
#######################################################
#                                                     #
#                        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   15 (  126),  selected   15 , name T0382TS009_2_3
# Molecule2: number of CA atoms  121 (  929),  selected   15 , name T0382.pdb
# PARAMETERS: T0382TS009_2_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:    15        65 - 79          4.87     4.87
  LCS_AVERAGE:     12.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        69 - 76          1.91     6.38
  LONGEST_CONTINUOUS_SEGMENT:     8        72 - 79          1.94     8.21
  LCS_AVERAGE:      6.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        70 - 74          0.84     7.17
  LONGEST_CONTINUOUS_SEGMENT:     5        72 - 76          0.78     7.56
  LCS_AVERAGE:      3.53

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     L      65     L      65      3    3   15     3    3    3    3    4    5    5    8    8    8    8    9    9   10   12   12   12   13   14   15 
LCS_GDT     F      66     F      66      4    6   15     3    4    5    5    5    5    6    8    8    9   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     E      67     E      67      4    6   15     3    4    5    5    5    6    7    8   10   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     Y      68     Y      68      4    7   15     3    4    5    5    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     P      69     P      69      4    8   15     3    4    5    5    5    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     N      70     N      70      5    8   15     3    4    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     M      71     M      71      5    8   15     3    4    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     Q      72     Q      72      5    8   15     3    5    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     V      73     V      73      5    8   15     3    5    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     R      74     R      74      5    8   15     3    5    5    7    7    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     L      75     L      75      5    8   15     3    5    5    7    7    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     Q      76     Q      76      5    8   15     3    5    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     A      77     A      77      4    8   15     3    4    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_GDT     A      78     A      78      3    8   15     3    3    3    4    4    8   10   12   12   12   12   12   13   14   14   14   14   14   14   15 
LCS_GDT     K      79     K      79      3    8   15     3    4    5    7    8    9   10   12   12   12   13   13   13   14   14   14   14   14   14   15 
LCS_AVERAGE  LCS_A:   7.33  (   3.53    6.06   12.40 )

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      5      5      7      8      9     10     12     12     12     13     13     13     14     14     14     14     14     14     15 
GDT PERCENT_CA   2.48   4.13   4.13   5.79   6.61   7.44   8.26   9.92   9.92   9.92  10.74  10.74  10.74  11.57  11.57  11.57  11.57  11.57  11.57  12.40
GDT RMS_LOCAL    0.07   0.78   0.78   1.35   1.85   2.04   2.25   2.69   2.69   2.69   3.76   3.76   3.39   4.05   4.05   4.05   4.05   4.05   4.05   4.87
GDT RMS_ALL_CA  16.63   7.56   7.56   7.73   5.63   5.62   5.62   5.95   5.95   5.95   5.02   5.02   5.39   5.03   5.03   5.03   5.03   5.03   5.03   4.87

#      Molecule1      Molecule2       DISTANCE
LGA    L      65      L      65         15.011
LGA    F      66      F      66         11.720
LGA    E      67      E      67          8.994
LGA    Y      68      Y      68          3.543
LGA    P      69      P      69          3.071
LGA    N      70      N      70          2.412
