
#######################################################
#                                                     #
#                        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   13 (   94),  selected   13 , name T0382TS009_3_3
# Molecule2: number of CA atoms  121 (  929),  selected   13 , name T0382.pdb
# PARAMETERS: T0382TS009_3_3.T0382.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        73 - 85          4.08     4.08
  LCS_AVERAGE:     10.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        76 - 83          1.94     5.16
  LCS_AVERAGE:      5.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        75 - 78          0.51     5.32
  LONGEST_CONTINUOUS_SEGMENT:     4        77 - 80          0.35     7.32
  LONGEST_CONTINUOUS_SEGMENT:     4        80 - 83          0.63     6.16
  LONGEST_CONTINUOUS_SEGMENT:     4        82 - 85          0.69     6.39
  LCS_AVERAGE:      3.18

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:  121
LCS_GDT     V      73     V      73      3    4   13     0    3    4    4    4    5    5    5    6    7    8   11   13   13   13   13   13   13   13   13 
LCS_GDT     R      74     R      74      3    6   13     3    4    4    6    7   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     L      75     L      75      4    6   13     3    5    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     Q      76     Q      76      4    8   13     3    4    5    5    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     A      77     A      77      4    8   13     4    4    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     A      78     A      78      4    8   13     4    5    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     K      79     K      79      4    8   13     4    4    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     L      80     L      80      4    8   13     4    4    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     T      81     T      81      4    8   13     3    4    4    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     L      82     L      82      4    8   13     3    4    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     A      83     A      83      4    8   13     3    5    5    6    9   10   10   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     V      84     V      84      4    5   13     3    5    5    6    6    7    8   10   11   11   11   11   13   13   13   13   13   13   13   13 
LCS_GDT     A      85     A      85      4    4   13     3    5    5    6    6    6    6    7   10   10   11   11   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   6.53  (   3.18    5.66   10.74 )

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      5      6      9     10     10     10     11     11     11     11     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   3.31   4.13   4.13   4.96   7.44   8.26   8.26   8.26   9.09   9.09   9.09   9.09  10.74  10.74  10.74  10.74  10.74  10.74  10.74  10.74
GDT RMS_LOCAL    0.35   0.47   0.47   0.87   2.06   2.26   2.26   2.26   2.81   2.81   2.81   2.81   4.08   4.08   4.08   4.08   4.08   4.08   4.08   4.08
GDT RMS_ALL_CA   7.32   5.20   5.20   5.27   4.92   4.69   4.69   4.69   4.35   4.35   4.35   4.35   4.08   4.08   4.08   4.08   4.08   4.08   4.08   4.08

#      Molecule1      Molecule2       DISTANCE
LGA    V      73      V      73          9.473
LGA    R      74      R      74          2.982
LGA    L      75      L      75          2.293
LGA    Q      76      Q      76          2.198
LGA    A      77      A      77          3.046
LGA    A      78      A      78          2.453
LGA    K      79      K      79          2.352
LGA    L      80      L      80          1.865
LGA    T      81      T      81          1.594
LGA    L      82      L      82          1.439
LGA    A      83      A      83          1.785
LGA    V      84      V      84          7.106
LGA    A      85      A      85          9.703

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  121    4.0     10    2.26     7.025     7.134     0.424

LGA_LOCAL      RMSD =  2.260  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.686  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  4.082  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.572955 * X  +   0.691876 * Y  +   0.439352 * Z  + -17.609926
  Y_new =   0.029211 * X  +  -0.518486 * Y  +   0.854587 * Z  +  49.618027
  Z_new =   0.819066 * X  +   0.502474 * Y  +   0.276858 * Z  + -23.771496 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.067193   -2.074399  [ DEG:    61.1457   -118.8543 ]
  Theta =  -0.959782   -2.181811  [ DEG:   -54.9914   -125.0086 ]
  Phi   =   3.090653   -0.050940  [ DEG:   177.0814     -2.9186 ]
 
