
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0338TS474_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected   33 , name T0338_D2.pdb
# PARAMETERS: T0338TS474_1-D2.T0338_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:    26       144 - 169         4.87     8.56
  LCS_AVERAGE:     21.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       162 - 167         1.94    16.58
  LCS_AVERAGE:      4.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       158 - 161         0.50    25.54
  LCS_AVERAGE:      2.76

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:  113
LCS_GDT     E     144     E     144      3    5   26     3    3    4    4    5    6    9   10   11   15   20   23   24   25   26   27   29   31   31   31 
LCS_GDT     H     145     H     145      3    5   26     3    3    3    4    5    5    7   11   15   18   20   23   24   25   26   27   29   31   31   31 
LCS_GDT     P     146     P     146      3    5   26     3    3    3    4    5    5    7    8   15   17   20   23   24   25   26   27   29   31   31   31 
LCS_GDT     H     147     H     147      3    5   26     3    3    3    4    5    5    7    8   11   11   13   21   23   25   26   26   27   28   28   31 
LCS_GDT     T     148     T     148      3    5   26     3    3    4    4    5    6    7    9   12   17   20   23   24   25   26   27   29   31   31   31 
LCS_GDT     D     149     D     149      3    4   26     3    3    4    4    6    7    8   11   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     V     150     V     150      3    4   26     3    3    4    4    5    7    7    9   14   17   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     V     151     V     151      3    4   26     3    3    3    4    6    7    8   11   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     K     152     K     152      3    5   26     2    3    4    5    6    7   10   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     C     153     C     153      3    5   26     3    3    4    8    8    9   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     T     154     T     154      3    5   26     3    3    4    5    6    6   11   11   14   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     Q     155     Q     155      3    5   26     3    3    5    8    8    9   11   12   14   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     L     156     L     156      3    5   26     3    3    4    5    6    7   10   12   14   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     V     157     V     157      3    5   26     3    3    4    4    6    7   10   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     R     158     R     158      4    5   26     3    4    4    8    8    9   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     A     159     A     159      4    5   26     3    4    4    4    5    8   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     S     160     S     160      4    5   26     3    4    4    6    8    9   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     K     161     K     161      4    5   26     3    4    4    8    8    9   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     D     162     D     162      3    6   26     3    3    5    8    8    9   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     L     163     L     163      3    6   26     0    3    3    5    6    8   10   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     A     164     A     164      3    6   26     3    3    3    4    5    7    9   11   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     Q     165     Q     165      3    6   26     3    3    3    4    6    7    8    9   14   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     T     166     T     166      3    6   26     3    3    3    4    5    7    7    9   10   14   18   23   24   25   26   27   29   31   31   31 
