
#######################################################
#                                                     #
#                        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   31 (  150),  selected   27 , name T0316TS102_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected   27 , name T0316_D2.pdb
# PARAMETERS: T0316TS102_2-D2.T0316_D2.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       239 - 272         4.92    18.18
  LCS_AVERAGE:     22.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       265 - 271         1.82    18.74
  LONGEST_CONTINUOUS_SEGMENT:     7       268 - 274         1.81    12.96
  LCS_AVERAGE:      9.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       265 - 270         0.82    20.46
  LONGEST_CONTINUOUS_SEGMENT:     6       269 - 274         0.65    12.30
  LCS_AVERAGE:      7.59

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:   60
LCS_GDT     G     220     G     220      4    4    9     3    5    5    5    5    5    5    5    6    7    9   10   12   15   16   16   17   18   20   20 
LCS_GDT     R     221     R     221      4    4    9     3    5    5    5    5    5    6    6    6    9   12   13   14   15   16   17   17   19   20   20 
LCS_GDT     M     222     M     222      4    4    9     3    5    5    5    5    5    6    7    8    9   12   13   14   15   17   17   17   19   20   20 
LCS_GDT     M     223     M     223      4    4    9     3    5    5    5    7    8    8    8    8    9   12   13   14   15   17   17   17   19   20   20 
LCS_GDT     Y     239     Y     239      3    4   15     3    3    3    4    4    5    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     T     240     T     240      3    4   15     3    3    3    4    4    5    6   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     I     241     I     241      3    4   15     3    3    3    4    4    5    6    7   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     G     242     G     242      3    4   15     3    3    3    4    4    5    6    7   10   11   12   14   15   15   16   17   17   18   20   20 
LCS_GDT     Q     243     Q     243      3    4   15     3    3    3    3    4    4    5    7   10   11   12   14   15   15   16   16   17   18   20   20 
LCS_GDT     R     244     R     244      3    4   15     3    3    3    3    4    4    5    6   10   11   12   14   15   15   15   15   17   18   20   20 
LCS_GDT     G     251     G     251      0    0   15     0    0    0    0    0    0    0    0    0    4    5   12   15   15   15   15   15   15   15   15 
LCS_GDT     K     265     K     265      6    7   15     4    5    6    6    6    6    7   10   11   11   12   14   15   15   16   17   17   19   20   20 
LCS_GDT     D     266     D     266      6    7   15     4    5    6    6    6    6    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     L     267     L     267      6    7   15     4    5    6    6    6    6    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     S     268     S     268      6    7   15     4    5    6    6    7    7    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     K     269     K     269      6    7   15     5    5    6    6    7    8    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     N     270     N     270      6    7   15     5    5    6    6    7    8    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     I     271     I     271      6    7   15     4    5    6    6    7    8    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     L     272     L     272      6    7   15     5    5    6    6    7    8    8   10   11   11   12   14   15   15   17   17   17   19   20   20 
