
#######################################################
#                                                     #
#                        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 (  126),  selected   14 , name T0386TS009_2_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   14 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_2_2-D1.T0386_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        74 - 87          4.06     4.06
  LCS_AVERAGE:      6.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        77 - 82          2.00     8.46
  LONGEST_CONTINUOUS_SEGMENT:     6        81 - 86          1.65    11.11
  LCS_AVERAGE:      2.57

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        75 - 78          0.95     9.54
  LONGEST_CONTINUOUS_SEGMENT:     4        77 - 80          0.57     6.68
  LONGEST_CONTINUOUS_SEGMENT:     4        80 - 83          0.93     9.53
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.67    11.69
  LCS_AVERAGE:      1.84

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:  206
LCS_GDT     Q      74     Q      74      3    3   14     3    3    4    4    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     L      75     L      75      4    4   14     3    3    4    5    5    5    7   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     F      76     F      76      4    4   14     3    3    4    5    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     K      77     K      77      4    6   14     3    4    5    5    5    5    8    9   10   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     N      78     N      78      4    6   14     3    4    5    5    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     T      79     T      79      4    6   14     3    4    5    5    5    6    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     F      80     F      80      4    6   14     3    4    5    5    5    5    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     E      81     E      81      4    6   14     3    4    4    5    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     W      82     W      82      4    6   14     3    4    4    5    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     A      83     A      83      4    6   14     3    4    4    5    5    6    8    9    9   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     G      84     G      84      4    6   14     3    4    5    5    5    6    8    9   10   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     Y      85     Y      85      4    6   14     3    4    4    5    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     L      86     L      86      3    6   14     0    3    4    5    5    7    8   10   11   12   13   13   14   14   14   14   14   14   14   14 
LCS_GDT     R      87     R      87      3    3   14     0    3    3    3    4    5    8    8   11   11   12   13   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   3.73  (   1.84    2.57    6.80 )

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      3      4      5      5      5      7      8     10     11     12     13     13     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   1.46   1.94   2.43   2.43   2.43   3.40   3.88   4.85   5.34   5.83   6.31   6.31   6.80   6.80   6.80   6.80   6.80   6.80   6.80   6.80
GDT RMS_LOCAL    0.14   0.35   0.68   0.68   0.68   2.15   2.42   2.93   3.16   3.60   3.79   3.79   4.06   4.06   4.06   4.06   4.06   4.06   4.06   4.06
GDT RMS_ALL_CA   8.25   8.16   7.03   7.03   7.03   4.31   7.13   4.20   4.30   4.61   4.20   4.20   4.06   4.06   4.06   4.06   4.06   4.06   4.06   4.06

#      Molecule1      Molecule2       DISTANCE
LGA    Q      74      Q      74          2.622
LGA    L      75      L      75          3.838
LGA    F      76      F      76          1.914
LGA    K      77      K      77          5.004
LGA    N      78      N      78          2.002
LGA    T      79      T      79          3.230
LGA    F      80      F      80          3.976
LGA    E      81      E      81          0.282
LGA    W      82      W      82          3.352
LGA    A      83      A      83          5.633
LGA    G      84      G      84          6.650
LGA    Y      85      Y      85          3.686
LGA    L      86      L      86          3.847
LGA    R      87      R      87          6.576

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  206    4.0     10    2.93     4.005     3.810     0.330

LGA_LOCAL      RMSD =  2.929  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.136  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  4.064  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.985054 * X  +   0.159877 * Y  +  -0.064085 * Z  +  33.427731
  Y_new =   0.169849 * X  +   0.839809 * Y  +  -0.515628 * Z  +  87.868904
  Z_new =  -0.028618 * X  +  -0.518806 * Y  +  -0.854413 * Z  +  31.565435 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.595890    0.545703  [ DEG:  -148.7335     31.2665 ]
  Theta =   0.028622    3.112971  [ DEG:     1.6399    178.3601 ]
  Phi   =   2.970846   -0.170747  [ DEG:   170.2169     -9.7831 ]
 