LGA    M      71      M      71          1.900
LGA    Q      72      Q      72          1.335
LGA    V      73      V      73          1.595
LGA    R      74      R      74          3.636
LGA    L      75      L      75          3.019
LGA    Q      76      Q      76          0.987
LGA    A      77      A      77          2.046
LGA    A      78      A      78          3.935
LGA    K      79      K      79          2.851

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  121    4.0     12    2.69     7.851     7.550     0.430

LGA_LOCAL      RMSD =  2.690  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.947  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  4.873  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.356470 * X  +  -0.919556 * Y  +  -0.165366 * Z  +  -5.022407
  Y_new =  -0.767901 * X  +  -0.187532 * Y  +  -0.612503 * Z  +  35.620495
  Z_new =   0.532219 * X  +   0.345324 * Y  +  -0.772978 * Z  +  -5.800373 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.721449   -0.420143  [ DEG:   155.9276    -24.0724 ]
  Theta =  -0.561220   -2.580373  [ DEG:   -32.1555   -147.8445 ]
  Phi   =  -1.136185    2.005407  [ DEG:   -65.0986    114.9014 ]
 
# 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_2_3                                
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_3.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  121   4.0   12   2.69   7.550     4.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    500  N   LEU    65     -23.313  38.322  13.684  1.00  0.00             
ATOM    501  CA  LEU    65     -24.648  38.287  14.271  1.00  0.00             
ATOM    502  C   LEU    65     -25.723  38.234  13.192  1.00  0.00             
ATOM    503  O   LEU    65     -26.094  37.158  12.722  1.00  0.00             
ATOM    504  CB  LEU    65     -24.788  37.089  15.212  1.00  0.00             
ATOM    505  CG  LEU    65     -24.896  37.408  16.705  1.00  0.00             
ATOM    506  CD1 LEU    65     -25.065  36.133  17.517  1.00  0.00             
ATOM    507  CD2 LEU    65     -26.043  38.372  16.966  1.00  0.00             
ATOM    508  N   PHE    66     -26.223  39.403  12.803  1.00  0.00             
ATOM    509  CA  PHE    66     -27.256  39.493  11.780  1.00  0.00             
ATOM    510  C   PHE    66     -26.819  38.803  10.491  1.00  0.00             
ATOM    511  O   PHE    66     -26.891  39.385   9.409  1.00  0.00             
ATOM    512  CB  PHE    66     -28.566  38.881  12.285  1.00  0.00             
ATOM    513  CG  PHE    66     -29.757  39.781  12.123  1.00  0.00             
ATOM    514  CD1 PHE    66     -29.620  41.041  11.567  1.00  0.00             
ATOM    515  CD2 PHE    66     -31.014  39.368  12.528  1.00  0.00             
ATOM    516  CE1 PHE    66     -30.717  41.869  11.419  1.00  0.00             
ATOM    517  CE2 PHE    66     -32.111  40.196  12.380  1.00  0.00             
ATOM    518  CZ  PHE    66     -31.966  41.442  11.828  1.00  0.00             
ATOM    519  N   GLU    67     -26.365  37.560  10.617  1.00  0.00             
ATOM    520  CA  GLU    67     -25.915  36.790   9.463  1.00  0.00             
ATOM    521  C   GLU    67     -25.295  37.694   8.404  1.00  0.00             
ATOM    522  O   GLU    67     -24.154  37.489   7.988  1.00  0.00             
ATOM    523  CB  GLU    67     -24.910  35.719   9.894  1.00  0.00             
ATOM    524  CG  GLU    67     -25.535  34.366  10.195  1.00  0.00             
ATOM    525  CD  GLU    67     -24.501  33.270  10.355  1.00  0.00             
ATOM    526  OE1 GLU    67     -23.862  33.208  11.426  1.00  0.00             
ATOM    527  OE2 GLU    67     -24.329  32.472   9.410  1.00  0.00             
ATOM    528  N   TYR    68     -26.053  38.695   7.970  1.00  0.00             
ATOM    529  CA  TYR    68     -25.581  39.633   6.958  1.00  0.00             
