
#######################################################
#                                                     #
#                        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 T0347AL381_3
# Molecule2: number of CA atoms  196 ( 1574),  selected   33 , name T0347.pdb
# PARAMETERS: T0347AL381_3.T0347.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:    25       173 - 197         4.83     8.70
  LONGEST_CONTINUOUS_SEGMENT:    25       174 - 198         4.86     8.51
  LONGEST_CONTINUOUS_SEGMENT:    25       175 - 199         4.99     8.32
  LONGEST_CONTINUOUS_SEGMENT:    25       176 - 200         4.98     8.54
  LONGEST_CONTINUOUS_SEGMENT:    25       177 - 201         4.99     8.82
  LCS_AVERAGE:     12.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       176 - 192         1.82    10.21
  LONGEST_CONTINUOUS_SEGMENT:    17       177 - 193         1.92    10.61
  LCS_AVERAGE:      6.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16       177 - 192         0.91    10.41
  LCS_AVERAGE:      5.63

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:  196
LCS_GDT     D     170     D     170      3    3   18     0    2    4    4    4    4    7    8    9   10   12   14   14   16   16   18   20   21   22   23 
LCS_GDT     R     171     R     171      3    3   22     3    3    4    4    4    4    7    8    9   12   15   17   20   21   25   25   27   28   29   29 
LCS_GDT     D     172     D     172      6    7   24     6    6    6    6    7    7    8    8   12   14   16   20   21   22   25   25   27   28   29   30 
LCS_GDT     L     173     L     173      6    7   25     6    6    6    6    7    7    9   11   11   14   16   20   20   22   25   25   27   28   29   30 
LCS_GDT     L     174     L     174      6    7   25     6    6    6    6    7    7    9   11   13   15   19   20   20   22   25   25   27   28   29   30 
LCS_GDT     S     175     S     175      6    7   25     6    6    6    6    7   10   13   16   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     D     176     D     176      6   17   25     6    6    6    6    7   11   15   17   18   19   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     S     177     S     177     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     F     178     F     178     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     D     179     D     179     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     D     180     D     180     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     A     181     A     181     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     L     182     L     182     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     A     183     A     183     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     E     184     E     184     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     A     185     A     185     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     M     186     M     186     16   17   25    12   15   15   15   16   16   17   17   18   19   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     K     187     K     187     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     L     188     L     188     16   17   25    12   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     A     189     A     189     16   17   25     6   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     K     190     K     190     16   17   25     6   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     S     191     S     191     16   17   25     6   15   15   15   16   16   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     R     192     R     192     16   17   25     4    5    7   12   16   16   16   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     E     193     E     193      5   17   25     4    5    7   11   11   11   11   12   15   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     A     194     A     194      8   11   25     6    7    7   11   11   11   11   12   17   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     R     195     R     195      8   11   25     6    7    7   11   11   14   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     H     196     H     196      8   11   25     6    7    7   11   11   14   17   17   18   20   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     L     197     L     197      8   11   25     6    7    7   11   11   11   11   13   15   18   21   23   24   25   26   26   27   28   29   30 
LCS_GDT     P     198     P     198      8   11   25     6    7    7   11   11   11   11   12   13   15   17   19   22   23   26   26   26   27   28   30 
LCS_GDT     G     199     G     199      8   11   25     6    7    7   11   11   11   11   12   12   13   14   18   19   20   22   25   26   27   28   30 