# 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: T0382TS009_3_3                                
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_3.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  121   4.0   10   2.26   7.134     4.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A  
ATOM    572  N   VAL    73     -18.882  51.917   5.027  1.00  0.00             
ATOM    573  CA  VAL    73     -19.533  50.933   4.116  1.00  0.00             
ATOM    574  C   VAL    73     -20.374  49.929   4.898  1.00  0.00             
ATOM    575  O   VAL    73     -21.190  50.309   5.737  1.00  0.00             
ATOM    576  CB  VAL    73     -20.427  51.634   3.074  1.00  0.00             
ATOM    577  CG1 VAL    73     -19.879  51.419   1.671  1.00  0.00             
ATOM    578  CG2 VAL    73     -20.545  53.118   3.387  1.00  0.00             
ATOM    579  N   ARG    74     -20.167  48.647   4.617  1.00  0.00             
ATOM    580  CA  ARG    74     -20.904  47.586   5.293  1.00  0.00             
ATOM    581  C   ARG    74     -20.139  47.071   6.507  1.00  0.00             
ATOM    582  O   ARG    74     -20.100  47.722   7.551  1.00  0.00             
ATOM    583  CB  ARG    74     -22.289  48.081   5.716  1.00  0.00             
ATOM    584  CG  ARG    74     -23.428  47.158   5.314  1.00  0.00             
ATOM    585  CD  ARG    74     -24.775  47.846   5.457  1.00  0.00             
ATOM    586  NE  ARG    74     -25.884  46.900   5.385  1.00  0.00             
ATOM    587  CZ  ARG    74     -26.266  46.120   6.390  1.00  0.00             
ATOM    588  NH1 ARG    74     -25.626  46.172   7.551  1.00  0.00             
ATOM    589  NH2 ARG    74     -27.287  45.288   6.233  1.00  0.00             
ATOM    590  N   LEU    75     -19.531  45.897   6.364  1.00  0.00             
ATOM    591  CA  LEU    75     -18.767  45.292   7.447  1.00  0.00             
ATOM    592  C   LEU    75     -17.323  45.786   7.446  1.00  0.00             
ATOM    593  O   LEU    75     -17.024  46.861   7.966  1.00  0.00             
ATOM    594  CB  LEU    75     -19.423  45.589   8.797  1.00  0.00             
ATOM    595  CG  LEU    75     -19.743  44.378   9.676  1.00  0.00             
ATOM    596  CD1 LEU    75     -19.318  44.631  11.114  1.00  0.00             
ATOM    597  CD2 LEU    75     -19.079  43.125   9.128  1.00  0.00             
ATOM    598  N   GLN    76     -16.433  44.993   6.859  1.00  0.00             
ATOM    599  CA  GLN    76     -15.020  45.347   6.789  1.00  0.00             
ATOM    600  C   GLN    76     -14.678  45.988   5.448  1.00  0.00             
ATOM    601  O   GLN    76     -14.455  47.196   5.366  1.00  0.00             
ATOM    602  CB  GLN    76     -14.648  46.292   7.934  1.00  0.00             
ATOM    603  CG  GLN    76     -13.914  45.618   9.081  1.00  0.00             
ATOM    604  CD  GLN    76     -13.696  46.547  10.259  1.00  0.00             
ATOM    605  OE1 GLN    76     -12.951  46.226  11.186  1.00  0.00             
ATOM    606  NE2 GLN    76     -14.347  47.704  10.228  1.00  0.00             
ATOM    607  N   ALA    77     -14.638  45.171   4.401  1.00  0.00             
ATOM    608  CA  ALA    77     -14.323  45.656   3.063  1.00  0.00             
ATOM    609  C   ALA    77     -14.506  47.166   2.966  1.00  0.00             
ATOM    610  O   ALA    77     -13.922  47.818   2.100  1.00  0.00             
ATOM    611  CB  ALA    77     -12.900  45.274   2.682  1.00  0.00             
ATOM    612  N   ALA    78     -15.321  47.717   3.860  1.00  0.00             
ATOM    613  CA  ALA    78     -15.582  49.151   3.878  1.00  0.00             
ATOM    614  C   ALA    78     -14.806  49.867   2.777  1.00  0.00             
ATOM    615  O   ALA    78     -15.376  50.273   1.765  1.00  0.00             
ATOM    616  CB  ALA    78     -17.072  49.421   3.728  1.00  0.00             