LCS_GDT     S     167     S     167      3    6   26     3    3    5    8    8    9   11   12   15   18   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     Y     168     Y     168      3    5   26     3    3    5    8    8    9   11   12   14   17   20   23   24   26   26   27   29   31   31   31 
LCS_GDT     F     169     F     169      3    5   26     3    3    5    8    8    9   11   12   14   17   20   21   24   26   26   27   29   31   31   31 
LCS_GDT     M     170     M     170      3    5   24     0    3    3    4    6    6    9   11   13   17   20   21   23   26   26   27   29   31   31   31 
LCS_GDT     A     171     A     171      3    4   24     0    3    4    4    5    7    9   11   12   14   17   19   22   26   26   27   29   31   31   31 
LCS_GDT     T     172     T     172      3    4   24     3    3    4    4    5    7    9   11   12   14   17   19   22   26   26   27   29   31   31   31 
LCS_GDT     N     173     N     173      3    4   22     3    3    4    4    5    6    9   10   12   12   17   19   22   26   26   27   29   31   31   31 
LCS_GDT     S     174     S     174      3    4   15     3    3    4    4    5    6    8    9   11   12   17   19   21   26   26   27   28   31   31   31 
LCS_GDT     L     175     L     175      3    4   14     3    3    3    3    4    5    6    8    9   11   13   16   20   21   22   25   27   28   29   31 
LCS_GDT     H     176     H     176      3    4   13     3    3    3    4    5    5    7    7   10   14   17   19   22   26   26   27   29   31   31   31 
LCS_AVERAGE  LCS_A:   9.63  (   2.76    4.34   21.78 )

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      8      8      9     11     12     15     18     20     23     24     26     26     27     29     31     31     31 
GDT PERCENT_CA   2.65   3.54   4.42   7.08   7.08   7.96   9.73  10.62  13.27  15.93  17.70  20.35  21.24  23.01  23.01  23.89  25.66  27.43  27.43  27.43
GDT RMS_LOCAL    0.03   0.50   1.03   1.59   1.59   1.81   2.26   2.65   3.56   3.92   4.11   4.41   4.53   5.23   4.87   5.32   5.63   6.02   6.02   6.02
GDT RMS_ALL_CA  15.02  25.54   9.86   9.92   9.92   9.84   9.91   9.49   8.87   9.07   8.62   8.71   8.87   7.27   8.56   6.82   6.70   6.49   6.49   6.49

#      Molecule1      Molecule2       DISTANCE
LGA    E     144      E     144         16.580
LGA    H     145      H     145         14.613
LGA    P     146      P     146         12.891
LGA    H     147      H     147         14.779
LGA    T     148      T     148         13.537
LGA    D     149      D     149          8.848
LGA    V     150      V     150          5.456
LGA    V     151      V     151          7.734
LGA    K     152      K     152          5.039
LGA    C     153      C     153          1.036
LGA    T     154      T     154          5.262
LGA    Q     155      Q     155          3.050
LGA    L     156      L     156          4.447
LGA    V     157      V     157          3.887
LGA    R     158      R     158          1.570
LGA    A     159      A     159          3.755
LGA    S     160      S     160          2.664
LGA    K     161      K     161          2.136
LGA    D     162      D     162          0.329