LCS_GDT     Y     273     Y     273      6    7   13     5    5    6    6    7    8    8    9    9   10   12   13   14   15   17   17   17   19   20   20 
LCS_GDT     V     274     V     274      6    7   13     5    5    6    6    7    8    8    9    9   10   12   13   14   15   17   17   17   19   20   20 
LCS_GDT     F     278     F     278      4    6   13     3    4    4    6    6    6    6    6    8   10   11   12   12   13   17   17   17   19   20   20 
LCS_GDT     Y     279     Y     279      5    6   13     3    4    5    6    6    6    8    9    9   10   11   12   12   14   17   17   17   19   20   20 
LCS_GDT     H     280     H     280      5    6   13     4    4    5    6    7    8    8    9    9   10   11   12   12   15   17   17   17   19   20   20 
LCS_GDT     D     281     D     281      5    6   13     4    4    5    6    6    6    6    6    9    9   11   11   11   13   15   16   17   18   20   20 
LCS_GDT     S     282     S     282      5    6   13     4    4    5    6    6    6    6    6    6    6    6    7    8   10   10   12   12   13   14   17 
LCS_GDT     L     283     L     283      5    6    7     4    4    5    6    6    6    6    6    6    6    8    8    9   11   11   12   12   17   18   20 
LCS_AVERAGE  LCS_A:  12.92  (   7.59    9.01   22.16 )

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      5      6      6      7      8      8     10     11     11     12     14     15     15     17     17     17     19     20     20 
GDT PERCENT_CA   8.33   8.33  10.00  10.00  11.67  13.33  13.33  16.67  18.33  18.33  20.00  23.33  25.00  25.00  28.33  28.33  28.33  31.67  33.33  33.33
GDT RMS_LOCAL    0.41   0.41   0.65   0.65   1.09   1.84   1.84   3.01   3.28   3.28   3.59   4.68   4.92   4.68   5.69   5.20   5.20   6.12   6.49   6.49
GDT RMS_ALL_CA  12.28  12.28  12.30  12.30  12.21  11.73  11.73  15.53  15.63  15.63  16.15  18.13  18.18  12.06  10.68  11.96  11.96  10.73  10.56  10.56

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         16.756
LGA    R     221      R     221         18.182
LGA    M     222      M     222         15.321
LGA    M     223      M     223         16.556
LGA    Y     239      Y     239          3.198
LGA    T     240      T     240          3.701
LGA    I     241      I     241          4.989
LGA    G     242      G     242          6.755
LGA    Q     243      Q     243         12.305
LGA    R     244      R     244         14.460
LGA    G     251      G     251         14.733
LGA    K     265      K     265          3.892
LGA    D     266      D     266          1.707
LGA    L     267      L     267          1.941
LGA    S     268      S     268          3.193
LGA    K     269      K     269          1.514
LGA    N     270      N     270          3.730
LGA    I     271      I     271          3.390
LGA    L     272      L     272          3.137
LGA    Y     273      Y     273          9.935
LGA    V     274      V     274         12.003
LGA    F     278      F     278         20.851
LGA    Y     279      Y     279         25.397
LGA    H     280      H     280         26.028
LGA    D     281      D     281         32.413
LGA    S     282      S     282         31.472
LGA    L     283      L     283         26.321

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   60    4.0     10    3.01    15.833    14.219     0.322

LGA_LOCAL      RMSD =  3.006  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.630  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  9.830  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.835773 * X  +   0.113010 * Y  +  -0.537320 * Z  +  79.200195