LCS_GDT     W     200     W     200      8   11   25     5    7    7   11   11   11   11   12   12   16   19   23   24   25   26   26   27   28   29   30 
LCS_GDT     C     201     C     201      8   11   25     3    3    6   11   11   11   11   12   12   13   18   20   23   25   26   26   27   28   29   30 
LCS_GDT     G     202     G     202      3    3   20     0    3    3    3    3    3    4    9    9    9   12   12   12   12   12   14   16   17   28   29 
LCS_AVERAGE  LCS_A:   8.27  (   5.63    6.66   12.51 )

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     12     15     15     15     16     16     17     17     18     20     21     23     24     25     26     26     27     28     29     30 
GDT PERCENT_CA   6.12   7.65   7.65   7.65   8.16   8.16   8.67   8.67   9.18  10.20  10.71  11.73  12.24  12.76  13.27  13.27  13.78  14.29  14.80  15.31
GDT RMS_LOCAL    0.30   0.58   0.58   0.58   0.91   0.91   1.99   1.99   2.21   3.46   3.47   4.07   4.37   4.63   4.86   4.86   5.71   5.64   6.02   6.05
GDT RMS_ALL_CA  10.48  10.24  10.24  10.24  10.41  10.41   9.98   9.98  10.04   9.40   9.52   8.89   8.49   8.16   8.19   8.19   7.59   7.51   7.30   7.49

#      Molecule1      Molecule2       DISTANCE
LGA    D     170      D     170         27.466
LGA    R     171      R     171         23.368
LGA    D     172      D     172         19.021
LGA    L     173      L     173         13.744
LGA    L     174      L     174         11.505
LGA    S     175      S     175         11.020
LGA    D     176      D     176         10.070
LGA    S     177      S     177          3.457
LGA    F     178      F     178          2.273
LGA    D     179      D     179          1.223
LGA    D     180      D     180          1.924
LGA    A     181      A     181          1.810
LGA    L     182      L     182          1.006
LGA    A     183      A     183          1.024
LGA    E     184      E     184          0.410
LGA    A     185      A     185          1.916
LGA    M     186      M     186          2.421
LGA    K     187      K     187          1.457
LGA    L     188      L     188          1.576
LGA    A     189      A     189          2.527
LGA    K     190      K     190          2.189
LGA    S     191      S     191          1.372
LGA    R     192      R     192          4.653
LGA    E     193      E     193          5.779
LGA    A     194      A     194          5.653
LGA    R     195      R     195          3.851
LGA    H     196      H     196          3.834
LGA    L     197      L     197          9.470
LGA    P     198      P     198         13.317
LGA    G     199      G     199         16.873
LGA    W     200      W     200         12.461
LGA    C     201      C     201         14.793
LGA    G     202      G     202         15.055

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  196    4.0     17    1.99     9.311     8.699     0.811

LGA_LOCAL      RMSD =  1.995  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.343  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  7.211  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.443072 * X  +  -0.879483 * Y  +   0.173770 * Z  +   5.618942
  Y_new =   0.819984 * X  +   0.319225 * Y  +  -0.475102 * Z  +  66.135468
  Z_new =   0.362372 * X  +   0.352993 * Y  +   0.862602 * Z  + -98.236031 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.388428   -2.753165  [ DEG:    22.2553   -157.7447 ]
  Theta =  -0.370812   -2.770781  [ DEG:   -21.2460   -158.7540 ]
  Phi   =   1.075398   -2.066195  [ DEG:    61.6158   -118.3842 ]
 
# 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: T0347AL381_3                                  
REMARK     2: T0347.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_3.T0347.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  196   4.0   17   1.99   8.699     7.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_3
REMARK Aligment from pdb entry: 1fcyA
ATOM      1  N   ASP   170      22.067  72.035 -21.013  1.00  0.00              
ATOM      2  CA  ASP   170      22.869  72.591 -19.948  1.00  0.00              
ATOM      3  C   ASP   170      22.359  72.163 -18.566  1.00  0.00              
ATOM      4  O   ASP   170      23.156  71.713 -17.741  1.00  0.00              
ATOM      5  N   ARG   171      21.059  72.294 -18.352  1.00  0.00              
ATOM      6  CA  ARG   171      20.423  71.926 -17.091  1.00  0.00              
ATOM      7  C   ARG   171      18.909  71.827 -17.290  1.00  0.00              
ATOM      8  O   ARG   171      18.308  72.731 -17.836  1.00  0.00              
ATOM      9  N   ASP   172      18.308  70.743 -16.840  1.00  0.00              
ATOM     10  CA  ASP   172      16.847  70.619 -16.801  1.00  0.00              
ATOM     11  C   ASP   172      16.435  70.877 -15.362  1.00  0.00              
ATOM     12  O   ASP   172      16.768  70.150 -14.419  1.00  0.00              
