
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0363TS383_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   27 , name T0363_D1.pdb
# PARAMETERS: T0363TS383_4-D1.T0363_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:    27        27 - 56          4.20     4.20
  LCS_AVERAGE:     58.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        36 - 54          1.99     5.54
  LONGEST_CONTINUOUS_SEGMENT:    17        37 - 55          1.98     5.63
  LCS_AVERAGE:     30.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        36 - 44          0.35     5.32
  LONGEST_CONTINUOUS_SEGMENT:     9        47 - 55          0.99     7.77
  LCS_AVERAGE:     16.02

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:   46
LCS_GDT     L      27     L      27      3    7   27     0    3    3    3    8   12   17   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     K      28     K      28      5    7   27     5    5    6    7    8   12   14   15   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     S      29     S      29      5    7   27     5    5    6   11   13   13   15   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     F      30     F      30      5    7   27     5    5    6   11   13   13   14   16   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     Q      31     Q      31      5    7   27     5    5    8   11   13   13   14   15   19   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     V      32     V      32      5    7   27     5    5    6   10   13   13   14   15   18   20   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     E      34     E      34      3    7   27     0    3    4    7    8    9   12   15   16   16   17   19   20   24   26   27   27   27   27   27 
LCS_GDT     G      35     G      35      3   10   27     3    3    5    7    8    9   12   15   16   19   21   23   25   26   26   27   27   27   27   27 
LCS_GDT     I      36     I      36      9   17   27     8    9    9   11   14   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     T      37     T      37      9   17   27     8    9    9   11   14   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     V      38     V      38      9   17   27     8    9    9   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     Q      39     Q      39      9   17   27     8    9    9   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     T      40     T      40      9   17   27     8    9    9   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     A      41     A      41      9   17   27     8    9    9   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     I      42     I      42      9   17   27     8    9   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     T      43     T      43      9   17   27     8    9   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     Q      44     Q      44      9   17   27     8    9    9   11   13   15   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     I      47     I      47      9   17   27     7    8   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     L      48     L      48      9   17   27     5    8   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     S      49     S      49      9   17   27     7    8   10   11   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     Q      50     Q      50      9   17   27     7    8   10   11   15   17   18   19   20   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     F      51     F      51      9   17   27     7    8   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     P      52     P      52      9   17   27     7    8   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     E      53     E      53      9   17   27     7    8   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     I      54     I      54      9   17   27     7    8   10   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     D      55     D      55      9   17   27     3    3    5   12   15   17   18   19   21   22   23   24   25   26   26   27   27   27   27   27 
LCS_GDT     L      56     L      56      3   10   27     3    5    6    7    8   10   12   13   16   17   21   23   25   26   26   27   27   27   27   27 
LCS_AVERAGE  LCS_A:  34.97  (  16.02   30.19   58.70 )

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      8      9     10     12     15     17     18     19     21     22     23     24     25     26     26     27     27     27     27     27 
GDT PERCENT_CA  17.39  19.57  21.74  26.09  32.61  36.96  39.13  41.30  45.65  47.83  50.00  52.17  54.35  56.52  56.52  58.70  58.70  58.70  58.70  58.70
GDT RMS_LOCAL    0.23   0.35   0.92   1.44   1.70   1.88   2.04   2.65   3.03   3.11   3.27   3.48   3.65   3.88   3.88   4.20   4.20   4.20   4.20   4.20
GDT RMS_ALL_CA   5.18   5.32   7.20   5.60   5.95   5.63   5.47   4.59   4.42   4.51   4.42   4.33   4.31   4.23   4.23   4.20   4.20   4.20   4.20   4.20

#      Molecule1      Molecule2       DISTANCE
LGA    L      27      L      27          3.643
LGA    K      28      K      28          5.118
LGA    S      29      S      29          4.433
LGA    F      30      F      30          5.917
LGA    Q      31      Q      31          6.628
LGA    V      32      V      32          7.873
LGA    E      34      E      34         11.831
LGA    G      35      G      35          9.454
LGA    I      36      I      36          3.952
LGA    T      37      T      37          3.376
LGA    V      38      V      38          2.736
LGA    Q      39      Q      39          1.948
LGA    T      40      T      40          1.633
LGA    A      41      A      41          1.500
LGA    I      42      I      42          1.605
LGA    T      43      T      43          1.859
LGA    Q      44      Q      44          2.927
LGA    I      47      I      47          3.252
LGA    L      48      L      48          1.710
LGA    S      49      S      49          3.282
LGA    Q      50      Q      50          3.950
LGA    F      51      F      51          2.828
LGA    P      52      P      52          2.082
LGA    E      53      E      53          3.086
LGA    I      54      I      54          2.610
LGA    D      55      D      55          2.540
LGA    L      56      L      56          6.091

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   46    4.0     19    2.40    36.413    36.438     0.759