  Y_new =   0.189778 * X  +  -0.858825 * Y  +  -0.475819 * Z  +  36.837017
  Z_new =  -0.515236 * X  +  -0.499649 * Y  +   0.696336 * Z  + -11.910810 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.622401    2.519192  [ DEG:   -35.6609    144.3391 ]
  Theta =   0.541283    2.600310  [ DEG:    31.0132    148.9868 ]
  Phi   =   2.918310   -0.223283  [ DEG:   167.2068    -12.7932 ]
 
# 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: T0316TS102_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_2-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   60   4.0   10   3.01  14.219     9.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_2-D2
PFRMAT TS
TARGET T0316
MODEL 2
PARENT 1b90_A
ATOM    675  N   GLY   220      46.998  30.766  -5.843  1.00  1.00
ATOM    676  CA  GLY   220      47.694  29.746  -6.596  1.00  1.00
ATOM    677  C   GLY   220      46.768  28.716  -7.223  1.00  1.00
ATOM    678  O   GLY   220      47.092  28.155  -8.271  1.00  1.00
ATOM    679  N   ARG   221      45.609  28.486  -6.595  1.00  1.00
ATOM    680  CA  ARG   221      44.613  27.532  -7.056  1.00  1.00
ATOM    681  C   ARG   221      43.976  27.767  -8.409  1.00  1.00
ATOM    682  O   ARG   221      43.935  28.899  -8.899  1.00  1.00
ATOM    683  CB  ARG   221      43.539  27.480  -6.021  1.00  1.00
ATOM    684  N   MET   222      43.447  26.709  -9.027  1.00  1.00
ATOM    685  CA  MET   222      42.807  26.872 -10.329  1.00  1.00
ATOM    686  C   MET   222      41.518  26.082 -10.387  1.00  1.00
ATOM    687  O   MET   222      41.394  25.060  -9.721  1.00  1.00
ATOM    688  CB  MET   222      43.688  26.399 -11.500  1.00  1.00
ATOM    689  N   MET   223      40.510  26.511 -11.145  1.00  1.00
ATOM    690  CA  MET   223      39.295  25.729 -11.150  1.00  1.00
ATOM    691  C   MET   223      39.064  25.144 -12.507  1.00  1.00
ATOM    692  O   MET   223      39.268  25.763 -13.533  1.00  1.00
ATOM    693  CB  MET   223      38.107  26.591 -10.713  1.00  1.00
ATOM    694  N   TYR   239      38.688  23.878 -12.409  1.00  1.00
ATOM    695  CA  TYR   239      38.393  23.000 -13.516  1.00  1.00
ATOM    696  C   TYR   239      37.056  22.285 -13.390  1.00  1.00
ATOM    697  O   TYR   239      36.461  22.212 -12.318  1.00  1.00
ATOM    698  CB  TYR   239      39.489  21.930 -13.633  1.00  1.00
ATOM    699  N   THR   240      36.492  21.810 -14.484  1.00  1.00
ATOM    700  CA  THR   240      35.267  21.045 -14.396  1.00  1.00
ATOM    701  C   THR   240      35.521  19.794 -15.186  1.00  1.00
ATOM    702  O   THR   240      36.269  19.724 -16.161  1.00  1.00
ATOM    703  CB  THR   240      33.946  21.629 -15.025  1.00  1.00
ATOM    704  N   ILE   241      34.936  18.765 -14.616  1.00  1.00
ATOM    705  CA  ILE   241      35.009  17.487 -15.252  1.00  1.00
ATOM    706  C   ILE   241      33.618  16.928 -15.113  1.00  1.00
ATOM    707  O   ILE   241      32.859  17.259 -14.206  1.00  1.00
ATOM    708  CB  ILE   241      36.066  16.658 -14.564  1.00  1.00
ATOM    709  N   GLY   242      33.275  16.137 -16.104  1.00  1.00
ATOM    710  CA  GLY   242      31.964  15.529 -16.135  1.00  1.00
ATOM    711  C   GLY   242      32.000  14.105 -16.632  1.00  1.00
ATOM    712  O   GLY   242      33.057  13.545 -16.924  1.00  1.00
ATOM    713  N   GLN   243      30.786  13.574 -16.755  1.00  1.00
ATOM    714  CA  GLN   243      30.535  12.214 -17.170  1.00  1.00
ATOM    715  C   GLN   243      30.695  11.824 -18.625  1.00  1.00
ATOM    716  O   GLN   243      31.020  10.679 -18.915  1.00  1.00
