
#######################################################
#                                                     #
#                        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   12 (   97),  selected   12 , name T0385TS009_2_1
# Molecule2: number of CA atoms  142 ( 1050),  selected   12 , name T0385.pdb
# PARAMETERS: T0385TS009_2_1.T0385.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:    12        64 - 75          2.71     2.71
  LCS_AVERAGE:      8.45

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        66 - 74          1.91     3.28
  LONGEST_CONTINUOUS_SEGMENT:     9        67 - 75          1.40     3.75
  LCS_AVERAGE:      5.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        68 - 74          0.78     3.26
  LCS_AVERAGE:      4.23

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:  142
LCS_GDT     H      64     H      64      5    6   12     3    4    5    5    6    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     R      65     R      65      5    6   12     3    4    5    5    6    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     R      66     R      66      5    9   12     3    4    5    5    6    8   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     D      67     D      67      5    9   12     3    4    5    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     D      68     D      68      7    9   12     4    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     V      69     V      69      7    9   12     4    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     I      70     I      70      7    9   12     5    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     V      71     V      71      7    9   12     5    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     M      72     M      72      7    9   12     5    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     L      73     L      73      7    9   12     5    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     S      74     S      74      7    9   12     5    6    7    8    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_GDT     A      75     A      75      3    9   12     0    3    5    6    9    9   10   12   12   12   12   12   12   12   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   6.22  (   4.23    5.99    8.45 )

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      5      6      7      8      9      9     10     12     12     12     12     12     12     12     12     12     12     12     12     12 
GDT PERCENT_CA   3.52   4.23   4.93   5.63   6.34   6.34   7.04   8.45   8.45   8.45   8.45   8.45   8.45   8.45   8.45   8.45   8.45   8.45   8.45   8.45
GDT RMS_LOCAL    0.23   0.55   0.78   1.16   1.40   1.40   2.07   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71
GDT RMS_ALL_CA   3.96   3.51   3.26   3.59   3.75   3.75   3.27   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71   2.71

#      Molecule1      Molecule2       DISTANCE
LGA    H      64      H      64          3.739
LGA    R      65      R      65          3.429
LGA    R      66      R      66          3.579
LGA    D      67      D      67          3.491
LGA    D      68      D      68          1.846
LGA    V      69      V      69          1.693
LGA    I      70      I      70          0.648
LGA    V      71      V      71          2.170
LGA    M      72      M      72          2.849
LGA    L      73      L      73          2.235
LGA    S      74      S      74          1.770
LGA    A      75      A      75          3.127

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  142    4.0     12    2.71     6.690     6.692     0.427

LGA_LOCAL      RMSD =  2.711  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.711  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  2.711  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.721783 * X  +  -0.064244 * Y  +  -0.689131 * Z  +  13.592862
  Y_new =   0.631064 * X  +  -0.347809 * Y  +   0.693388 * Z  + -24.856112
  Z_new =  -0.284232 * X  +  -0.935362 * Y  +  -0.210501 * Z  + -26.744970 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.792156    1.349437  [ DEG:  -102.6830     77.3170 ]
  Theta =   0.288205    2.853387  [ DEG:    16.5130    163.4870 ]
  Phi   =   0.718440   -2.423152  [ DEG:    41.1636   -138.8364 ]
 