LGA_LOCAL      RMSD =  2.405  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.711  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  4.197  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.713886 * X  +   0.699309 * Y  +  -0.036521 * Z  +  16.979582
  Y_new =  -0.525635 * X  +   0.569591 * Y  +   0.631881 * Z  +  -0.242809
  Z_new =   0.462682 * X  +  -0.431894 * Y  +   0.774204 * Z  +  19.604839 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.508854    2.632738  [ DEG:   -29.1552    150.8448 ]
  Theta =  -0.481018   -2.660574  [ DEG:   -27.5603   -152.4397 ]
  Phi   =  -0.634676    2.506917  [ DEG:   -36.3643    143.6357 ]
 
# 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: T0363TS383_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS383_4-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   46   4.0   19   2.40  36.438     4.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS383_4-D1
PFRMAT TS
TARGET T0363
MODEL 4
PARENT 1v8cA
ATOM      1  N   LEU    27      27.392  19.999  -3.947  1.00  0.00
ATOM      2  CA  LEU    27      26.448  18.932  -3.644  1.00  0.00
ATOM      3  C   LEU    27      25.453  19.298  -2.553  1.00  0.00
ATOM      4  O   LEU    27      25.808  19.960  -1.585  1.00  0.00
ATOM      5  N   LYS    28      24.206  18.863  -2.718  1.00  0.00
ATOM      6  CA  LYS    28      23.167  19.117  -1.725  1.00  0.00
ATOM      7  C   LYS    28      22.938  17.859  -0.890  1.00  0.00
ATOM      8  O   LYS    28      22.638  17.945   0.299  1.00  0.00
ATOM      9  N   SER    29      23.054  16.690  -1.515  1.00  0.00
ATOM     10  CA  SER    29      22.867  15.444  -0.779  1.00  0.00
ATOM     11  C   SER    29      23.824  14.362  -1.243  1.00  0.00
ATOM     12  O   SER    29      24.162  14.272  -2.425  1.00  0.00
ATOM     13  N   PHE    30      24.263  13.545  -0.293  1.00  0.00
ATOM     14  CA  PHE    30      25.188  12.460  -0.571  1.00  0.00
ATOM     15  C   PHE    30      24.777  11.240   0.235  1.00  0.00
ATOM     16  O   PHE    30      24.141  11.367   1.276  1.00  0.00
ATOM     17  N   GLN    31      25.120  10.064  -0.272  1.00  0.00
ATOM     18  CA  GLN    31      24.847   8.812   0.418  1.00  0.00
ATOM     19  C   GLN    31      26.233   8.306   0.816  1.00  0.00
ATOM     20  O   GLN    31      27.089   8.087  -0.046  1.00  0.00
ATOM     21  N   VAL    32      26.458   8.134   2.117  1.00  0.00
ATOM     22  CA  VAL    32      27.756   7.680   2.616  1.00  0.00
ATOM     23  C   VAL    32      27.580   6.587   3.650  1.00  0.00
ATOM     24  O   VAL    32      26.635   6.619   4.432  1.00  0.00
ATOM     25  N   GLU    34      28.493   5.604   3.672  1.00  0.00
ATOM     26  CA  GLU    34      28.385   4.513   4.645  1.00  0.00
ATOM     27  C   GLU    34      28.789   4.929   6.059  1.00  0.00
ATOM     28  O   GLU    34      29.470   5.939   6.257  1.00  0.00
ATOM     29  N   GLY    35      28.346   4.153   7.042  1.00  0.00
ATOM     30  CA  GLY    35      28.689   4.446   8.424  1.00  0.00
ATOM     31  C   GLY    35      27.579   4.050   9.372  1.00  0.00
ATOM     32  O   GLY    35      26.407   4.291   9.079  1.00  0.00
ATOM     33  N   ILE    36      27.957   3.451  10.503  1.00  0.00
ATOM     34  CA  ILE    36      27.008   2.994  11.514  1.00  0.00
ATOM     35  C   ILE    36      26.849   3.970  12.682  1.00  0.00
ATOM     36  O   ILE    36      26.042   3.735  13.585  1.00  0.00
ATOM     37  N   THR    37      27.636   5.045  12.670  1.00  0.00
ATOM     38  CA  THR    37      27.541   6.094  13.690  1.00  0.00
ATOM     39  C   THR    37      27.716   7.418  12.970  1.00  0.00
ATOM     40  O   THR    37      28.232   7.465  11.843  1.00  0.00
ATOM     41  N   VAL    38      27.285   8.493  13.613  1.00  0.00
ATOM     42  CA  VAL    38      27.412   9.814  13.017  1.00  0.00
ATOM     43  C   VAL    38      28.879  10.084  12.672  1.00  0.00
ATOM     44  O   VAL    38      29.191  10.588  11.589  1.00  0.00
ATOM     45  N   GLN    39      29.778   9.726  13.584  1.00  0.00
ATOM     46  CA  GLN    39      31.199   9.931  13.354  1.00  0.00
ATOM     47  C   GLN    39      31.714   9.207  12.123  1.00  0.00