ATOM     13  N   LEU   173      15.728  71.966 -15.147  1.00  0.00              
ATOM     14  CA  LEU   173      15.442  72.393 -13.785  1.00  0.00              
ATOM     15  C   LEU   173      14.524  71.429 -13.047  1.00  0.00              
ATOM     16  O   LEU   173      14.681  71.331 -11.817  1.00  0.00              
ATOM     17  N   LEU   174      13.634  70.747 -13.751  1.00  0.00              
ATOM     18  CA  LEU   174      12.788  69.760 -13.051  1.00  0.00              
ATOM     19  C   LEU   174      13.678  68.602 -12.565  1.00  0.00              
ATOM     20  O   LEU   174      13.460  68.136 -11.440  1.00  0.00              
ATOM     21  N   SER   175      14.636  68.137 -13.380  1.00  0.00              
ATOM     22  CA  SER   175      15.521  67.090 -12.891  1.00  0.00              
ATOM     23  C   SER   175      16.433  67.643 -11.795  1.00  0.00              
ATOM     24  O   SER   175      16.668  66.916 -10.808  1.00  0.00              
ATOM     25  N   ASP   176      16.935  68.846 -11.906  1.00  0.00              
ATOM     26  CA  ASP   176      17.750  69.417 -10.825  1.00  0.00              
ATOM     27  C   ASP   176      16.969  69.463  -9.526  1.00  0.00              
ATOM     28  O   ASP   176      17.479  69.116  -8.486  1.00  0.00              
ATOM     29  N   SER   177      15.724  69.903  -9.559  1.00  0.00              
ATOM     30  CA  SER   177      14.958  69.991  -8.311  1.00  0.00              
ATOM     31  C   SER   177      14.821  68.630  -7.687  1.00  0.00              
ATOM     32  O   SER   177      15.017  68.474  -6.487  1.00  0.00              
ATOM     33  N   PHE   178      14.506  67.597  -8.447  1.00  0.00              
ATOM     34  CA  PHE   178      14.415  66.273  -7.837  1.00  0.00              
ATOM     35  C   PHE   178      15.762  65.737  -7.372  1.00  0.00              
ATOM     36  O   PHE   178      15.843  65.156  -6.285  1.00  0.00              
ATOM     37  N   ASP   179      16.803  65.924  -8.184  1.00  0.00              
ATOM     38  CA  ASP   179      18.167  65.444  -7.851  1.00  0.00              
ATOM     39  C   ASP   179      18.638  66.045  -6.545  1.00  0.00              
ATOM     40  O   ASP   179      19.176  65.407  -5.655  1.00  0.00              
ATOM     41  N   ASP   180      18.433  67.366  -6.448  1.00  0.00              
ATOM     42  CA  ASP   180      18.936  68.078  -5.283  1.00  0.00              
ATOM     43  C   ASP   180      18.142  67.719  -4.050  1.00  0.00              
ATOM     44  O   ASP   180      18.726  67.646  -2.961  1.00  0.00              
ATOM     45  N   ALA   181      16.838  67.488  -4.156  1.00  0.00              
ATOM     46  CA  ALA   181      16.053  66.981  -3.055  1.00  0.00              
ATOM     47  C   ALA   181      16.531  65.609  -2.580  1.00  0.00              
ATOM     48  O   ALA   181      16.671  65.350  -1.368  1.00  0.00              
ATOM     49  N   LEU   182      16.787  64.737  -3.530  1.00  0.00              
ATOM     50  CA  LEU   182      17.301  63.413  -3.197  1.00  0.00              
ATOM     51  C   LEU   182      18.689  63.508  -2.570  1.00  0.00              
ATOM     52  O   LEU   182      19.004  62.754  -1.626  1.00  0.00              
ATOM     53  N   ALA   183      19.544  64.412  -3.035  1.00  0.00              
ATOM     54  CA  ALA   183      20.855  64.616  -2.406  1.00  0.00              
ATOM     55  C   ALA   183      20.701  65.054  -0.956  1.00  0.00              
ATOM     56  O   ALA   183      21.400  64.527  -0.091  1.00  0.00              
ATOM     57  N   GLU   184      19.852  66.042  -0.653  1.00  0.00              
ATOM     58  CA  GLU   184      19.611  66.416   0.738  1.00  0.00              
ATOM     59  C   GLU   184      19.237  65.226   1.592  1.00  0.00              
ATOM     60  O   GLU   184      19.737  65.009   2.702  1.00  0.00              
ATOM     61  N   ALA   185      18.277  64.432   1.129  1.00  0.00              
ATOM     62  CA  ALA   185      17.845  63.285   1.908  1.00  0.00              
ATOM     63  C   ALA   185      19.001  62.315   2.164  1.00  0.00              
ATOM     64  O   ALA   185      19.119  61.793   3.265  1.00  0.00              
ATOM     65  N   MET   186      19.804  62.110   1.106  1.00  0.00              
ATOM     66  CA  MET   186      20.973  61.205   1.321  1.00  0.00              
ATOM     67  C   MET   186      22.034  61.757   2.241  1.00  0.00              
ATOM     68  O   MET   186      22.632  61.034   2.991  1.00  0.00              
ATOM     69  N   LYS   187      22.214  63.109   2.234  1.00  0.00              
ATOM     70  CA  LYS   187      23.131  63.706   3.210  1.00  0.00              
ATOM     71  C   LYS   187      22.659  63.366   4.640  1.00  0.00              
ATOM     72  O   LYS   187      23.493  62.997   5.465  1.00  0.00              
