
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0363AL243_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   26 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_2-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:    26        29 - 56          4.35     4.35
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        36 - 52          1.98     5.56
  LCS_AVERAGE:     26.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        36 - 44          0.55     5.62
  LCS_AVERAGE:     12.96

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     S      29     S      29      5    7   26     4    5    6   10   13   13   16   16   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     F      30     F      30      5    7   26     4    5    6    7   13   13   16   16   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     Q      31     Q      31      5    7   26     4    6   10   11   13   13   16   16   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     V      32     V      32      5    7   26     4    5   10   11   13   13   16   16   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     D      33     D      33      5    7   26     3    5   10   11   13   13   16   16   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     E      34     E      34      3   11   26     1    3    4    7    9   12   16   16   16   17   19   22   25   26   26   26   26   26   26   26 
LCS_GDT     G      35     G      35      3   11   26     3    5    6    7    9   12   16   16   17   20   22   24   25   26   26   26   26   26   26   26 
LCS_GDT     I      36     I      36      9   15   26     5    8    9   10   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     T      37     T      37      9   15   26     8    8    9   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     V      38     V      38      9   15   26     8    8   10   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     Q      39     Q      39      9   15   26     8    8   10   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     T      40     T      40      9   15   26     8    8   10   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     A      41     A      41      9   15   26     8    8   10   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     I      42     I      42      9   15   26     8    8   10   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     T      43     T      43      9   15   26     8    8   10   11   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     Q      44     Q      44      9   15   26     8    8   10   11   13   14   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     I      47     I      47      5   15   26     4    5    6   10   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     L      48     L      48      5   15   26     4    5    9   10   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     S      49     S      49      5   15   26     4    5    6    9   13   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     Q      50     Q      50      5   15   26     4    5    6    9   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     F      51     F      51      5   15   26     3    4    7   10   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     P      52     P      52      4   15   26     3    4    7   10   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     E      53     E      53      4   12   26     3    5    7   10   14   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     I      54     I      54      4   12   26     3    4    7   10   13   16   17   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     D      55     D      55      3    5   26     3    3    3    4    5    5   10   18   18   20   23   24   25   26   26   26   26   26   26   26 
LCS_GDT     L      56     L      56      3    3   26     2    3    3    7    7    7   11   12   17   18   19   21   25   26   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  31.91  (  12.96   26.25   56.52 )

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      8     10     11     14     16     17     18     18     20     23     24     25     26     26     26     26     26     26     26 
GDT PERCENT_CA  17.39  17.39  21.74  23.91  30.43  34.78  36.96  39.13  39.13  43.48  50.00  52.17  54.35  56.52  56.52  56.52  56.52  56.52  56.52  56.52
GDT RMS_LOCAL    0.32   0.32   0.91   1.06   1.83   1.95   2.09   2.30   2.30   3.36   3.84   4.01   4.20   4.35   4.35   4.35   4.35   4.35   4.35   4.35
GDT RMS_ALL_CA   5.67   5.67   7.05   6.96   6.02   6.31   6.07   5.96   5.96   4.81   4.48   4.41   4.38   4.35   4.35   4.35   4.35   4.35   4.35   4.35

#      Molecule1      Molecule2       DISTANCE
LGA    S      29      S      29         11.532
LGA    F      30      F      30         11.425
LGA    Q      31      Q      31         11.339
LGA    V      32      V      32         10.031
LGA    D      33      D      33         11.182
LGA    E      34      E      34          9.172
LGA    G      35      G      35          8.597
LGA    I      36      I      36          2.523
LGA    T      37      T      37          2.206
LGA    V      38      V      38          1.268
LGA    Q      39      Q      39          1.666
LGA    T      40      T      40          1.104
LGA    A      41      A      41          1.507
LGA    I      42      I      42          2.385
LGA    T      43      T      43          1.360
LGA    Q      44      Q      44          3.412
LGA    I      47      I      47          3.147
LGA    L      48      L      48          2.654
LGA    S      49      S      49          3.256
LGA    Q      50      Q      50          2.684
LGA    F      51      F      51          1.862
LGA    P      52      P      52          1.212
LGA    E      53      E      53          1.246
LGA    I      54      I      54          2.111
LGA    D      55      D      55          3.873
LGA    L      56      L      56          5.984

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26   46    4.0     18    2.30    34.239    34.014     0.750

LGA_LOCAL      RMSD =  2.299  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.918  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  4.351  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.793226 * X  +   0.605142 * Y  +   0.067790 * Z  +  21.703278
  Y_new =  -0.492068 * X  +  -0.702591 * Y  +   0.514037 * Z  +  47.019958
  Z_new =   0.358694 * X  +   0.374390 * Y  +   0.855085 * Z  +  -8.211630 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.412696   -2.728897  [ DEG:    23.6457   -156.3543 ]
  Theta =  -0.366868   -2.774724  [ DEG:   -21.0200   -158.9800 ]
  Phi   =  -2.586353    0.555240  [ DEG:  -148.1871     31.8129 ]
 