ATOM    617  N   LYS    79     -13.502  50.018   2.982  1.00  0.00             
ATOM    618  CA  LYS    79     -12.644  50.684   2.009  1.00  0.00             
ATOM    619  C   LYS    79     -13.211  50.559   0.599  1.00  0.00             
ATOM    620  O   LYS    79     -12.960  51.405  -0.259  1.00  0.00             
ATOM    621  CB  LYS    79     -12.465  52.159   2.375  1.00  0.00             
ATOM    622  CG  LYS    79     -11.021  52.566   2.620  1.00  0.00             
ATOM    623  CD  LYS    79     -10.824  54.058   2.406  1.00  0.00             
ATOM    624  CE  LYS    79      -9.349  54.420   2.363  1.00  0.00             
ATOM    625  NZ  LYS    79      -9.139  55.865   2.074  1.00  0.00             
ATOM    626  N   LEU    80     -13.976  49.497   0.366  1.00  0.00             
ATOM    627  CA  LEU    80     -14.580  49.259  -0.940  1.00  0.00             
ATOM    628  C   LEU    80     -14.514  50.507  -1.813  1.00  0.00             
ATOM    629  O   LEU    80     -13.518  50.745  -2.498  1.00  0.00             
ATOM    630  CB  LEU    80     -13.890  48.088  -1.643  1.00  0.00             
ATOM    631  CG  LEU    80     -14.790  47.169  -2.470  1.00  0.00             
ATOM    632  CD1 LEU    80     -13.965  46.115  -3.194  1.00  0.00             
ATOM    633  CD2 LEU    80     -15.621  47.976  -3.456  1.00  0.00             
ATOM    634  N   THR    81     -15.580  51.300  -1.786  1.00  0.00             
ATOM    635  CA  THR    81     -15.647  52.552  -2.593  1.00  0.00             
ATOM    636  C   THR    81     -15.740  53.782  -1.695  1.00  0.00             
ATOM    637  O   THR    81     -14.947  54.715  -1.820  1.00  0.00             
ATOM    638  CB  THR    81     -14.423  52.694  -3.516  1.00  0.00             
ATOM    639  OG1 THR    81     -13.224  52.472  -2.764  1.00  0.00             
ATOM    640  CG2 THR    81     -14.495  51.689  -4.655  1.00  0.00             
ATOM    641  N   LEU    82     -16.714  53.776  -0.792  1.00  0.00             
ATOM    642  CA  LEU    82     -16.914  54.890   0.128  1.00  0.00             
ATOM    643  C   LEU    82     -15.947  56.032  -0.172  1.00  0.00             
ATOM    644  O   LEU    82     -15.445  56.688   0.739  1.00  0.00             
ATOM    645  CB  LEU    82     -18.357  55.390   0.058  1.00  0.00             
ATOM    646  CG  LEU    82     -19.261  55.018   1.235  1.00  0.00             
ATOM    647  CD1 LEU    82     -19.922  56.259   1.818  1.00  0.00             
ATOM    648  CD2 LEU    82     -18.475  54.273   2.303  1.00  0.00             
ATOM    649  N   ALA    83     -15.693  56.263  -1.457  1.00  0.00             
ATOM    650  CA  ALA    83     -14.787  57.324  -1.878  1.00  0.00             
ATOM    651  C   ALA    83     -13.480  57.278  -1.095  1.00  0.00             
ATOM    652  O   ALA    83     -13.420  57.706   0.057  1.00  0.00             
ATOM    653  CB  ALA    83     -14.509  57.222  -3.370  1.00  0.00             
ATOM    654  N   VAL    84     -12.434  56.756  -1.728  1.00  0.00             
ATOM    655  CA  VAL    84     -11.097  56.650  -1.078  1.00  0.00             
ATOM    656  C   VAL    84     -10.649  55.196  -0.970  1.00  0.00             
ATOM    657  O   VAL    84     -10.234  54.744   0.097  1.00  0.00             
ATOM    658  CB  VAL    84     -10.030  57.449  -1.850  1.00  0.00             
ATOM    659  CG1 VAL    84     -10.079  58.918  -1.461  1.00  0.00             
ATOM    660  CG2 VAL    84     -10.219  57.280  -3.350  1.00  0.00             
ATOM    661  N   ALA    85     -10.739  54.470  -2.080  1.00  0.00             
ATOM    662  CA  ALA    85     -10.344  53.067  -2.110  1.00  0.00             
ATOM    663  C   ALA    85     -10.928  52.304  -0.926  1.00  0.00             
ATOM    664  O   ALA    85     -11.300  52.892   0.088  1.00  0.00             
ATOM    665  CB  ALA    85     -10.781  52.422  -3.417  1.00  0.00             
TER
END
