ARG   324      53.580  59.879  82.042  1.00  9.99
ATOM    498  CB  ARG   324      53.175  58.667  82.899  1.00  9.99
ATOM    499  CG  ARG   324      52.202  57.713  82.199  1.00  9.99
ATOM    500  CD  ARG   324      51.762  56.536  83.074  1.00  9.99
ATOM    501  NE  ARG   324      50.767  55.742  82.299  1.00  9.99
ATOM    502  CZ  ARG   324      51.182  54.756  81.453  1.00  9.99
ATOM    503  NH1 ARG   324      52.512  54.491  81.307  1.00  9.99
ATOM    504  NH2 ARG   324      50.259  54.031  80.755  1.00  9.99
ATOM    505  C   ARG   324      52.336  60.637  81.725  1.00  9.99
ATOM    506  O   ARG   324      51.775  61.326  82.575  1.00  9.99
ATOM    507  N   PRO   325      51.922  60.536  80.495  1.00  9.99
ATOM    508  CA  PRO   325      50.668  61.109  80.121  1.00  9.99
ATOM    509  CD  PRO   325      52.883  60.624  79.414  1.00  9.99
ATOM    510  CB  PRO   325      50.620  61.028  78.600  1.00  9.99
ATOM    511  CG  PRO   325      52.104  61.174  78.208  1.00  9.99
ATOM    512  C   PRO   325      49.668  60.287  80.848  1.00  9.99
ATOM    513  O   PRO   325      49.877  59.080  80.947  1.00  9.99
ATOM    514  N   PRO   326      48.638  60.898  81.352  1.00  9.99
ATOM    515  CA  PRO   326      47.693  60.202  82.182  1.00  9.99
ATOM    516  CD  PRO   326      48.703  62.315  81.669  1.00  9.99
ATOM    517  CB  PRO   326      46.803  61.286  82.787  1.00  9.99
ATOM    518  CG  PRO   326      47.721  62.520  82.837  1.00  9.99
ATOM    519  C   PRO   326      46.940  59.078  81.551  1.00  9.99
ATOM    520  O   PRO   326      46.671  58.095  82.240  1.00  9.99
ATOM    521  N   ASP   327      46.575  59.183  80.263  1.00  9.99
ATOM    522  CA  ASP   327      45.846  58.110  79.660  1.00  9.99
ATOM    523  CB  ASP   327      45.091  58.541  78.390  1.00  9.99
ATOM    524  CG  ASP   327      44.236  57.381  77.894  1.00  9.99
ATOM    525  OD1 ASP   327      44.449  56.234  78.370  1.00  9.99
ATOM    526  OD2 ASP   327      43.357  57.630  77.026  1.00  9.99
ATOM    527  C   ASP   327      46.902  57.088  79.254  1.00  9.99
ATOM    528  O   ASP   327      47.794  57.452  78.440  1.00  9.99
ATOM    529  OXT ASP   327      46.837  55.935  79.758  1.00  9.99
TER
END