# 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: T0386TS009_2_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_2_2-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  206   4.0   10   2.93   3.810     4.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_2_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                                                                      
ATOM    595  N   GLN    74       6.466  73.170  48.918  1.00  0.00             
ATOM    596  CA  GLN    74       6.129  71.916  49.579  1.00  0.00             
ATOM    597  C   GLN    74       6.871  70.742  48.950  1.00  0.00             
ATOM    598  O   GLN    74       7.469  69.925  49.650  1.00  0.00             
ATOM    599  CB  GLN    74       6.444  71.998  51.074  1.00  0.00             
ATOM    600  CG  GLN    74       7.805  72.598  51.389  1.00  0.00             
ATOM    601  CD  GLN    74       7.705  73.872  52.204  1.00  0.00             
ATOM    602  OE1 GLN    74       8.271  73.971  53.292  1.00  0.00             
ATOM    603  NE2 GLN    74       6.982  74.854  51.677  1.00  0.00             
ATOM    604  N   LEU    75       6.830  70.666  47.623  1.00  0.00             
ATOM    605  CA  LEU    75       7.499  69.593  46.897  1.00  0.00             
ATOM    606  C   LEU    75       8.919  69.381  47.411  1.00  0.00             
ATOM    607  O   LEU    75       9.820  69.035  46.647  1.00  0.00             
ATOM    608  CB  LEU    75       6.700  68.293  47.006  1.00  0.00             
ATOM    609  CG  LEU    75       6.911  67.272  45.886  1.00  0.00             
ATOM    610  CD1 LEU    75       6.892  65.855  46.440  1.00  0.00             
ATOM    611  CD2 LEU    75       8.211  67.546  45.147  1.00  0.00             
ATOM    612  N   PHE    76       9.111  69.592  48.709  1.00  0.00             
ATOM    613  CA  PHE    76      10.421  69.424  49.326  1.00  0.00             
ATOM    614  C   PHE    76      11.514  70.082  48.490  1.00  0.00             
ATOM    615  O   PHE    76      11.771  71.279  48.620  1.00  0.00             
ATOM    616  CB  PHE    76      10.422  70.002  50.744  1.00  0.00             
ATOM    617  CG  PHE    76      11.748  69.888  51.443  1.00  0.00             
ATOM    618  CD1 PHE    76      12.816  70.683  51.066  1.00  0.00             
ATOM    619  CD2 PHE    76      11.926  68.986  52.477  1.00  0.00             
ATOM    620  CE1 PHE    76      14.035  70.578  51.709  1.00  0.00             
ATOM    621  CE2 PHE    76      13.144  68.882  53.121  1.00  0.00             
ATOM    622  CZ  PHE    76      14.196  69.673  52.740  1.00  0.00             
ATOM    623  N   LYS    77      12.153  69.292  47.634  1.00  0.00             
ATOM    624  CA  LYS    77      13.218  69.796  46.776  1.00  0.00             
ATOM    625  C   LYS    77      12.858  71.158  46.193  1.00  0.00             
ATOM    626  O   LYS    77      13.181  71.457  45.043  1.00  0.00             
ATOM    627  CB  LYS    77      14.534  69.887  47.552  1.00  0.00             
ATOM    628  CG  LYS    77      15.768  69.579  46.720  1.00  0.00             
ATOM    629  CD  LYS    77      16.620  68.504  47.375  1.00  0.00             
ATOM    630  CE  LYS    77      18.099  68.732  47.105  1.00  0.00             
ATOM    631  NZ  LYS    77      18.955  68.158  48.179  1.00  0.00             
ATOM    632  N   ASN    78      12.188  71.981  46.993  1.00  0.00             
ATOM    633  CA  ASN    78      11.784  73.313  46.558  1.00  0.00             
