
#######################################################
#                                                     #
#                        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 (  129),  selected   15 , name T0347TS249_5_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   15 , name T0347_D1.pdb
# PARAMETERS: T0347TS249_5_2-D1.T0347_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:    15        94 - 108         2.77     2.77
  LCS_AVERAGE:     16.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       103 - 108         1.88     6.24
  LCS_AVERAGE:      5.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        94 - 96          0.28     3.35
  LONGEST_CONTINUOUS_SEGMENT:     3        95 - 97          0.25    14.52
  LONGEST_CONTINUOUS_SEGMENT:     3        96 - 98          0.22    14.53
  LONGEST_CONTINUOUS_SEGMENT:     3        97 - 99          0.26    12.39
  LONGEST_CONTINUOUS_SEGMENT:     3        98 - 100         0.16    10.22
  LONGEST_CONTINUOUS_SEGMENT:     3        99 - 101         0.20     9.96
  LONGEST_CONTINUOUS_SEGMENT:     3       100 - 102         0.49    10.40
  LONGEST_CONTINUOUS_SEGMENT:     3       101 - 103         0.25    10.40
  LONGEST_CONTINUOUS_SEGMENT:     3       102 - 104         0.43     6.43
  LONGEST_CONTINUOUS_SEGMENT:     3       103 - 105         0.89     5.35
  LONGEST_CONTINUOUS_SEGMENT:     3       104 - 106         0.30    15.19
  LONGEST_CONTINUOUS_SEGMENT:     3       105 - 107         0.11    14.28
  LONGEST_CONTINUOUS_SEGMENT:     3       106 - 108         0.28     4.36
  LCS_AVERAGE:      3.37

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:   89
LCS_GDT     L      94     L      94      3    5   15     4    5    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G      95     G      95      3    5   15     4    5    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K      96     K      96      3    5   15     4    5    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     D      97     D      97      3    5   15     3    3    5    6    9    9   11   13   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E      98     E      98      3    5   15     3    5    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     F      99     F      99      3    4   15     3    3    5    5    7   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     W     100     W     100      3    4   15     3    5    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     S     101     S     101      3    4   15     3    4    6    7    9    9   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     102     V     102      3    4   15     3    3    5    6    7   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     M     103     M     103      3    6   15     3    4    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     D     104     D     104      3    6   15     3    3    6    7   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     H     105     H     105      3    6   15     3    3    4    7    8    9   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     106     R     106      3    6   15     4    5    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     N     107     N     107      3    6   15     4    5    6    9   10   12   12   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     108     L     108      3    6   15     3    3    6    9   10   12   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   8.66  (   3.37    5.77   16.85 )