LGA    L     163      L     163          3.396
LGA    A     164      A     164          6.809
LGA    Q     165      Q     165          7.233
LGA    T     166      T     166          7.537
LGA    S     167      S     167          1.841
LGA    Y     168      Y     168          3.586
LGA    F     169      F     169          3.435
LGA    M     170      M     170          5.391
LGA    A     171      A     171          9.060
LGA    T     172      T     172         10.834
LGA    N     173      N     173         13.428
LGA    S     174      S     174         15.172
LGA    L     175      L     175         17.983
LGA    H     176      H     176         13.997

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  113    4.0     12    2.65    11.283     9.893     0.437

LGA_LOCAL      RMSD =  2.646  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.052  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  6.469  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.401575 * X  +   0.787668 * Y  +   0.467244 * Z  + -36.454594
  Y_new =  -0.613772 * X  +  -0.610127 * Y  +   0.501028 * Z  +  68.994514
  Z_new =   0.679721 * X  +  -0.085581 * Y  +   0.728460 * Z  +   7.213295 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.116946    3.024647  [ DEG:    -6.7005    173.2995 ]
  Theta =  -0.747383   -2.394210  [ DEG:   -42.8219   -137.1781 ]
  Phi   =  -2.150171    0.991422  [ DEG:  -123.1957     56.8043 ]
 
# 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: T0338TS474_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0338TS474_1-D2.T0338_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  113   4.0   12   2.65   9.893     6.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS474_1-D2
PFRMAT TS
TARGET T0338
MODEL 1
PARENT N/A
ATOM    573  N   GLU   144     -13.692  12.746  63.427  1.00 18.46
ATOM    574  CA  GLU   144     -12.753  12.088  64.321  1.00 21.33
ATOM    575  C   GLU   144     -13.245  10.685  64.753  1.00 17.80
ATOM    576  O   GLU   144     -12.561   9.967  65.467  1.00 24.44
ATOM    577  N   HIS   145     -14.439  10.319  64.311  1.00 19.89
ATOM    578  CA  HIS   145     -15.058   9.027  64.647  1.00 19.35
ATOM    579  C   HIS   145     -15.820   9.191  65.960  1.00 19.59
ATOM    580  O   HIS   145     -16.783   9.949  66.029  1.00 21.97
ATOM    581  N   PRO   146     -15.424   8.462  67.020  1.00 17.87
ATOM    582  CA  PRO   146     -16.149   8.625  68.284  1.00 21.70
ATOM    583  C   PRO   146     -17.615   8.212  68.271  1.00 28.52
ATOM    584  O   PRO   146     -18.356   8.528  69.200  1.00 23.07
ATOM    585  N   HIS   147     -18.043   7.539  67.209  1.00 16.22
ATOM    586  CA  HIS   147     -19.431   7.088  67.129  1.00 28.05
ATOM    587  C   HIS   147     -20.332   7.977  66.274  1.00 28.78
ATOM    588  O   HIS   147     -21.486   7.637  66.038  1.00 24.83
ATOM    589  N   THR   148     -19.839   9.123  65.821  1.00 24.83
ATOM    590  CA  THR   148     -20.667   9.949  64.937  1.00 25.20
ATOM    591  C   THR   148     -21.470  11.082  65.570  1.00 13.90
ATOM    592  O   THR   148     -21.991  11.936  64.857  1.00 21.58
ATOM    593  N   ASP   149     -21.581  11.117  66.890  1.00 18.21
ATOM    594  CA  ASP   149     -22.333  12.213  67.499  1.00 22.90
ATOM    595  C   ASP   149     -23.750  12.377  66.991  1.00 31.52
ATOM    596  O   ASP   149     -24.407  11.397  66.625  1.00 22.10
ATOM    597  N   VAL   150     -24.224  13.625  66.975  1.00 21.29
ATOM    598  CA  VAL   150     -25.616  13.881  66.626  1.00 27.37
