
#######################################################
#                                                     #
#                        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_5_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   14 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_5_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:    13       314 - 326         4.88     5.28
  LCS_AVERAGE:     10.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       314 - 320         1.89     7.53
  LONGEST_CONTINUOUS_SEGMENT:     7       316 - 322         0.98     7.92
  LCS_AVERAGE:      5.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       316 - 322         0.98     7.92
  LCS_AVERAGE:      3.86

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      3    7   13     3    3    4    5    6    8    8    9    9   10   10   10   11   13   14   14   14   14   14   14 
LCS_GDT     A     315     A     315      3    7   13     3    3    4    4    5    7    7    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     I     316     I     316      7    7   13     4    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     Y     317     Y     317      7    7   13     4    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     H     318     H     318      7    7   13     4    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     S     319     S     319      7    7   13     4    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     T     320     T     320      7    7   13     4    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     Y     321     Y     321      7    7   13     3    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     T     322     T     322      7    7   13     3    5    7    7    7    8    8    9    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     G     323     G     323      3    6   13     3    3    4    4    6    6    7    8    9   10   10   10   12   13   14   14   14   14   14   14 
LCS_GDT     R     324     R     324      3    6   13     1    3    4    4    6    6    6    6    7    7    8   10   12   13   14   14   14   14   14   14 
LCS_GDT     P     325     P     325      3    6   13     1    3    4    4    6    6    6    6    7    7    8   10   12   13   14   14   14   14   14   14 
LCS_GDT     P     326     P     326      3    6   13     0    3    4    4    6    6    6    6    7    7    8   10   12   13   14   14   14   14   14   14 
LCS_GDT     D     327     D     327      0    4   10     0    0    2    3    4    4    6    6    7    7    8    9    9   13   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   6.47  (   3.86    5.24   10.31 )

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      7      7      7      8      8      9      9     10     10     10     12     13     14     14     14     14     14     14 
GDT PERCENT_CA   3.23   4.03   5.65   5.65   5.65   6.45   6.45   7.26   7.26   8.06   8.06   8.06   9.68  10.48  11.29  11.29  11.29  11.29  11.29  11.29
GDT RMS_LOCAL    0.36   0.60   0.98   0.98   0.98   1.80   1.80   2.25   2.25   2.88   2.88   2.88   4.80   4.88   5.21   5.21   5.21   5.21   5.21   5.21
GDT RMS_ALL_CA   7.81   7.87   7.92   7.92   7.92   7.75   7.75   7.48   7.48   7.77   7.77   7.77   5.32   5.28   5.21   5.21   5.21   5.21   5.21   5.21

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          2.510
LGA    A     315      A     315          3.915
LGA    I     316      I     316          1.802
LGA    Y     317      Y     317          2.515
LGA    H     318      H     318          1.402
LGA    S     319      S     319          0.471
LGA    T     320      T     320          1.214
LGA    Y     321      Y     321          2.134
LGA    T     322      T     322          2.509
LGA    G     323      G     323          7.345
LGA    R     324      R     324         11.852
LGA    P     325      P     325         14.357
LGA    P     326      P     326         13.758
LGA    D     327      D     327         12.177

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  124    4.0      9    2.25     7.056     6.584     0.382

LGA_LOCAL      RMSD =  2.254  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.482  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  5.207  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.162100 * X  +  -0.946031 * Y  +   0.280622 * Z  + 190.415878
  Y_new =  -0.692996 * X  +  -0.093312 * Y  +  -0.714877 * Z  +  97.684341
  Z_new =   0.702481 * X  +  -0.310352 * Y  +  -0.640470 * Z  + 158.416077 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.690366    0.451227  [ DEG:  -154.1466     25.8534 ]
  Theta =  -0.778878   -2.362715  [ DEG:   -44.6264   -135.3736 ]
  Phi   =  -1.800577    1.341016  [ DEG:  -103.1654     76.8346 ]
 