ATOM    717  CB  GLN   243      29.132  11.854 -16.693  1.00  1.00
ATOM    718  N   ARG   244      30.410  12.703 -19.566  1.00  1.00
ATOM    719  CA  ARG   244      30.554  12.411 -20.978  1.00  1.00
ATOM    720  C   ARG   244      31.972  12.715 -21.407  1.00  1.00
ATOM    721  O   ARG   244      32.631  13.568 -20.817  1.00  1.00
ATOM    722  CB  ARG   244      29.607  13.276 -21.805  1.00  1.00
ATOM    723  N   GLY   251      32.426  12.096 -22.498  1.00  1.00
ATOM    724  CA  GLY   251      33.773  12.328 -22.994  1.00  1.00
ATOM    725  C   GLY   251      34.037  13.778 -23.385  1.00  1.00
ATOM    726  O   GLY   251      35.184  14.244 -23.349  1.00  1.00
ATOM    727  N   GLN   252      32.978  14.537 -23.704  1.00  1.00
ATOM    728  CA  GLN   252      33.149  15.943 -24.069  1.00  1.00
ATOM    729  C   GLN   252      33.461  16.793 -22.856  1.00  1.00
ATOM    730  O   GLN   252      33.888  17.940 -22.988  1.00  1.00
ATOM    731  CB  GLN   252      31.915  16.523 -24.770  1.00  1.00
ATOM    732  N   HIS   253      33.271  16.217 -21.659  1.00  1.00
ATOM    733  CA  HIS   253      33.567  16.908 -20.414  1.00  1.00
ATOM    734  C   HIS   253      34.738  16.213 -19.715  1.00  1.00
ATOM    735  O   HIS   253      35.059  16.503 -18.565  1.00  1.00
ATOM    736  CB  HIS   253      32.346  16.902 -19.497  1.00  1.00
ATOM    737  N   GLY   254      35.374  15.232 -20.369  1.00  1.00
ATOM    738  CA  GLY   254      36.524  14.536 -19.802  1.00  1.00
ATOM    739  C   GLY   254      36.332  13.177 -19.139  1.00  1.00
ATOM    740  O   GLY   254      37.304  12.680 -18.577  1.00  1.00
ATOM    741  N   GLY   255      35.161  12.538 -19.153  1.00  1.00
ATOM    742  CA  GLY   255      34.915  11.247 -18.532  1.00  1.00
ATOM    743  C   GLY   255      35.447  11.118 -17.103  1.00  1.00
ATOM    744  O   GLY   255      36.134  10.168 -16.702  1.00  1.00
ATOM    745  N   LYS   265      35.229  12.199 -16.354  1.00  1.00
ATOM    746  CA  LYS   265      35.603  12.314 -14.953  1.00  1.00
ATOM    747  C   LYS   265      37.070  12.421 -14.589  1.00  1.00
ATOM    748  O   LYS   265      37.457  12.473 -13.413  1.00  1.00
ATOM    749  CB  LYS   265      34.964  11.141 -14.162  1.00  1.00
ATOM    750  N   ASP   266      37.879  12.502 -15.634  1.00  1.00
ATOM    751  CA  ASP   266      39.303  12.626 -15.489  1.00  1.00
ATOM    752  C   ASP   266      39.650  14.004 -14.962  1.00  1.00
ATOM    753  O   ASP   266      39.004  14.988 -15.304  1.00  1.00
ATOM    754  CB  ASP   266      39.931  12.409 -16.833  1.00  1.00
ATOM    755  N   LEU   267      40.710  14.097 -14.167  1.00  1.00
ATOM    756  CA  LEU   267      41.132  15.350 -13.594  1.00  1.00
ATOM    757  C   LEU   267      42.537  15.745 -13.941  1.00  1.00
ATOM    758  O   LEU   267      42.879  16.878 -13.608  1.00  1.00
ATOM    759  CB  LEU   267      41.062  15.328 -12.078  1.00  1.00
ATOM    760  N   SER   268      43.409  14.903 -14.531  1.00  1.00
ATOM    761  CA  SER   268      44.773  15.367 -14.825  1.00  1.00
ATOM    762  C   SER   268      45.097  15.710 -16.251  1.00  1.00
ATOM    763  O   SER   268      45.865  16.636 -16.493  1.00  1.00
ATOM    764  CB  SER   268      45.896  14.389 -14.451  1.00  1.00
ATOM    765  N   LYS   269      44.554  14.938 -17.184  1.00  1.00
ATOM    766  CA  LYS   269      44.801  15.142 -18.584  1.00  1.00
ATOM    767  C   LYS   269      43.787  15.984 -19.288  1.00  1.00
ATOM    768  O   LYS   269      44.135  16.985 -19.900  1.00  1.00
ATOM    769  CB  LYS   269      44.858  13.811 -19.295  1.00  1.00
ATOM    770  N   ASN   270      42.530  15.567 -19.144  1.00  1.00