ATOM     48  O   GLN    39      32.460   9.787  11.338  1.00  0.00
ATOM     49  N   THR    40      31.329   7.942  11.959  1.00  0.00
ATOM     50  CA  THR    40      31.780   7.163  10.806  1.00  0.00
ATOM     51  C   THR    40      31.314   7.832   9.517  1.00  0.00
ATOM     52  O   THR    40      32.078   7.945   8.553  1.00  0.00
ATOM     53  N   ALA    41      30.068   8.289   9.504  1.00  0.00
ATOM     54  CA  ALA    41      29.536   8.948   8.316  1.00  0.00
ATOM     55  C   ALA    41      30.296  10.236   8.011  1.00  0.00
ATOM     56  O   ALA    41      30.654  10.489   6.858  1.00  0.00
ATOM     57  N   ILE    42      30.548  11.047   9.035  1.00  0.00
ATOM     58  CA  ILE    42      31.263  12.298   8.837  1.00  0.00
ATOM     59  C   ILE    42      32.717  12.082   8.427  1.00  0.00
ATOM     60  O   ILE    42      33.255  12.864   7.652  1.00  0.00
ATOM     61  N   THR    43      33.353  11.024   8.933  1.00  0.00
ATOM     62  CA  THR    43      34.731  10.747   8.545  1.00  0.00
ATOM     63  C   THR    43      34.714  10.394   7.062  1.00  0.00
ATOM     64  O   THR    43      35.601  10.802   6.306  1.00  0.00
ATOM     65  N   GLN    44      33.702   9.646   6.628  1.00  0.00
ATOM     66  CA  GLN    44      33.631   9.307   5.211  1.00  0.00
ATOM     67  C   GLN    44      33.326  10.533   4.363  1.00  0.00
ATOM     68  O   GLN    44      33.809  10.650   3.234  1.00  0.00
ATOM     69  N   ILE    47      32.550  11.462   4.910  1.00  0.00
ATOM     70  CA  ILE    47      32.218  12.678   4.178  1.00  0.00
ATOM     71  C   ILE    47      33.486  13.452   3.812  1.00  0.00
ATOM     72  O   ILE    47      33.627  13.922   2.677  1.00  0.00
ATOM     73  N   LEU    48      34.415  13.573   4.761  1.00  0.00
ATOM     74  CA  LEU    48      35.642  14.312   4.491  1.00  0.00
ATOM     75  C   LEU    48      36.638  13.508   3.656  1.00  0.00
ATOM     76  O   LEU    48      37.557  14.072   3.065  1.00  0.00
ATOM     77  N   SER    49      36.462  12.191   3.609  1.00  0.00
ATOM     78  CA  SER    49      37.322  11.358   2.774  1.00  0.00
ATOM     79  C   SER    49      36.840  11.565   1.337  1.00  0.00
ATOM     80  O   SER    49      37.622  11.470   0.387  1.00  0.00
ATOM     81  N   GLN    50      35.550  11.866   1.191  1.00  0.00
ATOM     82  CA  GLN    50      34.953  12.094  -0.130  1.00  0.00
ATOM     83  C   GLN    50      35.123  13.541  -0.599  1.00  0.00
ATOM     84  O   GLN    50      35.365  13.794  -1.784  1.00  0.00
ATOM     85  N   PHE    51      34.990  14.479   0.332  1.00  0.00
ATOM     86  CA  PHE    51      35.113  15.906   0.046  1.00  0.00
ATOM     87  C   PHE    51      35.975  16.552   1.116  1.00  0.00
ATOM     88  O   PHE    51      35.473  17.205   2.031  1.00  0.00
ATOM     89  N   PRO    52      37.300  16.392   0.999  1.00  0.00
ATOM     90  CA  PRO    52      38.243  16.957   1.967  1.00  0.00
ATOM     91  C   PRO    52      38.169  18.467   2.176  1.00  0.00
ATOM     92  O   PRO    52      38.660  18.975   3.183  1.00  0.00
ATOM     93  N   GLU    53      37.547  19.182   1.240  1.00  0.00
ATOM     94  CA  GLU    53      37.400  20.627   1.355  1.00  0.00
ATOM     95  C   GLU    53      36.573  20.979   2.591  1.00  0.00
ATOM     96  O   GLU    53      36.661  22.086   3.114  1.00  0.00
ATOM     97  N   ILE    54      35.781  20.022   3.065  1.00  0.00
ATOM     98  CA  ILE    54      34.940  20.229   4.242  1.00  0.00
ATOM     99  C   ILE    54      35.634  19.932   5.568  1.00  0.00
ATOM    100  O   ILE    54      35.110  20.261   6.631  1.00  0.00
ATOM    101  N   ASP    55      36.809  19.315   5.513  1.00  0.00
ATOM    102  CA  ASP    55      37.514  18.950   6.739  1.00  0.00
ATOM    103  C   ASP    55      37.775  20.121   7.682  1.00  0.00
ATOM    104  O   ASP    55      37.514  20.030   8.885  1.00  0.00
ATOM    105  N   LEU    56      38.289  21.211   7.121  1.00  0.00
ATOM    106  CA  LEU    56      38.621  22.415   7.874  1.00  0.00
ATOM    107  C   LEU    56      37.431  23.028   8.601  1.00  0.00
ATOM    108  O   LEU    56      37.585  23.591   9.681  1.00  0.00
TER
END
