
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0363AL044_2
# Molecule2: number of CA atoms   80 (  645),  selected   24 , name T0363.pdb
# PARAMETERS: T0363AL044_2.T0363.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:    13        31 - 47          4.80    21.35
  LONGEST_CONTINUOUS_SEGMENT:    13        32 - 57          4.88    13.56
  LCS_AVERAGE:     13.02

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        38 - 47          1.61    17.06
  LCS_AVERAGE:      6.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        38 - 46          0.68    16.00
  LCS_AVERAGE:      4.84

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:   80
LCS_GDT     Q      31     Q      31      0    3   13     0    0    3    3    3    3    3    6    8    8    9    9   13   13   14   17   18   19   20   20 
LCS_GDT     V      32     V      32      0    3   13     0    1    3    4    4    6    7    8    9   11   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     D      33     D      33      0    3   13     0    0    3    3    3    6    6    7    9   11   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     V      38     V      38      9   10   13     8    8    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     Q      39     Q      39      9   10   13     8    8    9    9   10   10   11   11   11   12   12   13   15   15   16   18   18   19   20   20 
LCS_GDT     T      40     T      40      9   10   13     8    8    9    9   10   10   11   11   11   12   12   14   15   15   16   18   18   19   20   20 
LCS_GDT     A      41     A      41      9   10   13     8    8    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     I      42     I      42      9   10   13     8    8    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     T      43     T      43      9   10   13     8    8    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     Q      44     Q      44      9   10   13     8    8    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     S      45     S      45      9   10   13     8    8    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     G      46     G      46      9   10   13     3    4    9    9   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     I      47     I      47      3   10   13     3    3    3    3    9    9   10   10   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     S      57     S      57      0    0   13     0    0    1    1    3    3    4    6    7    8    9   11   14   15   16   17   18   19   20   20 
LCS_GDT     T      58     T      58      0    0    6     0    0    0    0    0    3    4    5    5    5    5   11   13   13   13   14   16   16   20   20 
LCS_GDT     K      60     K      60      0    0    6     1    1    1    2    2    3    3    5    8    9   10   11   13   15   16   18   18   19   20   20 
LCS_GDT     I      63     I      63      0    3    7     0    0    1    2    3    4    5    6    9   11   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     F      64     F      64      0    4    7     1    2    2    2    3    4    6    6    6    7    8   10   13   15   16   18   18   19   20   20 
LCS_GDT     S      65     S      65      0    4    7     0    2    3    3    3    4    6    6    6    6    6    8   11   15   16   18   18   19   20   20 
LCS_GDT     R      66     R      66      3    4    7     3    3    4    6   10   10   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     P      67     P      67      3    4    7     1    2    3    3    3    5   11   11   11   12   13   14   15   15   16   18   18   19   20   20 
LCS_GDT     I      68     I      68      3    4    7     0    2    3    3    3    4    6    6    6    6    7    9   11   15   16   17   18   19   20   20 
LCS_GDT     T      71     T      71      0    0    7     0    0    0    0    0    0    6    6    6    6    6    6    6    6    6    7    8    8    8    8 
LCS_GDT     D      72     D      72      0    0    7     0    0    0    0    0    0    0    0    0    3    4    5    7    7    8    9   10   10   11   11 
LCS_AVERAGE  LCS_A:   8.25  (   4.84    6.88   13.02 )

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      9      9     10     10     11     11     11     12     13     14     15     15     16     18     18     19     20     20 
GDT PERCENT_CA  10.00  10.00  11.25  11.25  12.50  12.50  13.75  13.75  13.75  15.00  16.25  17.50  18.75  18.75  20.00  22.50  22.50  23.75  25.00  25.00
GDT RMS_LOCAL    0.24   0.24   0.68   0.68   2.02   2.02   2.30   2.30   2.30   2.91   4.19   4.36   4.53   4.53   4.88   5.59   5.59   6.04   6.37   6.27
GDT RMS_ALL_CA  16.08  16.08  16.00  16.00  12.60  12.60  12.50  12.50  12.50  12.04  10.05  10.13  10.35  10.35  10.35  10.16  10.16  10.00  10.14   9.64

#      Molecule1      Molecule2       DISTANCE
LGA    Q      31      Q      31         18.714
LGA    V      32      V      32         13.339
LGA    D      33      D      33         11.608
LGA    V      38      V      38          2.395
LGA    Q      39      Q      39          0.428
LGA    T      40      T      40          2.140
LGA    A      41      A      41          2.069
LGA    I      42      I      42          1.424
LGA    T      43      T      43          2.415
LGA    Q      44      Q      44          2.553
LGA    S      45      S      45          1.026
LGA    G      46      G      46          2.402
LGA    I      47      I      47          7.668
LGA    S      57      S      57         18.798
LGA    T      58      T      58         21.585
LGA    K      60      K      60         19.479
LGA    I      63      I      63         10.158
LGA    F      64      F      64         10.543
LGA    S      65      S      65         11.281
LGA    R      66      R      66          2.596
LGA    P      67      P      67          3.917
LGA    I      68      I      68          9.371
LGA    T      71      T      71         20.700
LGA    D      72      D      72         30.228

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   80    4.0     11    2.30    14.375    12.327     0.459