# 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: T0385TS009_2_1                                
REMARK     2: T0385.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_2_1.T0385.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  142   4.0   12   2.71   6.692     2.71
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_2_1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM    453  N   HIS    64      38.022  11.710  25.997  1.00  0.00              
ATOM    454  CA  HIS    64      38.434  12.798  26.877  1.00  0.00              
ATOM    455  C   HIS    64      37.700  14.090  26.534  1.00  0.00              
ATOM    456  O   HIS    64      37.173  14.768  27.417  1.00  0.00              
ATOM    457  CB  HIS    64      38.189  12.425  28.340  1.00  0.00              
ATOM    458  CG  HIS    64      39.371  12.659  29.229  1.00  0.00              
ATOM    459  ND1 HIS    64      40.633  12.913  28.737  1.00  0.00              
ATOM    460  CD2 HIS    64      39.482  12.678  30.578  1.00  0.00              
ATOM    461  CE1 HIS    64      41.470  13.077  29.746  1.00  0.00              
ATOM    462  NE2 HIS    64      40.799  12.940  30.873  1.00  0.00              
ATOM    463  N   ARG    65      37.672  14.426  25.249  1.00  0.00              
ATOM    464  CA  ARG    65      37.004  15.638  24.789  1.00  0.00              
ATOM    465  C   ARG    65      35.614  15.768  25.402  1.00  0.00              
ATOM    466  O   ARG    65      35.415  16.514  26.360  1.00  0.00              
ATOM    467  CB  ARG    65      37.844  16.872  25.122  1.00  0.00              
ATOM    468  CG  ARG    65      37.954  17.874  23.983  1.00  0.00              
ATOM    469  CD  ARG    65      39.001  18.935  24.281  1.00  0.00              
ATOM    470  NE  ARG    65      39.481  19.585  23.065  1.00  0.00              
ATOM    471  CZ  ARG    65      39.072  20.777  22.644  1.00  0.00              
ATOM    472  NH1 ARG    65      38.170  21.453  23.343  1.00  0.00              
ATOM    473  NH2 ARG    65      39.564  21.290  21.525  1.00  0.00              
ATOM    474  N   ARG    66      34.654  15.037  24.842  1.00  0.00              
ATOM    475  CA  ARG    66      33.282  15.070  25.333  1.00  0.00              
ATOM    476  C   ARG    66      33.103  14.143  26.532  1.00  0.00              
ATOM    477  O   ARG    66      32.626  14.564  27.586  1.00  0.00              
ATOM    478  CB  ARG    66      32.880  16.498  25.706  1.00  0.00              
ATOM    479  CG  ARG    66      31.698  17.036  24.917  1.00  0.00              
ATOM    480  CD  ARG    66      31.110  18.272  25.576  1.00  0.00              
ATOM    481  NE  ARG    66      29.986  18.814  24.820  1.00  0.00              
ATOM    482  CZ  ARG    66      28.717  18.473  25.020  1.00  0.00              
ATOM    483  NH1 ARG    66      28.408  17.587  25.958  1.00  0.00              
ATOM    484  NH2 ARG    66      27.759  19.018  24.282  1.00  0.00              
ATOM    485  N   ASP    67      33.488  12.883  26.362  1.00  0.00              
ATOM    486  CA  ASP    67      33.370  11.896  27.428  1.00  0.00              
ATOM    487  C   ASP    67      33.765  12.490  28.776  1.00  0.00              
ATOM    488  O   ASP    67      33.305  12.039  29.825  1.00  0.00              
ATOM    489  CB  ASP    67      31.944  11.345  27.495  1.00  0.00              
ATOM    490  CG  ASP    67      31.894   9.838  27.335  1.00  0.00              
ATOM    491  OD1 ASP    67      30.868   9.235  27.714  1.00  0.00              
ATOM    492  OD2 ASP    67      32.879   9.261  26.831  1.00  0.00              
ATOM    493  N   ASP    68      34.620  13.507  28.741  1.00  0.00              
ATOM    494  CA  ASP    68      35.079  14.165  29.958  1.00  0.00              
ATOM    495  C   ASP    68      34.482  13.510  31.198  1.00  0.00              
ATOM    496  O   ASP    68      35.052  13.583  32.287  1.00  0.00              
ATOM    497  CB  ASP    68      36.606  14.145  30.036  1.00  0.00              
ATOM    498  CG  ASP    68      37.170  15.357  30.752  1.00  0.00              