# 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_5_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_5_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    9   2.25   6.584     5.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_5_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1fx7_D
ATOM    417  N   ASP   314      75.462  73.660  98.463  1.00  9.99
ATOM    418  CA  ASP   314      76.081  73.043  97.326  1.00  9.99
ATOM    419  CB  ASP   314      77.102  71.934  97.664  1.00  9.99
ATOM    420  CG  ASP   314      76.393  70.712  98.241  1.00  9.99
ATOM    421  OD1 ASP   314      75.665  70.009  97.490  1.00  9.99
ATOM    422  OD2 ASP   314      76.591  70.456  99.456  1.00  9.99
ATOM    423  C   ASP   314      75.100  72.439  96.357  1.00  9.99
ATOM    424  O   ASP   314      75.532  71.641  95.531  1.00  9.99
ATOM    425  N   ALA   315      73.771  72.637  96.480  1.00  9.99
ATOM    426  CA  ALA   315      72.935  71.881  95.566  1.00  9.99
ATOM    427  CB  ALA   315      71.569  71.527  96.171  1.00  9.99
ATOM    428  C   ALA   315      72.659  72.583  94.243  1.00  9.99
ATOM    429  O   ALA   315      71.630  73.234  94.064  1.00  9.99
ATOM    430  N   ILE   316      73.587  72.439  93.268  1.00  9.99
ATOM    431  CA  ILE   316      73.584  73.029  91.941  1.00  9.99
ATOM    432  CB  ILE   316      74.961  73.346  91.430  1.00  9.99
ATOM    433  CG2 ILE   316      74.732  74.443  90.373  1.00  9.99
ATOM    434  CG1 ILE   316      75.860  73.933  92.532  1.00  9.99
ATOM    435  CD1 ILE   316      75.392  75.285  93.065  1.00  9.99
ATOM    436  C   ILE   316      72.834  72.318  90.804  1.00  9.99
ATOM    437  O   ILE   316      72.478  72.968  89.823  1.00  9.99
ATOM    438  N   TYR   317      72.709  70.970  90.831  1.00  9.99
ATOM    439  CA  TYR   317      72.243  70.052  89.798  1.00  9.99
ATOM    440  CB  TYR   317      72.250  68.583  90.249  1.00  9.99
ATOM    441  CG  TYR   317      73.648  68.094  90.343  1.00  9.99
ATOM    442  CD1 TYR   317      74.424  68.355  91.448  1.00  9.99
ATOM    443  CD2 TYR   317      74.176  67.353  89.314  1.00  9.99
ATOM    444  CE1 TYR   317      75.716  67.881  91.514  1.00  9.99
ATOM    445  CE2 TYR   317      75.464  66.878  89.376  1.00  9.99
ATOM    446  CZ  TYR   317      76.239  67.141  90.479  1.00  9.99
ATOM    447  OH  TYR   317      77.561  66.651  90.544  1.00  9.99
ATOM    448  C   TYR   317      70.867  70.240  89.233  1.00  9.99
ATOM    449  O   TYR   317      70.006  70.920  89.780  1.00  9.99
ATOM    450  N   HIS   318      70.644  69.636  88.042  1.00  9.99
ATOM    451  CA  HIS   318      69.340  69.643  87.453  1.00  9.99
ATOM    452  ND1 HIS   318      68.749  72.615  86.016  1.00  9.99
ATOM    453  CG  HIS   318      69.685  71.609  85.927  1.00  9.99
ATOM    454  CB  HIS   318      69.339  70.151  86.003  1.00  9.99
ATOM    455  NE2 HIS   318      70.727  73.608  85.792  1.00  9.99
ATOM    456  CD2 HIS   318      70.889  72.234  85.792  1.00  9.99
ATOM    457  CE1 HIS   318      69.425  73.788  85.929  1.00  9.99
ATOM    458  C   HIS   318      68.863  68.240  87.468  1.00  9.99
ATOM    459  O   HIS   318      69.339  67.438  86.688  1.00  9.99
ATOM    460  N   SER   319      67.917  67.861  88.340  1.00  9.99
ATOM    461  CA  SER   319      67.553  66.464  88.291  1.00  9.99
ATOM    462  CB  SER   319      67.256  65.846  89.667  1.00  9.99
ATOM    463  OG  SER   319      68.420  65.887  90.480  1.00  9.99
ATOM    464  C   SER   319      66.329  66.344  87.450  1.00  9.99
ATOM    465  O   SER   319      65.563  67.284  87.361  1.00  9.99
ATOM    466  N   THR   320      66.092  65.215  86.763  1.00  9.99
ATOM    467  CA  THR   320      64.861  65.168  86.014  1.00  9.99
ATOM    468  CB  THR   320      65.046  64.787  84.581  1.00  9.99
ATOM    469  OG1 THR   320      65.800  65.800  83.939  1.00  9.99
ATOM    470  CG2 THR   320      63.674  64.637  83.909  1.00  9.99