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      6      9     10     12     13     14     15     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   4.49   5.62   6.74  10.11  11.24  13.48  14.61  15.73  16.85  16.85  16.85  16.85  16.85  16.85  16.85  16.85  16.85  16.85  16.85  16.85
GDT RMS_LOCAL    0.13   0.41   0.72   1.49   1.63   1.91   2.46   2.49   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77
GDT RMS_ALL_CA   3.62   3.39   3.33   2.95   2.87   2.98   2.85   2.82   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77   2.77

#      Molecule1      Molecule2       DISTANCE
LGA    L      94      L      94          1.504
LGA    G      95      G      95          1.937
LGA    K      96      K      96          1.219
LGA    D      97      D      97          4.936
LGA    E      98      E      98          1.001
LGA    F      99      F      99          3.796
LGA    W     100      W     100          1.569
LGA    S     101      S     101          3.563
LGA    V     102      V     102          3.417
LGA    M     103      M     103          1.326
LGA    D     104      D     104          1.441
LGA    H     105      H     105          3.996
LGA    R     106      R     106          2.435
LGA    N     107      N     107          3.058
LGA    L     108      L     108          2.733

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   89    4.0     14    2.49    12.079    11.204     0.541

LGA_LOCAL      RMSD =  2.488  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.789  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  2.766  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.224800 * X  +   0.622326 * Y  +  -0.749784 * Z  +  16.927856
  Y_new =   0.711982 * X  +  -0.630242 * Y  +  -0.309640 * Z  +  38.591354
  Z_new =  -0.665242 * X  +  -0.464225 * Y  +  -0.584763 * Z  +   1.577415 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.470601    0.670991  [ DEG:  -141.5550     38.4450 ]
  Theta =   0.727818    2.413774  [ DEG:    41.7009    138.2991 ]
  Phi   =   1.264964   -1.876628  [ DEG:    72.4771   -107.5229 ]
 
# 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: T0347TS249_5_2-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS249_5_2-D1.T0347_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   89   4.0   14   2.49  11.204     2.77
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS249_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0347
PARENT 1oe8_A
ATOM    760  N   LEU    94      -1.817  25.742   6.590  1.00  9.99
ATOM    761  CA  LEU    94      -2.076  25.842   7.994  1.00  9.99
ATOM    762  CB  LEU    94      -0.994  26.620   8.762  1.00  9.99
ATOM    763  CG  LEU    94       0.387  25.939   8.749  1.00  9.99
ATOM    764  CD1 LEU    94       1.421  26.768   9.532  1.00  9.99
ATOM    765  CD2 LEU    94       0.291  24.484   9.239  1.00  9.99
ATOM    766  C   LEU    94      -3.370  26.631   8.008  1.00  9.99
ATOM    767  O   LEU    94      -3.947  26.847   6.943  1.00  9.99
ATOM    768  N   GLY    95      -3.911  27.035   9.181  1.00  9.99
ATOM    769  CA  GLY    95      -5.215  27.671   9.199  1.00  9.99
ATOM    770  C   GLY    95      -5.316  28.978   8.457  1.00  9.99
ATOM    771  O   GLY    95      -5.992  29.057   7.437  1.00  9.99
ATOM    772  N   LYS    96      -4.625  30.063   8.853  1.00  9.99
ATOM    773  CA  LYS    96      -4.603  31.173   7.938  1.00  9.99
ATOM    774  CB  LYS    96      -4.136  32.454   8.626  1.00  9.99
ATOM    775  CG  LYS    96      -4.865  32.567   9.970  1.00  9.99
ATOM    776  CD  LYS    96      -6.391  32.505   9.828  1.00  9.99
ATOM    777  CE  LYS    96      -7.146  32.745  11.136  1.00  9.99
ATOM    778  NZ  LYS    96      -8.597  32.859  10.875  1.00  9.99
ATOM    779  C   LYS    96      -3.571  30.549   7.040  1.00  9.99