# 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: T0363AL243_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_2-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26   46   4.0   18   2.30  34.014     4.35
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_2-D1
REMARK Aligment from pdb entry: 1fmaD
ATOM      1  N   SER    29      24.772  24.007   2.748  1.00  0.00              
ATOM      2  CA  SER    29      23.906  22.837   2.945  1.00  0.00              
ATOM      3  C   SER    29      24.077  21.861   1.894  1.00  0.00              
ATOM      4  O   SER    29      24.259  22.293   0.732  1.00  0.00              
ATOM      5  N   PHE    30      23.911  20.619   2.197  1.00  0.00              
ATOM      6  CA  PHE    30      23.958  19.600   1.208  1.00  0.00              
ATOM      7  C   PHE    30      23.180  18.411   1.650  1.00  0.00              
ATOM      8  O   PHE    30      22.849  18.246   2.784  1.00  0.00              
ATOM      9  N   GLN    31      22.854  17.545   0.734  1.00  0.00              
ATOM     10  CA  GLN    31      22.138  16.306   1.058  1.00  0.00              
ATOM     11  C   GLN    31      23.011  15.118   0.832  1.00  0.00              
ATOM     12  O   GLN    31      23.794  15.097  -0.154  1.00  0.00              
ATOM     13  N   VAL    32      22.850  14.136   1.714  1.00  0.00              
ATOM     14  CA  VAL    32      23.491  12.839   1.653  1.00  0.00              
ATOM     15  C   VAL    32      22.476  11.674   1.868  1.00  0.00              
ATOM     16  O   VAL    32      21.413  11.785   2.473  1.00  0.00              
ATOM     17  N   ASP    33      22.709  10.524   1.243  1.00  0.00              
ATOM     18  CA  ASP    33      21.808   9.379   1.501  1.00  0.00              
ATOM     19  C   ASP    33      21.846   8.948   2.999  1.00  0.00              
ATOM     20  O   ASP    33      22.840   9.173   3.694  1.00  0.00              
ATOM     21  N   GLU    34      22.736   6.492   4.523  1.00  0.00              
ATOM     22  CA  GLU    34      23.536   5.292   4.564  1.00  0.00              
ATOM     23  C   GLU    34      24.619   5.414   5.588  1.00  0.00              
ATOM     24  O   GLU    34      25.685   4.857   5.341  1.00  0.00              
ATOM     25  N   GLY    35      24.417   6.185   6.660  1.00  0.00              
ATOM     26  CA  GLY    35      25.431   6.231   7.689  1.00  0.00              
ATOM     27  C   GLY    35      24.829   5.943   9.008  1.00  0.00              
ATOM     28  O   GLY    35      23.775   6.470   9.314  1.00  0.00              
ATOM     29  N   ILE    36      25.483   5.136   9.808  1.00  0.00              
ATOM     30  CA  ILE    36      24.842   4.778  11.063  1.00  0.00              
ATOM     31  C   ILE    36      24.848   5.901  12.090  1.00  0.00              
ATOM     32  O   ILE    36      23.976   5.894  12.909  1.00  0.00              
ATOM     33  N   THR    37      25.830   6.783  12.035  1.00  0.00              
ATOM     34  CA  THR    37      26.054   7.772  13.106  1.00  0.00              
ATOM     35  C   THR    37      26.514   9.031  12.457  1.00  0.00              
ATOM     36  O   THR    37      26.988   9.071  11.320  1.00  0.00              
ATOM     37  N   VAL    38      26.422  10.061  13.254  1.00  0.00              
ATOM     38  CA  VAL    38      26.977  11.382  12.904  1.00  0.00              
ATOM     39  C   VAL    38      28.438  11.221  12.565  1.00  0.00              
ATOM     40  O   VAL    38      28.928  11.826  11.599  1.00  0.00              
ATOM     41  N   GLN    39      29.173  10.478  13.353  1.00  0.00              
ATOM     42  CA  GLN    39      30.571  10.258  13.077  1.00  0.00              
ATOM     43  C   GLN    39      30.816   9.639  11.730  1.00  0.00              
ATOM     44  O   GLN    39      31.726  10.017  11.042  1.00  0.00              
ATOM     45  N   THR    40      30.066   8.630  11.380  1.00  0.00              
ATOM     46  CA  THR    40      30.246   7.969  10.098  1.00  0.00              
ATOM     47  C   THR    40      30.009   8.956   8.986  1.00  0.00              
ATOM     48  O   THR    40      30.715   9.023   7.983  1.00  0.00              
ATOM     49  N   ALA    41      28.992   9.777   9.169  1.00  0.00              
ATOM     50  CA  ALA    41      28.712  10.827   8.182  1.00  0.00              