ATOM    530  C   TYR    68     -24.090  39.909   7.117  1.00  0.00             
ATOM    531  O   TYR    68     -23.687  40.966   7.600  1.00  0.00             
ATOM    532  CB  TYR    68     -25.872  39.098   5.554  1.00  0.00             
ATOM    533  CG  TYR    68     -26.911  39.893   4.798  1.00  0.00             
ATOM    534  CD1 TYR    68     -27.155  41.224   5.113  1.00  0.00             
ATOM    535  CD2 TYR    68     -27.643  39.313   3.771  1.00  0.00             
ATOM    536  CE1 TYR    68     -28.102  41.960   4.427  1.00  0.00             
ATOM    537  CE2 TYR    68     -28.594  40.033   3.075  1.00  0.00             
ATOM    538  CZ  TYR    68     -28.819  41.367   3.411  1.00  0.00             
ATOM    539  OH  TYR    68     -29.765  42.093   2.724  1.00  0.00             
ATOM    540  N   PRO    69     -23.249  38.949   6.705  1.00  0.00             
ATOM    541  CA  PRO    69     -21.791  39.083   6.798  1.00  0.00             
ATOM    542  C   PRO    69     -21.369  39.800   8.076  1.00  0.00             
ATOM    543  O   PRO    69     -20.180  40.006   8.320  1.00  0.00             
ATOM    544  CB  PRO    69     -21.313  37.630   6.827  1.00  0.00             
ATOM    545  CG  PRO    69     -22.338  36.917   7.644  1.00  0.00             
ATOM    546  CD  PRO    69     -23.657  37.662   6.118  1.00  0.00             
ATOM    547  N   ASN    70     -22.351  40.178   8.888  1.00  0.00             
ATOM    548  CA  ASN    70     -22.083  40.873  10.142  1.00  0.00             
ATOM    549  C   ASN    70     -20.881  41.803  10.012  1.00  0.00             
ATOM    550  O   ASN    70     -19.918  41.699  10.771  1.00  0.00             
ATOM    551  CB  ASN    70     -23.314  41.662  10.591  1.00  0.00             
ATOM    552  CG  ASN    70     -24.116  40.938  11.654  1.00  0.00             
ATOM    553  OD1 ASN    70     -24.914  41.547  12.366  1.00  0.00             
ATOM    554  ND2 ASN    70     -23.905  39.631  11.764  1.00  0.00             
ATOM    555  N   MET    71     -20.946  42.712   9.045  1.00  0.00             
ATOM    556  CA  MET    71     -19.865  43.662   8.813  1.00  0.00             
ATOM    557  C   MET    71     -18.592  42.951   8.368  1.00  0.00             
ATOM    558  O   MET    71     -17.822  43.478   7.565  1.00  0.00             
ATOM    559  CB  MET    71     -20.279  44.701   7.769  1.00  0.00             
ATOM    560  CG  MET    71     -20.606  46.068   8.350  1.00  0.00             
ATOM    561  SD  MET    71     -21.586  47.084   7.228  1.00  0.00             
ATOM    562  CE  MET    71     -21.257  48.719   7.878  1.00  0.00             
ATOM    563  N   GLN    72     -18.375  41.751   8.897  1.00  0.00             
ATOM    564  CA  GLN    72     -17.194  40.965   8.556  1.00  0.00             
ATOM    565  C   GLN    72     -17.024  40.855   7.045  1.00  0.00             
ATOM    566  O   GLN    72     -15.977  41.210   6.501  1.00  0.00             
ATOM    567  CB  GLN    72     -15.942  41.579   9.184  1.00  0.00             
ATOM    568  CG  GLN    72     -15.222  40.661  10.159  1.00  0.00             
ATOM    569  CD  GLN    72     -13.783  41.074  10.393  1.00  0.00             
ATOM    570  OE1 GLN    72     -13.152  40.638  11.356  1.00  0.00             
ATOM    571  NE2 GLN    72     -13.259  41.918   9.513  1.00  0.00             
ATOM    572  N   VAL    73     -18.057  40.362   6.371  1.00  0.00             
ATOM    573  CA  VAL    73     -18.023  40.201   4.890  1.00  0.00             
ATOM    574  C   VAL    73     -18.046  41.555   4.187  1.00  0.00             
ATOM    575  O   VAL    73     -17.115  42.349   4.318  1.00  0.00             
ATOM    576  CB  VAL    73     -16.775  39.420   4.436  1.00  0.00             
ATOM    577  CG1 VAL    73     -17.177  38.095   3.806  1.00  0.00             