ATOM    780  O   LYS    96      -3.793  29.578   6.323  1.00  9.99
ATOM    781  N   ASP    97      -2.343  31.021   7.081  1.00  9.99
ATOM    782  CA  ASP    97      -1.368  30.020   6.776  1.00  9.99
ATOM    783  CB  ASP    97      -0.014  30.581   6.328  1.00  9.99
ATOM    784  CG  ASP    97      -0.311  31.460   5.122  1.00  9.99
ATOM    785  OD1 ASP    97      -0.867  30.939   4.120  1.00  9.99
ATOM    786  OD2 ASP    97      -0.021  32.682   5.209  1.00  9.99
ATOM    787  C   ASP    97      -1.298  29.578   8.217  1.00  9.99
ATOM    788  O   ASP    97      -2.254  29.049   8.780  1.00  9.99
ATOM    789  N   GLU    98      -0.181  29.638   8.915  1.00  9.99
ATOM    790  CA  GLU    98      -0.597  29.641  10.288  1.00  9.99
ATOM    791  CB  GLU    98       0.589  29.586  11.259  1.00  9.99
ATOM    792  CG  GLU    98       0.207  29.091  12.652  1.00  9.99
ATOM    793  CD  GLU    98       1.490  28.836  13.424  1.00  9.99
ATOM    794  OE1 GLU    98       2.488  29.561  13.169  1.00  9.99
ATOM    795  OE2 GLU    98       1.491  27.907  14.276  1.00  9.99
ATOM    796  C   GLU    98      -1.264  31.004  10.355  1.00  9.99
ATOM    797  O   GLU    98      -2.474  31.097  10.278  1.00  9.99
ATOM    798  N   PHE    99      -0.472  32.086  10.255  1.00  9.99
ATOM    799  CA  PHE    99      -0.808  33.492  10.113  1.00  9.99
ATOM    800  CB  PHE    99      -0.102  34.309  11.230  1.00  9.99
ATOM    801  CG  PHE    99       0.014  35.802  11.384  1.00  9.99
ATOM    802  CD1 PHE    99      -0.999  36.627  11.743  1.00  9.99
ATOM    803  CD2 PHE    99       1.214  36.431  11.319  1.00  9.99
ATOM    804  CE1 PHE    99      -0.902  37.981  11.940  1.00  9.99
ATOM    805  CE2 PHE    99       1.363  37.788  11.503  1.00  9.99
ATOM    806  CZ  PHE    99       0.306  38.593  11.824  1.00  9.99
ATOM    807  C   PHE    99      -0.161  33.462   8.802  1.00  9.99
ATOM    808  O   PHE    99      -0.581  32.642   8.000  1.00  9.99
ATOM    809  N   TRP   100       0.921  34.157   8.481  1.00  9.99
ATOM    810  CA  TRP   100       1.490  33.506   7.341  1.00  9.99
ATOM    811  CB  TRP   100       2.523  34.309   6.681  1.00  9.99
ATOM    812  CG  TRP   100       2.523  33.982   5.254  1.00  9.99
ATOM    813  CD2 TRP   100       1.707  34.767   4.424  1.00  9.99
ATOM    814  CD1 TRP   100       3.096  33.031   4.481  1.00  9.99
ATOM    815  NE1 TRP   100       2.628  33.159   3.200  1.00  9.99
ATOM    816  CE2 TRP   100       1.768  34.242   3.164  1.00  9.99
ATOM    817  CE3 TRP   100       0.942  35.822   4.705  1.00  9.99
ATOM    818  CZ2 TRP   100       1.018  34.797   2.176  1.00  9.99
ATOM    819  CZ3 TRP   100       0.232  36.383   3.690  1.00  9.99
ATOM    820  CH2 TRP   100       0.253  35.891   2.422  1.00  9.99
ATOM    821  C   TRP   100       2.182  32.435   8.135  1.00  9.99
ATOM    822  O   TRP   100       1.567  31.515   8.666  1.00  9.99
ATOM    823  N   SER   101       3.497  32.401   8.296  1.00  9.99
ATOM    824  CA  SER   101       3.687  31.680   9.536  1.00  9.99
ATOM    825  CB  SER   101       5.162  31.445   9.877  1.00  9.99
ATOM    826  OG  SER   101       5.269  30.738  11.105  1.00  9.99
ATOM    827  C   SER   101       3.193  32.803  10.350  1.00  9.99
ATOM    828  O   SER   101       2.062  32.903  10.736  1.00  9.99
ATOM    829  N   VAL   102       4.054  33.762  10.489  1.00  9.99
ATOM    830  CA  VAL   102       3.696  35.100  10.616  1.00  9.99
ATOM    831  CB  VAL   102       4.419  35.667  11.803  1.00  9.99
ATOM    832  CG1 VAL   102       4.199  37.179  11.924  1.00  9.99
ATOM    833  CG2 VAL   102       3.877  34.900  13.024  1.00  9.99
ATOM    834  C   VAL   102       4.452  35.057   9.323  1.00  9.99