ATOM    634  C   ASN    78      11.643  73.378  45.040  1.00  0.00             
ATOM    635  O   ASN    78      10.574  73.693  44.519  1.00  0.00             
ATOM    636  CB  ASN    78      10.468  73.717  47.225  1.00  0.00             
ATOM    637  CG  ASN    78      10.401  75.201  47.529  1.00  0.00             
ATOM    638  OD1 ASN    78       9.320  75.757  47.727  1.00  0.00             
ATOM    639  ND2 ASN    78      11.559  75.849  47.566  1.00  0.00             
ATOM    640  N   THR    79      12.731  73.077  44.337  1.00  0.00             
ATOM    641  CA  THR    79      12.731  73.102  42.847  1.00  0.00             
ATOM    642  C   THR    79      12.339  71.746  42.272  1.00  0.00             
ATOM    643  O   THR    79      13.045  71.187  41.434  1.00  0.00             
ATOM    644  CB  THR    79      11.774  74.177  42.300  1.00  0.00             
ATOM    645  OG1 THR    79      10.444  73.917  42.763  1.00  0.00             
ATOM    646  CG2 THR    79      12.206  75.561  42.763  1.00  0.00             
ATOM    647  N   PHE    80      11.206  71.220  42.731  1.00  0.00             
ATOM    648  CA  PHE    80      10.718  69.929  42.263  1.00  0.00             
ATOM    649  C   PHE    80      11.643  69.339  41.203  1.00  0.00             
ATOM    650  O   PHE    80      11.898  68.134  41.189  1.00  0.00             
ATOM    651  CB  PHE    80      10.572  68.955  43.435  1.00  0.00             
ATOM    652  CG  PHE    80       9.275  68.197  43.435  1.00  0.00             
ATOM    653  CD1 PHE    80       8.854  67.518  42.304  1.00  0.00             
ATOM    654  CD2 PHE    80       8.477  68.162  44.564  1.00  0.00             
ATOM    655  CE1 PHE    80       7.661  66.820  42.305  1.00  0.00             
ATOM    656  CE2 PHE    80       7.284  67.464  44.565  1.00  0.00             
ATOM    657  CZ  PHE    80       6.875  66.796  43.441  1.00  0.00             
ATOM    658  N   GLU    81      12.143  70.195  40.319  1.00  0.00             
ATOM    659  CA  GLU    81      13.041  69.760  39.256  1.00  0.00             
ATOM    660  C   GLU    81      14.068  68.759  39.775  1.00  0.00             
ATOM    661  O   GLU    81      14.867  68.221  39.008  1.00  0.00             
ATOM    662  CB  GLU    81      12.246  69.148  38.100  1.00  0.00             
ATOM    663  CG  GLU    81      11.360  70.139  37.363  1.00  0.00             
ATOM    664  CD  GLU    81      10.942  69.639  35.994  1.00  0.00             
ATOM    665  OE1 GLU    81      11.133  68.437  35.716  1.00  0.00             
ATOM    666  OE2 GLU    81      10.422  70.451  35.199  1.00  0.00             
ATOM    667  N   TRP    82      14.039  68.514  41.080  1.00  0.00             
ATOM    668  CA  TRP    82      14.966  67.577  41.704  1.00  0.00             
ATOM    669  C   TRP    82      14.636  66.138  41.324  1.00  0.00             
ATOM    670  O   TRP    82      14.740  65.228  42.147  1.00  0.00             
ATOM    671  CB  TRP    82      16.408  67.907  41.311  1.00  0.00             
ATOM    672  CG  TRP    82      17.276  68.283  42.472  1.00  0.00             
ATOM    673  CD1 TRP    82      18.608  68.576  42.438  1.00  0.00             
ATOM    674  CD2 TRP    82      16.870  68.407  43.841  1.00  0.00             
ATOM    675  NE1 TRP    82      19.060  68.874  43.701  1.00  0.00             
ATOM    676  CE2 TRP    82      18.011  68.778  44.581  1.00  0.00             