ATOM     51  C   ALA    41      29.847  11.852   8.125  1.00  0.00              
ATOM     52  O   ALA    41      30.329  12.203   7.048  1.00  0.00              
ATOM     53  N   ILE    42      30.347  12.278   9.271  1.00  0.00              
ATOM     54  CA  ILE    42      31.422  13.247   9.326  1.00  0.00              
ATOM     55  C   ILE    42      32.632  12.688   8.558  1.00  0.00              
ATOM     56  O   ILE    42      33.261  13.384   7.763  1.00  0.00              
ATOM     57  N   THR    43      32.946  11.425   8.820  1.00  0.00              
ATOM     58  CA  THR    43      34.100  10.832   8.147  1.00  0.00              
ATOM     59  C   THR    43      33.880  10.782   6.643  1.00  0.00              
ATOM     60  O   THR    43      34.746  11.040   5.900  1.00  0.00              
ATOM     61  N   GLN    44      32.664  10.409   6.219  1.00  0.00              
ATOM     62  CA  GLN    44      32.364  10.322   4.793  1.00  0.00              
ATOM     63  C   GLN    44      32.539  11.733   4.132  1.00  0.00              
ATOM     64  O   GLN    44      33.210  11.837   3.102  1.00  0.00              
ATOM     65  N   ILE    47      31.976  12.741   4.787  1.00  0.00              
ATOM     66  CA  ILE    47      32.082  14.126   4.254  1.00  0.00              
ATOM     67  C   ILE    47      33.513  14.575   4.264  1.00  0.00              
ATOM     68  O   ILE    47      33.986  15.214   3.306  1.00  0.00              
ATOM     69  N   LEU    48      34.263  14.262   5.328  1.00  0.00              
ATOM     70  CA  LEU    48      35.655  14.676   5.435  1.00  0.00              
ATOM     71  C   LEU    48      36.435  14.101   4.304  1.00  0.00              
ATOM     72  O   LEU    48      37.397  14.704   3.827  1.00  0.00              
ATOM     73  N   SER    49      36.067  12.910   3.844  1.00  0.00              
ATOM     74  CA  SER    49      36.814  12.224   2.835  1.00  0.00              
ATOM     75  C   SER    49      36.604  12.741   1.446  1.00  0.00              
ATOM     76  O   SER    49      37.306  12.291   0.565  1.00  0.00              
ATOM     77  N   GLN    50      35.717  13.719   1.255  1.00  0.00              
ATOM     78  CA  GLN    50      35.373  14.233  -0.084  1.00  0.00              
ATOM     79  C   GLN    50      36.409  15.092  -0.632  1.00  0.00              
ATOM     80  O   GLN    50      36.576  15.142  -1.836  1.00  0.00              
ATOM     81  N   PHE    51      37.141  15.810   0.206  1.00  0.00              
ATOM     82  CA  PHE    51      38.210  16.691  -0.278  1.00  0.00              
ATOM     83  C   PHE    51      39.074  17.141   0.864  1.00  0.00              
ATOM     84  O   PHE    51      38.702  17.011   2.011  1.00  0.00              
ATOM     85  N   PRO    52      40.242  17.740   0.554  1.00  0.00              
ATOM     86  CA  PRO    52      41.128  18.211   1.576  1.00  0.00              
ATOM     87  C   PRO    52      40.458  19.370   2.346  1.00  0.00              
ATOM     88  O   PRO    52      40.656  19.445   3.568  1.00  0.00              
ATOM     89  N   GLU    53      39.684  20.201   1.641  1.00  0.00              
ATOM     90  CA  GLU    53      38.988  21.313   2.317  1.00  0.00              
ATOM     91  C   GLU    53      37.950  20.755   3.290  1.00  0.00              
ATOM     92  O   GLU    53      37.818  21.264   4.357  1.00  0.00              
ATOM     93  N   ILE    54      37.167  19.774   2.841  1.00  0.00              
ATOM     94  CA  ILE    54      36.161  19.154   3.691  1.00  0.00              
ATOM     95  C   ILE    54      36.802  18.463   4.859  1.00  0.00              
ATOM     96  O   ILE    54      36.322  18.500   5.926  1.00  0.00              
ATOM     97  N   ASP    55      37.966  17.865   4.643  1.00  0.00              
ATOM     98  CA  ASP    55      38.615  17.183   5.753  1.00  0.00              
ATOM     99  C   ASP    55      39.104  18.145   6.764  1.00  0.00              
ATOM    100  O   ASP    55      38.916  17.976   7.916  1.00  0.00              
ATOM    101  N   LEU    56      39.645  19.258   6.304  1.00  0.00              
ATOM    102  CA  LEU    56      40.097  20.330   7.190  1.00  0.00              
ATOM    103  C   LEU    56      38.977  20.897   8.010  1.00  0.00              
ATOM    104  O   LEU    56      39.030  21.061   9.209  1.00  0.00              
END