ATOM    771  CA  ASN   270      41.414  16.217 -19.804  1.00  1.00
ATOM    772  C   ASN   270      40.453  17.260 -19.169  1.00  1.00
ATOM    773  O   ASN   270      39.510  17.660 -19.865  1.00  1.00
ATOM    774  CB  ASN   270      40.611  15.075 -20.381  1.00  1.00
ATOM    775  N   ILE   271      40.537  17.810 -17.942  1.00  1.00
ATOM    776  CA  ILE   271      39.583  18.785 -17.422  1.00  1.00
ATOM    777  C   ILE   271      39.557  20.128 -18.128  1.00  1.00
ATOM    778  O   ILE   271      40.576  20.558 -18.675  1.00  1.00
ATOM    779  CB  ILE   271      39.960  18.877 -15.988  1.00  1.00
ATOM    780  N   LEU   272      38.384  20.767 -18.155  1.00  1.00
ATOM    781  CA  LEU   272      38.290  22.052 -18.807  1.00  1.00
ATOM    782  C   LEU   272      38.456  23.109 -17.740  1.00  1.00
ATOM    783  O   LEU   272      38.009  22.964 -16.620  1.00  1.00
ATOM    784  CB  LEU   272      36.954  22.267 -19.486  1.00  1.00
ATOM    785  N   TYR   273      39.095  24.196 -18.116  1.00  1.00
ATOM    786  CA  TYR   273      39.392  25.282 -17.243  1.00  1.00
ATOM    787  C   TYR   273      38.452  26.469 -17.229  1.00  1.00
ATOM    788  O   TYR   273      38.004  27.009 -18.239  1.00  1.00
ATOM    789  CB  TYR   273      40.816  25.639 -17.628  1.00  1.00
ATOM    790  N   VAL   274      38.246  26.908 -16.008  1.00  1.00
ATOM    791  CA  VAL   274      37.397  28.033 -15.704  1.00  1.00
ATOM    792  C   VAL   274      38.297  29.171 -15.220  1.00  1.00
ATOM    793  O   VAL   274      39.357  28.950 -14.638  1.00  1.00
ATOM    794  CB  VAL   274      36.414  27.590 -14.646  1.00  1.00
ATOM    795  N   PHE   278      37.921  30.419 -15.496  1.00  1.00
ATOM    796  CA  PHE   278      38.683  31.603 -15.131  1.00  1.00
ATOM    797  C   PHE   278      37.963  32.555 -14.170  1.00  1.00
ATOM    798  O   PHE   278      36.799  32.917 -14.366  1.00  1.00
ATOM    799  CB  PHE   278      39.046  32.387 -16.392  1.00  1.00
ATOM    800  N   TYR   279      38.685  33.006 -13.133  1.00  1.00
ATOM    801  CA  TYR   279      38.153  33.926 -12.136  1.00  1.00
ATOM    802  C   TYR   279      37.816  35.272 -12.679  1.00  1.00
ATOM    803  O   TYR   279      38.625  35.920 -13.334  1.00  1.00
ATOM    804  CB  TYR   279      39.133  34.157 -11.022  1.00  1.00
ATOM    805  N   HIS   280      36.612  35.639 -12.302  1.00  1.00
ATOM    806  CA  HIS   280      36.037  36.901 -12.668  1.00  1.00
ATOM    807  C   HIS   280      36.085  37.632 -11.350  1.00  1.00
ATOM    808  O   HIS   280      35.311  37.369 -10.422  1.00  1.00
ATOM    809  CB  HIS   280      34.610  36.722 -13.114  1.00  1.00
ATOM    810  N   ASP   281      36.979  38.612 -11.383  1.00  1.00
ATOM    811  CA  ASP   281      37.282  39.490 -10.274  1.00  1.00
ATOM    812  C   ASP   281      36.160  40.423  -9.886  1.00  1.00
ATOM    813  O   ASP   281      36.019  40.789  -8.717  1.00  1.00
ATOM    814  CB  ASP   281      38.493  40.309 -10.625  1.00  1.00
ATOM    815  N   SER   282      35.374  40.802 -10.897  1.00  1.00
ATOM    816  CA  SER   282      34.259  41.711 -10.711  1.00  1.00
ATOM    817  C   SER   282      33.089  41.087  -9.967  1.00  1.00
ATOM    818  O   SER   282      32.427  41.769  -9.183  1.00  1.00
ATOM    819  CB  SER   282      33.776  42.230 -12.085  1.00  1.00
ATOM    820  N   LEU   283      32.834  39.791 -10.187  1.00  1.00
ATOM    821  CA  LEU   283      31.732  39.130  -9.518  1.00  1.00
ATOM    822  C   LEU   283      32.200  38.023  -8.603  1.00  1.00
ATOM    823  O   LEU   283      31.381  37.292  -8.070  1.00  1.00
ATOM    824  CB  LEU   283      30.753  38.565 -10.546  1.00  1.00
TER
END