ATOM    677  CE3 TRP    82      15.655  68.241  44.512  1.00  0.00             
ATOM    678  CZ2 TRP    82      17.973  68.985  45.958  1.00  0.00             
ATOM    679  CZ3 TRP    82      15.619  68.447  45.878  1.00  0.00             
ATOM    680  CH2 TRP    82      16.772  68.815  46.590  1.00  0.00             
ATOM    681  N   ALA    83      14.238  65.939  40.071  1.00  0.00             
ATOM    682  CA  ALA    83      13.891  64.610  39.579  1.00  0.00             
ATOM    683  C   ALA    83      13.535  63.672  40.727  1.00  0.00             
ATOM    684  O   ALA    83      12.493  63.020  40.708  1.00  0.00             
ATOM    685  CB  ALA    83      12.736  64.695  38.594  1.00  0.00             
ATOM    686  N   GLY    84      14.409  63.611  41.728  1.00  0.00             
ATOM    687  CA  GLY    84      14.167  62.749  42.869  1.00  0.00             
ATOM    688  C   GLY    84      12.757  62.887  43.411  1.00  0.00             
ATOM    689  O   GLY    84      12.212  61.951  43.997  1.00  0.00             
ATOM    690  N   TYR    85      12.161  64.059  43.216  1.00  0.00             
ATOM    691  CA  TYR    85      10.807  64.318  43.688  1.00  0.00             
ATOM    692  C   TYR    85       9.906  63.108  43.471  1.00  0.00             
ATOM    693  O   TYR    85       9.230  62.651  44.393  1.00  0.00             
ATOM    694  CB  TYR    85      10.821  64.704  45.169  1.00  0.00             
ATOM    695  CG  TYR    85      10.642  63.534  46.109  1.00  0.00             
ATOM    696  CD1 TYR    85      11.741  62.862  46.626  1.00  0.00             
ATOM    697  CD2 TYR    85       9.372  63.105  46.476  1.00  0.00             
ATOM    698  CE1 TYR    85      11.587  61.791  47.486  1.00  0.00             
ATOM    699  CE2 TYR    85       9.199  62.035  47.334  1.00  0.00             
ATOM    700  CZ  TYR    85      10.320  61.378  47.839  1.00  0.00             
ATOM    701  OH  TYR    85      10.159  60.312  48.694  1.00  0.00             
ATOM    702  N   LEU    86       9.901  62.592  42.245  1.00  0.00             
ATOM    703  CA  LEU    86       9.084  61.434  41.904  1.00  0.00             
ATOM    704  C   LEU    86       9.064  60.419  43.042  1.00  0.00             
ATOM    705  O   LEU    86       8.620  59.284  42.867  1.00  0.00             
ATOM    706  CB  LEU    86       7.657  61.868  41.561  1.00  0.00             
ATOM    707  CG  LEU    86       6.610  60.756  41.491  1.00  0.00             
ATOM    708  CD1 LEU    86       5.513  61.111  40.498  1.00  0.00             
ATOM    709  CD2 LEU    86       6.023  60.482  42.868  1.00  0.00             
ATOM    710  N   ARG    87       9.547  60.834  44.208  1.00  0.00             
ATOM    711  CA  ARG    87       9.586  59.962  45.376  1.00  0.00             
ATOM    712  C   ARG    87       9.357  58.507  44.986  1.00  0.00             
ATOM    713  O   ARG    87       8.612  57.786  45.649  1.00  0.00             
ATOM    714  CB  ARG    87      10.922  60.107  46.109  1.00  0.00             
ATOM    715  CG  ARG    87      11.005  59.321  47.407  1.00  0.00             
ATOM    716  CD  ARG    87      10.195  59.985  48.507  1.00  0.00             
ATOM    717  NE  ARG    87      10.919  61.089  49.131  1.00  0.00             
ATOM    718  CZ  ARG    87      10.411  62.301  49.328  1.00  0.00             
ATOM    719  NH1 ARG    87       9.168  62.568  48.948  1.00  0.00             
ATOM    720  NH2 ARG    87      11.144  63.243  49.903  1.00  0.00             
TER
END