ATOM    599  C   VAL   150     -26.266  13.505  67.957  1.00 33.30
ATOM    600  O   VAL   150     -25.807  13.958  69.014  1.00 21.95
ATOM    601  N   VAL   151     -27.304  12.673  67.913  1.00 23.79
ATOM    602  CA  VAL   151     -27.951  12.189  69.133  1.00 23.83
ATOM    603  C   VAL   151     -29.211  12.947  69.495  1.00 26.09
ATOM    604  O   VAL   151     -30.101  13.131  68.669  1.00 22.49
ATOM    605  N   LYS   152     -29.277  13.355  70.751  1.00 16.95
ATOM    606  CA  LYS   152     -30.411  14.107  71.284  1.00 22.70
ATOM    607  C   LYS   152     -31.639  13.182  71.303  1.00 33.28
ATOM    608  O   LYS   152     -31.495  11.997  71.577  1.00 21.52
ATOM    609  N   CYS   153     -32.835  13.690  71.009  1.00 26.58
ATOM    610  CA  CYS   153     -34.005  12.813  71.041  1.00 27.49
ATOM    611  C   CYS   153     -34.393  12.481  72.476  1.00 29.15
ATOM    612  O   CYS   153     -33.944  13.127  73.439  1.00 19.41
ATOM    613  N   THR   154     -35.243  11.473  72.611  1.00 24.42
ATOM    614  CA  THR   154     -35.670  11.004  73.917  1.00 28.20
ATOM    615  C   THR   154     -36.330  12.090  74.730  1.00 31.58
ATOM    616  O   THR   154     -35.966  12.293  75.886  1.00 33.89
ATOM    617  N   GLN   155     -37.283  12.815  74.136  1.00 25.98
ATOM    618  CA  GLN   155     -37.986  13.845  74.897  1.00 29.83
ATOM    619  C   GLN   155     -37.148  15.042  75.311  1.00 37.45
ATOM    620  O   GLN   155     -37.388  15.626  76.371  1.00 28.36
ATOM    621  N   LEU   156     -36.180  15.444  74.490  1.00 31.09
ATOM    622  CA  LEU   156     -35.368  16.583  74.911  1.00 36.98
ATOM    623  C   LEU   156     -34.352  16.108  75.942  1.00 22.35
ATOM    624  O   LEU   156     -33.946  16.870  76.818  1.00 43.54
ATOM    625  N   VAL   157     -33.963  14.843  75.851  1.00 33.48
ATOM    626  CA  VAL   157     -33.015  14.288  76.808  1.00 40.32
ATOM    627  C   VAL   157     -33.612  14.341  78.217  1.00 51.27
ATOM    628  O   VAL   157     -33.071  14.995  79.112  1.00 48.17
ATOM    629  N   ARG   158     -34.750  13.684  78.409  1.00 54.74
ATOM    630  CA  ARG   158     -35.361  13.650  79.736  1.00 63.54
ATOM    631  C   ARG   158     -35.884  15.004  80.220  1.00 57.11
ATOM    632  O   ARG   158     -36.037  15.224  81.417  1.00 65.77
ATOM    633  N   ALA   159     -36.144  15.912  79.293  1.00 52.52
ATOM    634  CA  ALA   159     -36.623  17.244  79.642  1.00 52.55
ATOM    635  C   ALA   159     -35.446  18.209  79.910  1.00 63.71
ATOM    636  O   ALA   159     -35.650  19.366  80.288  1.00 62.49
ATOM    637  N   SER   160     -34.217  17.716  79.740  1.00 60.38
ATOM    638  CA  SER   160     -33.012  18.533  79.925  1.00 58.15
ATOM    639  C   SER   160     -32.637  18.862  81.366  1.00 63.82
ATOM    640  O   SER   160     -32.587  17.972  82.220  1.00 63.98
ATOM    641  N   LYS   161     -32.344  20.139  81.620  1.00 59.23
ATOM    642  CA  LYS   161     -31.948  20.592  82.953  1.00 68.12
ATOM    643  C   LYS   161     -30.503  21.090  83.019  1.00 67.33
ATOM    644  O   LYS   161     -30.110  21.757  83.974  1.00 68.15
ATOM    645  N   ASP   162     -29.721  20.765  81.994  1.00 63.69
ATOM    646  CA  ASP   162     -28.311  21.137  81.931  1.00 60.16
ATOM    647  C   ASP   162     -27.525  19.839  81.884  1.00 48.51
ATOM    648  O   ASP   162     -27.814  18.963  81.071  1.00 51.04
ATOM    649  N   LEU   163     -26.540  19.706  82.758  1.00 41.95
ATOM    650  CA  LEU   163     -25.736  18.494  82.784  1.00 47.13
ATOM    651  C   LEU   163     -24.578  18.611  81.790  1.00 41.22