ATOM    499  OD1 ASP    68      38.164  15.199  31.492  1.00  0.00              
ATOM    500  OD2 ASP    68      36.618  16.462  30.573  1.00  0.00              
ATOM    501  N   VAL    69      33.331  12.867  31.027  1.00  0.00              
ATOM    502  CA  VAL    69      32.640  12.183  32.155  1.00  0.00              
ATOM    503  C   VAL    69      33.642  11.545  33.111  1.00  0.00              
ATOM    504  O   VAL    69      33.614  11.799  34.316  1.00  0.00              
ATOM    505  CB  VAL    69      31.742  13.156  32.942  1.00  0.00              
ATOM    506  CG1 VAL    69      30.274  12.855  32.683  1.00  0.00              
ATOM    507  CG2 VAL    69      32.070  14.596  32.578  1.00  0.00              
ATOM    508  N   ILE    70      34.528  10.718  32.567  1.00  0.00              
ATOM    509  CA  ILE    70      35.564  10.029  33.388  1.00  0.00              
ATOM    510  C   ILE    70      36.010  10.900  34.557  1.00  0.00              
ATOM    511  O   ILE    70      36.224  10.405  35.665  1.00  0.00              
ATOM    512  CB  ILE    70      35.051   8.682  33.930  1.00  0.00              
ATOM    513  CG2 ILE    70      35.489   7.541  33.022  1.00  0.00              
ATOM    514  CG1 ILE    70      33.528   8.708  34.067  1.00  0.00              
ATOM    515  CD1 ILE    70      32.859   7.402  33.701  1.00  0.00              
ATOM    516  N   VAL    71      36.150  12.197  34.304  1.00  0.00              
ATOM    517  CA  VAL    71      36.580  13.160  35.358  1.00  0.00              
ATOM    518  C   VAL    71      35.738  13.007  36.621  1.00  0.00              
ATOM    519  O   VAL    71      36.271  12.885  37.724  1.00  0.00              
ATOM    520  CB  VAL    71      38.066  12.975  35.718  1.00  0.00              
ATOM    521  CG1 VAL    71      38.923  13.987  34.974  1.00  0.00              
ATOM    522  CG2 VAL    71      38.517  11.556  35.411  1.00  0.00              
ATOM    523  N   MET    72      34.420  13.015  36.452  1.00  0.00              
ATOM    524  CA  MET    72      33.502  12.877  37.577  1.00  0.00              
ATOM    525  C   MET    72      33.843  11.653  38.420  1.00  0.00              
ATOM    526  O   MET    72      33.492  11.582  39.597  1.00  0.00              
ATOM    527  CB  MET    72      33.526  14.138  38.444  1.00  0.00              
ATOM    528  CG  MET    72      32.308  15.032  38.274  1.00  0.00              
ATOM    529  SD  MET    72      31.727  15.722  39.835  1.00  0.00              
ATOM    530  CE  MET    72      30.787  17.130  39.253  1.00  0.00              
ATOM    531  N   LEU    73      34.529  10.693  37.809  1.00  0.00              
ATOM    532  CA  LEU    73      34.918   9.471  38.503  1.00  0.00              
ATOM    533  C   LEU    73      36.138   9.704  39.389  1.00  0.00              
ATOM    534  O   LEU    73      36.069   9.550  40.608  1.00  0.00              
ATOM    535  CB  LEU    73      33.755   8.936  39.339  1.00  0.00              
ATOM    536  CG  LEU    73      32.951   7.787  38.727  1.00  0.00              
ATOM    537  CD1 LEU    73      32.470   6.830  39.807  1.00  0.00              
ATOM    538  CD2 LEU    73      33.776   7.051  37.682  1.00  0.00              
ATOM    539  N   SER    74      37.252  10.076  38.767  1.00  0.00              
ATOM    540  CA  SER    74      38.487  10.330  39.497  1.00  0.00              
ATOM    541  C   SER    74      38.791  11.823  39.564  1.00  0.00              
ATOM    542  O   SER    74      38.265  12.536  40.419  1.00  0.00              
ATOM    543  CB  SER    74      38.406   9.747  40.910  1.00  0.00              
ATOM    544  OG  SER    74      39.673   9.285  41.345  1.00  0.00              
ATOM    545  N   ALA    75      39.644  12.290  38.657  1.00  0.00              
ATOM    546  CA  ALA    75      40.019  13.697  38.612  1.00  0.00              
ATOM    547  C   ALA    75      39.207  14.451  37.563  1.00  0.00              
ATOM    548  O   ALA    75      39.618  15.511  37.089  1.00  0.00              
ATOM    549  CB  ALA    75      39.835  14.341  39.978  1.00  0.00              
TER
END