ATOM    578  CG2 VAL    73     -15.831  39.197   5.607  1.00  0.00             
ATOM    579  N   ARG    74     -19.116  41.810   3.442  1.00  0.00             
ATOM    580  CA  ARG    74     -19.263  43.067   2.717  1.00  0.00             
ATOM    581  C   ARG    74     -18.949  44.260   3.614  1.00  0.00             
ATOM    582  O   ARG    74     -18.369  45.250   3.166  1.00  0.00             
ATOM    583  CB  ARG    74     -18.358  43.083   1.484  1.00  0.00             
ATOM    584  CG  ARG    74     -19.064  43.493   0.201  1.00  0.00             
ATOM    585  CD  ARG    74     -18.219  43.173  -1.021  1.00  0.00             
ATOM    586  NE  ARG    74     -18.723  43.832  -2.222  1.00  0.00             
ATOM    587  CZ  ARG    74     -18.516  45.113  -2.514  1.00  0.00             
ATOM    588  NH1 ARG    74     -17.812  45.875  -1.688  1.00  0.00             
ATOM    589  NH2 ARG    74     -19.013  45.627  -3.630  1.00  0.00             
ATOM    590  N   LEU    75     -19.335  44.159   4.882  1.00  0.00             
ATOM    591  CA  LEU    75     -19.096  45.229   5.843  1.00  0.00             
ATOM    592  C   LEU    75     -17.822  45.997   5.507  1.00  0.00             
ATOM    593  O   LEU    75     -17.790  47.226   5.580  1.00  0.00             
ATOM    594  CB  LEU    75     -20.290  46.184   5.890  1.00  0.00             
ATOM    595  CG  LEU    75     -20.908  46.430   7.268  1.00  0.00             
ATOM    596  CD1 LEU    75     -21.168  47.912   7.484  1.00  0.00             
ATOM    597  CD2 LEU    75     -20.013  45.872   8.364  1.00  0.00             
ATOM    598  N   GLN    76     -16.775  45.266   5.139  1.00  0.00             
ATOM    599  CA  GLN    76     -15.498  45.877   4.790  1.00  0.00             
ATOM    600  C   GLN    76     -15.699  47.140   3.960  1.00  0.00             
ATOM    601  O   GLN    76     -14.794  47.966   3.839  1.00  0.00             
ATOM    602  CB  GLN    76     -14.697  46.199   6.053  1.00  0.00             
ATOM    603  CG  GLN    76     -13.581  45.211   6.349  1.00  0.00             
ATOM    604  CD  GLN    76     -12.909  45.473   7.683  1.00  0.00             
ATOM    605  OE1 GLN    76     -11.866  44.894   7.987  1.00  0.00             
ATOM    606  NE2 GLN    76     -13.506  46.348   8.483  1.00  0.00             
ATOM    607  N   ALA    77     -16.891  47.285   3.390  1.00  0.00             
ATOM    608  CA  ALA    77     -17.213  48.446   2.571  1.00  0.00             
ATOM    609  C   ALA    77     -16.222  49.581   2.810  1.00  0.00             
ATOM    610  O   ALA    77     -16.611  50.742   2.932  1.00  0.00             
ATOM    611  CB  ALA    77     -17.233  48.069   1.098  1.00  0.00             
ATOM    612  N   ALA    78     -14.940  49.236   2.874  1.00  0.00             
ATOM    613  CA  ALA    78     -13.891  50.224   3.097  1.00  0.00             
ATOM    614  C   ALA    78     -14.021  50.864   4.474  1.00  0.00             
ATOM    615  O   ALA    78     -13.103  50.794   5.291  1.00  0.00             
ATOM    616  CB  ALA    78     -12.519  49.585   2.942  1.00  0.00             
ATOM    617  N   LYS    79     -15.166  51.489   4.725  1.00  0.00             
ATOM    618  CA  LYS    79     -15.419  52.142   6.004  1.00  0.00             
ATOM    619  C   LYS    79     -14.440  51.663   7.071  1.00  0.00             
ATOM    620  O   LYS    79     -14.008  52.439   7.924  1.00  0.00             
ATOM    621  CB  LYS    79     -15.332  53.662   5.855  1.00  0.00             
ATOM    622  CG  LYS    79     -16.612  54.396   6.221  1.00  0.00             
ATOM    623  CD  LYS    79     -16.330  55.838   6.611  1.00  0.00             
ATOM    624  CE  LYS    79     -17.549  56.485   7.251  1.00  0.00             
ATOM    625  NZ  LYS    79     -17.262  57.871   7.713  1.00  0.00             
TER
END