ATOM    652  O   LEU   163     -23.978  19.674  81.671  1.00 40.78
ATOM    653  N   ALA   164     -24.279  17.540  81.029  1.00 42.34
ATOM    654  CA  ALA   164     -24.926  16.216  80.995  1.00 50.26
ATOM    655  C   ALA   164     -26.249  16.323  80.229  1.00 43.69
ATOM    656  O   ALA   164     -26.318  16.971  79.190  1.00 40.71
ATOM    657  N   GLN   165     -27.292  15.690  80.746  1.00 38.17
ATOM    658  CA  GLN   165     -28.615  15.785  80.145  1.00 43.31
ATOM    659  C   GLN   165     -28.774  15.239  78.739  1.00 37.38
ATOM    660  O   GLN   165     -29.644  15.695  77.987  1.00 34.10
ATOM    661  N   THR   166     -27.940  14.281  78.366  1.00 29.93
ATOM    662  CA  THR   166     -28.071  13.707  77.034  1.00 42.34
ATOM    663  C   THR   166     -27.206  14.371  75.960  1.00 37.65
ATOM    664  O   THR   166     -27.195  13.908  74.817  1.00 35.86
ATOM    665  N   SER   167     -26.477  15.443  76.300  1.00 28.64
ATOM    666  CA  SER   167     -25.654  16.087  75.270  1.00 22.87
ATOM    667  C   SER   167     -26.561  16.908  74.352  1.00 26.06
ATOM    668  O   SER   167     -27.468  17.604  74.812  1.00 28.24
ATOM    669  N   TYR   168     -26.322  16.814  73.053  1.00 22.71
ATOM    670  CA  TYR   168     -27.121  17.552  72.087  1.00 21.55
ATOM    671  C   TYR   168     -26.869  19.069  72.230  1.00 27.43
ATOM    672  O   TYR   168     -27.773  19.899  72.026  1.00 20.64
ATOM    673  N   PHE   169     -25.646  19.420  72.617  1.00 20.92
ATOM    674  CA  PHE   169     -25.256  20.823  72.728  1.00 25.94
ATOM    675  C   PHE   169     -24.495  21.156  74.002  1.00 26.09
ATOM    676  O   PHE   169     -23.949  20.276  74.655  1.00 25.42
ATOM    677  N   MET   170     -24.443  22.442  74.329  1.00 24.47
ATOM    678  CA  MET   170     -23.730  22.916  75.512  1.00 24.94
ATOM    679  C   MET   170     -22.924  24.179  75.189  1.00 34.26
ATOM    680  O   MET   170     -23.159  24.853  74.178  1.00 23.39
ATOM    681  N   ALA   171     -21.977  24.486  76.065  1.00 28.05
ATOM    682  CA  ALA   171     -21.102  25.636  75.913  1.00 23.66
ATOM    683  C   ALA   171     -21.379  26.609  77.060  1.00 28.52
ATOM    684  O   ALA   171     -21.350  26.229  78.233  1.00 30.83
ATOM    685  N   THR   172     -21.654  27.865  76.721  1.00 29.99
ATOM    686  CA  THR   172     -21.947  28.881  77.727  1.00 30.02
ATOM    687  C   THR   172     -21.119  30.138  77.465  1.00 28.26
ATOM    688  O   THR   172     -20.635  30.372  76.342  1.00 24.19
ATOM    689  N   ASN   173     -20.983  30.952  78.504  1.00 27.90
ATOM    690  CA  ASN   173     -20.219  32.191  78.429  1.00 19.60
ATOM    691  C   ASN   173     -18.867  31.931  77.797  1.00 24.98
ATOM    692  O   ASN   173     -18.411  32.690  76.948  1.00 24.74
ATOM    693  N   SER   174     -18.223  30.854  78.229  1.00 22.22
ATOM    694  CA  SER   174     -16.920  30.506  77.694  1.00 17.93
ATOM    695  C   SER   174     -15.870  31.289  78.431  1.00 32.80
ATOM    696  O   SER   174     -15.829  31.275  79.682  1.00 22.03
ATOM    697  N   LEU   175     -15.019  31.966  77.668  1.00 19.16
ATOM    698  CA  LEU   175     -13.946  32.743  78.264  1.00 35.16
ATOM    699  C   LEU   175     -12.931  31.749  78.848  1.00 32.16
ATOM    700  O   LEU   175     -12.260  32.045  79.823  1.00 26.88
ATOM    701  N   HIS   176     -12.843  30.562  78.250  1.00 29.22
ATOM    702  CA  HIS   176     -11.921  29.532  78.710  1.00 31.28
ATOM    703  C   HIS   176     -12.541  28.493  79.625  1.00 29.96
ATOM    704  O   HIS   176     -13.734  28.179  79.523  1.00 24.52
TER
END