ATOM    835  O   VAL   102       5.258  34.142   9.226  1.00  9.99
ATOM    836  N   MET   103       4.285  35.774   8.235  1.00  9.99
ATOM    837  CA  MET   103       5.258  35.558   7.178  1.00  9.99
ATOM    838  CB  MET   103       4.939  35.543   5.710  1.00  9.99
ATOM    839  CG  MET   103       5.830  34.421   5.192  1.00  9.99
ATOM    840  SD  MET   103       5.640  32.885   6.171  1.00  9.99
ATOM    841  CE  MET   103       6.669  31.817   5.126  1.00  9.99
ATOM    842  C   MET   103       6.204  36.615   7.356  1.00  9.99
ATOM    843  O   MET   103       7.147  36.861   6.603  1.00  9.99
ATOM    844  N   ASP   104       5.892  37.370   8.350  1.00  9.99
ATOM    845  CA  ASP   104       7.040  37.574   9.015  1.00  9.99
ATOM    846  CB  ASP   104       6.553  38.049  10.396  1.00  9.99
ATOM    847  CG  ASP   104       6.052  39.461  10.388  1.00  9.99
ATOM    848  OD1 ASP   104       5.785  40.000   9.284  1.00  9.99
ATOM    849  OD2 ASP   104       5.936  40.017  11.513  1.00  9.99
ATOM    850  C   ASP   104       7.225  36.053   9.195  1.00  9.99
ATOM    851  O   ASP   104       6.710  35.785  10.248  1.00  9.99
ATOM    852  N   HIS   105       7.947  35.126   8.350  1.00  9.99
ATOM    853  CA  HIS   105       7.774  33.700   8.303  1.00  9.99
ATOM    854  ND1 HIS   105      10.747  33.770   6.366  1.00  9.99
ATOM    855  CG  HIS   105       9.419  33.454   6.424  1.00  9.99
ATOM    856  CB  HIS   105       8.859  32.860   7.649  1.00  9.99
ATOM    857  NE2 HIS   105       9.861  34.349   4.414  1.00  9.99
ATOM    858  CD2 HIS   105       8.884  33.814   5.227  1.00  9.99
ATOM    859  CE1 HIS   105      10.957  34.291   5.149  1.00  9.99
ATOM    860  C   HIS   105       8.036  33.540   9.726  1.00  9.99
ATOM    861  O   HIS   105       7.169  33.205  10.526  1.00  9.99
ATOM    862  N   ARG   106       9.260  33.913  10.105  1.00  9.99
ATOM    863  CA  ARG   106       9.429  34.149  11.502  1.00  9.99
ATOM    864  CB  ARG   106      10.902  34.214  11.951  1.00  9.99
ATOM    865  CG  ARG   106      11.820  33.159  11.321  1.00  9.99
ATOM    866  CD  ARG   106      12.160  31.960  12.208  1.00  9.99
ATOM    867  NE  ARG   106      13.161  31.142  11.462  1.00  9.99
ATOM    868  CZ  ARG   106      12.755  30.131  10.640  1.00  9.99
ATOM    869  NH1 ARG   106      11.432  29.807  10.555  1.00  9.99
ATOM    870  NH2 ARG   106      13.676  29.447   9.901  1.00  9.99
ATOM    871  C   ARG   106       8.871  35.525  11.767  1.00  9.99
ATOM    872  O   ARG   106       7.837  35.703  12.402  1.00  9.99
ATOM    873  N   ASN   107       9.479  36.500  11.058  1.00  9.99
ATOM    874  CA  ASN   107       9.321  37.931  10.841  1.00  9.99
ATOM    875  CB  ASN   107      10.419  38.793  11.455  1.00  9.99
ATOM    876  CG  ASN   107      10.223  38.722  12.956  1.00  9.99
ATOM    877  OD1 ASN   107       9.117  38.893  13.468  1.00  9.99
ATOM    878  ND2 ASN   107      11.334  38.443  13.686  1.00  9.99
ATOM    879  C   ASN   107       9.620  37.775   9.427  1.00  9.99
ATOM    880  O   ASN   107       9.743  36.593   9.232  1.00  9.99
ATOM    881  N   LEU   108       9.427  38.758   8.473  1.00  9.99
ATOM    882  CA  LEU   108       9.398  38.524   7.021  1.00  9.99
ATOM    883  CB  LEU   108      10.090  39.674   6.279  1.00  9.99
ATOM    884  CG  LEU   108       9.359  41.014   6.514  1.00  9.99
ATOM    885  CD1 LEU   108      10.113  42.214   5.915  1.00  9.99
ATOM    886  CD2 LEU   108       7.904  40.937   6.023  1.00  9.99
ATOM    887  C   LEU   108      10.163  37.264   6.835  1.00  9.99
ATOM    888  O   LEU   108       9.583  36.208   6.671  1.00  9.99
TER
END