ATOM    471  C   THR   320      63.992  64.182  86.714  1.00  9.99
ATOM    472  O   THR   320      64.467  63.119  87.070  1.00  9.99
ATOM    473  N   TYR   321      62.703  64.507  86.948  1.00  9.99
ATOM    474  CA  TYR   321      61.831  63.739  87.813  1.00  9.99
ATOM    475  CB  TYR   321      60.454  64.386  88.008  1.00  9.99
ATOM    476  CG  TYR   321      60.518  65.522  88.968  1.00  9.99
ATOM    477  CD1 TYR   321      60.874  66.792  88.571  1.00  9.99
ATOM    478  CD2 TYR   321      60.186  65.302  90.285  1.00  9.99
ATOM    479  CE1 TYR   321      60.906  67.823  89.483  1.00  9.99
ATOM    480  CE2 TYR   321      60.215  66.326  91.202  1.00  9.99
ATOM    481  CZ  TYR   321      60.576  67.589  90.798  1.00  9.99
ATOM    482  OH  TYR   321      60.606  68.645  91.734  1.00  9.99
ATOM    483  C   TYR   321      61.494  62.334  87.428  1.00  9.99
ATOM    484  O   TYR   321      61.626  61.437  88.253  1.00  9.99
ATOM    485  N   THR   322      61.035  62.084  86.194  1.00  9.99
ATOM    486  CA  THR   322      60.602  60.769  85.798  1.00  9.99
ATOM    487  CB  THR   322      59.787  60.780  84.536  1.00  9.99
ATOM    488  OG1 THR   322      58.795  61.787  84.606  1.00  9.99
ATOM    489  CG2 THR   322      59.092  59.417  84.383  1.00  9.99
ATOM    490  C   THR   322      61.883  60.162  85.397  1.00  9.99
ATOM    491  O   THR   322      62.914  60.514  85.948  1.00  9.99
ATOM    492  N   GLY   323      61.898  59.213  84.460  1.00  9.99
ATOM    493  CA  GLY   323      63.213  58.844  84.064  1.00  9.99
ATOM    494  C   GLY   323      63.480  59.659  82.844  1.00  9.99
ATOM    495  O   GLY   323      63.269  59.195  81.726  1.00  9.99
ATOM    496  N   ARG   324      63.994  60.895  83.012  1.00  9.99
ATOM    497  CA  ARG   324      64.139  61.683  81.824  1.00  9.99
ATOM    498  CB  ARG   324      62.983  62.672  81.629  1.00  9.99
ATOM    499  CG  ARG   324      61.636  61.959  81.503  1.00  9.99
ATOM    500  CD  ARG   324      60.435  62.885  81.327  1.00  9.99
ATOM    501  NE  ARG   324      59.966  62.718  79.928  1.00  9.99
ATOM    502  CZ  ARG   324      58.630  62.718  79.659  1.00  9.99
ATOM    503  NH1 ARG   324      57.726  62.865  80.671  1.00  9.99
ATOM    504  NH2 ARG   324      58.198  62.574  78.373  1.00  9.99
ATOM    505  C   ARG   324      65.413  62.467  81.831  1.00  9.99
ATOM    506  O   ARG   324      65.966  62.857  82.855  1.00  9.99
ATOM    507  N   PRO   325      65.853  62.671  80.618  1.00  9.99
ATOM    508  CA  PRO   325      67.064  63.409  80.334  1.00  9.99
ATOM    509  CD  PRO   325      65.608  61.632  79.627  1.00  9.99
ATOM    510  CB  PRO   325      67.424  63.053  78.889  1.00  9.99
ATOM    511  CG  PRO   325      66.813  61.657  78.680  1.00  9.99
ATOM    512  C   PRO   325      67.140  64.908  80.582  1.00  9.99
ATOM    513  O   PRO   325      68.269  65.391  80.472  1.00  9.99
ATOM    514  N   PRO   326      66.123  65.674  80.892  1.00  9.99
ATOM    515  CA  PRO   326      66.255  67.117  80.897  1.00  9.99
ATOM    516  CD  PRO   326      64.762  65.285  80.545  1.00  9.99
ATOM    517  CB  PRO   326      64.870  67.674  80.568  1.00  9.99
ATOM    518  CG  PRO   326      63.899  66.517  80.819  1.00  9.99
ATOM    519  C   PRO   326      66.863  67.942  81.988  1.00  9.99
ATOM    520  O   PRO   326      67.493  67.459  82.932  1.00  9.99
ATOM    521  N   ASP   327      66.701  69.263  81.761  1.00  9.99
ATOM    522  CA  ASP   327      67.042  70.367  82.605  1.00  9.99
ATOM    523  CB  ASP   327      67.455  71.597  81.764  1.00  9.99
ATOM    524  CG  ASP   327      67.756  72.827  82.615  1.00  9.99
ATOM    525  OD1 ASP   327      67.169  72.984  83.719  1.00  9.99
ATOM    526  OD2 ASP   327      68.579  73.653  82.137  1.00  9.99
ATOM    527  C   ASP   327      65.722  70.708  83.300  1.00  9.99
ATOM    528  O   ASP   327      64.752  71.050  82.570  1.00  9.99
ATOM    529  OXT ASP   327      65.666  70.635  84.558  1.00  9.99
TER
END