ATOM     73  N   LEU   188      21.385  63.497   4.918  1.00  0.00              
ATOM     74  CA  LEU   188      20.871  63.157   6.243  1.00  0.00              
ATOM     75  C   LEU   188      21.096  61.692   6.513  1.00  0.00              
ATOM     76  O   LEU   188      21.496  61.348   7.620  1.00  0.00              
ATOM     77  N   ALA   189      20.934  60.784   5.578  1.00  0.00              
ATOM     78  CA  ALA   189      21.197  59.377   5.770  1.00  0.00              
ATOM     79  C   ALA   189      22.684  59.149   6.018  1.00  0.00              
ATOM     80  O   ALA   189      23.005  58.254   6.832  1.00  0.00              
ATOM     81  N   LYS   190      23.593  59.868   5.380  1.00  0.00              
ATOM     82  CA  LYS   190      25.011  59.702   5.627  1.00  0.00              
ATOM     83  C   LYS   190      25.361  60.160   7.037  1.00  0.00              
ATOM     84  O   LYS   190      26.183  59.524   7.725  1.00  0.00              
ATOM     85  N   SER   191      24.784  61.236   7.527  1.00  0.00              
ATOM     86  CA  SER   191      24.947  61.645   8.904  1.00  0.00              
ATOM     87  C   SER   191      24.464  60.552   9.862  1.00  0.00              
ATOM     88  O   SER   191      25.158  60.221  10.824  1.00  0.00              
ATOM     89  N   ARG   192      23.297  59.965   9.564  1.00  0.00              
ATOM     90  CA  ARG   192      22.747  58.879  10.396  1.00  0.00              
ATOM     91  C   ARG   192      23.680  57.680  10.409  1.00  0.00              
ATOM     92  O   ARG   192      23.921  57.056  11.453  1.00  0.00              
ATOM     93  N   GLU   193      24.193  57.339   9.223  1.00  0.00              
ATOM     94  CA  GLU   193      25.182  56.270   9.108  1.00  0.00              
ATOM     95  C   GLU   193      26.409  56.564   9.982  1.00  0.00              
ATOM     96  O   GLU   193      26.856  55.713  10.748  1.00  0.00              
ATOM     97  N   ALA   194      26.916  57.789   9.822  1.00  0.00              
ATOM     98  CA  ALA   194      28.127  58.177  10.575  1.00  0.00              
ATOM     99  C   ALA   194      27.925  57.996  12.072  1.00  0.00              
ATOM    100  O   ALA   194      28.810  57.466  12.773  1.00  0.00              
ATOM    101  N   ARG   195      26.764  58.417  12.556  1.00  0.00              
ATOM    102  CA  ARG   195      26.551  58.351  14.033  1.00  0.00              
ATOM    103  C   ARG   195      26.392  56.942  14.547  1.00  0.00              
ATOM    104  O   ARG   195      26.483  56.734  15.745  1.00  0.00              
ATOM    105  N   HIS   196      26.191  55.969  13.674  1.00  0.00              
ATOM    106  CA  HIS   196      26.175  54.565  14.039  1.00  0.00              
ATOM    107  C   HIS   196      27.533  53.900  13.987  1.00  0.00              
ATOM    108  O   HIS   196      27.669  52.725  14.341  1.00  0.00              
ATOM    109  N   LEU   197      28.562  54.614  13.503  1.00  0.00              
ATOM    110  CA  LEU   197      29.891  54.035  13.458  1.00  0.00              
ATOM    111  C   LEU   197      30.521  54.080  14.836  1.00  0.00              
ATOM    112  O   LEU   197      30.562  55.147  15.434  1.00  0.00              
ATOM    113  N   PRO   198      31.006  52.958  15.333  1.00  0.00              
ATOM    114  CA  PRO   198      31.560  52.970  16.670  1.00  0.00              
ATOM    115  C   PRO   198      32.627  54.067  16.871  1.00  0.00              
ATOM    116  O   PRO   198      33.514  54.275  16.064  1.00  0.00              
ATOM    117  N   GLY   199      32.362  54.837  17.941  1.00  0.00              
ATOM    118  CA  GLY   199      33.222  55.896  18.368  1.00  0.00              
ATOM    119  C   GLY   199      32.992  57.242  17.732  1.00  0.00              
ATOM    120  O   GLY   199      33.491  58.257  18.213  1.00  0.00              
ATOM    121  N   TRP   200      32.213  57.335  16.651  1.00  0.00              
ATOM    122  CA  TRP   200      32.085  58.594  15.947  1.00  0.00              
ATOM    123  C   TRP   200      31.502  59.681  16.841  1.00  0.00              
ATOM    124  O   TRP   200      31.954  60.826  16.863  1.00  0.00              
ATOM    125  N   CYS   201      30.461  59.316  17.634  1.00  0.00              
ATOM    126  CA  CYS   201      29.834  60.307  18.525  1.00  0.00              
ATOM    127  C   CYS   201      30.667  60.626  19.750  1.00  0.00              
ATOM    128  O   CYS   201      30.352  61.557  20.497  1.00  0.00              
ATOM    129  N   GLY   202      31.756  59.901  19.976  1.00  0.00              
ATOM    130  CA  GLY   202      32.715  60.289  20.990  1.00  0.00              
ATOM    131  C   GLY   202      33.749  61.293  20.512  1.00  0.00              
ATOM    132  O   GLY   202      34.510  61.818  21.348  1.00  0.00              
END