LGA_LOCAL      RMSD =  2.297  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.500  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  9.380  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.312430 * X  +  -0.166094 * Y  +  -0.935308 * Z  +  92.543388
  Y_new =  -0.536819 * X  +  -0.781438 * Y  +   0.318089 * Z  +  36.419220
  Z_new =  -0.783717 * X  +   0.601471 * Y  +   0.154982 * Z  +   8.738154 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.318611   -1.822982  [ DEG:    75.5508   -104.4492 ]
  Theta =   0.900628    2.240964  [ DEG:    51.6022    128.3978 ]
  Phi   =  -2.097877    1.043715  [ DEG:  -120.1995     59.8005 ]
 
# 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: T0363AL044_2                                  
REMARK     2: T0363.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL044_2.T0363.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   80   4.0   11   2.30  12.327     9.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL044_2
REMARK Aligment from pdb entry: 1t6l_A
ATOM      1  N   GLN    31      28.144  15.253  17.713  1.00  0.00              
ATOM      2  CA  GLN    31      29.392  14.880  17.092  1.00  0.00              
ATOM      3  C   GLN    31      29.343  13.495  16.460  1.00  0.00              
ATOM      4  O   GLN    31      29.848  13.318  15.351  1.00  0.00              
ATOM      5  N   VAL    32      28.720  12.516  17.142  1.00  0.00              
ATOM      6  CA  VAL    32      28.508  11.189  16.542  1.00  0.00              
ATOM      7  C   VAL    32      27.777  11.172  15.192  1.00  0.00              
ATOM      8  O   VAL    32      28.025  10.314  14.316  1.00  0.00              
ATOM      9  N   ASP    33      26.878  12.130  14.999  1.00  0.00              
ATOM     10  CA  ASP    33      26.175  12.268  13.734  1.00  0.00              
ATOM     11  C   ASP    33      27.121  12.785  12.662  1.00  0.00              
ATOM     12  O   ASP    33      27.093  12.308  11.536  1.00  0.00              
ATOM     13  N   VAL    38      27.954  13.760  13.023  1.00  0.00              
ATOM     14  CA  VAL    38      28.961  14.292  12.114  1.00  0.00              
ATOM     15  C   VAL    38      29.931  13.183  11.690  1.00  0.00              
ATOM     16  O   VAL    38      30.260  13.029  10.500  1.00  0.00              
ATOM     17  N   GLN    39      30.385  12.407  12.673  1.00  0.00              
ATOM     18  CA  GLN    39      31.263  11.276  12.389  1.00  0.00              
ATOM     19  C   GLN    39      30.618  10.274  11.421  1.00  0.00              
ATOM     20  O   GLN    39      31.262   9.833  10.487  1.00  0.00              
ATOM     21  N   THR    40      29.360   9.923  11.652  1.00  0.00              
ATOM     22  CA  THR    40      28.627   9.026  10.758  1.00  0.00              
ATOM     23  C   THR    40      28.507   9.562   9.346  1.00  0.00              
ATOM     24  O   THR    40      28.626   8.797   8.375  1.00  0.00              
ATOM     25  N   ALA    41      28.244  10.861   9.218  1.00  0.00              
ATOM     26  CA  ALA    41      28.154  11.459   7.885  1.00  0.00              
ATOM     27  C   ALA    41      29.490  11.366   7.166  1.00  0.00              
ATOM     28  O   ALA    41      29.528  11.055   5.988  1.00  0.00              
ATOM     29  N   ILE    42      30.576  11.653   7.887  1.00  0.00              
ATOM     30  CA  ILE    42      31.945  11.636   7.339  1.00  0.00              
ATOM     31  C   ILE    42      32.361  10.235   6.872  1.00  0.00              
ATOM     32  O   ILE    42      33.007  10.083   5.835  1.00  0.00              
ATOM     33  N   THR    43      31.988   9.230   7.642  1.00  0.00              
ATOM     34  CA  THR    43      32.335   7.841   7.327  1.00  0.00              
ATOM     35  C   THR    43      31.549   7.356   6.124  1.00  0.00              
ATOM     36  O   THR    43      32.098   6.646   5.269  1.00  0.00              
ATOM     37  N   GLN    44      30.279   7.768   6.065  1.00  0.00              
ATOM     38  CA  GLN    44      29.371   7.508   4.940  1.00  0.00              
ATOM     39  C   GLN    44      29.888   8.170   3.676  1.00  0.00              
ATOM     40  O   GLN    44      30.079   7.495   2.658  1.00  0.00              
ATOM     41  N   SER    45      30.168   9.476   3.742  1.00  0.00              
ATOM     42  CA  SER    45      30.577  10.217   2.560  1.00  0.00              
ATOM     43  C   SER    45      32.028   9.931   2.167  1.00  0.00              
ATOM     44  O   SER    45      32.349   9.927   0.981  1.00  0.00              
ATOM     45  N   GLY    46      32.883   9.681   3.153  1.00  0.00              
ATOM     46  CA  GLY    46      34.265   9.316   2.904  1.00  0.00              
ATOM     47  C   GLY    46      34.334   7.899   2.342  1.00  0.00              
ATOM     48  O   GLY    46      34.126   6.918   3.076  1.00  0.00              
ATOM     49  N   ILE    47      34.594   7.783   1.041  1.00  0.00              
ATOM     50  CA  ILE    47      34.729   6.471   0.403  1.00  0.00              
ATOM     51  C   ILE    47      36.204   6.047   0.346  1.00  0.00              
ATOM     52  O   ILE    47      36.798   5.755   1.399  1.00  0.00              
ATOM     53  N   SER    57      37.789  10.186  -2.124  1.00  0.00              
ATOM     54  CA  SER    57      37.545  11.321  -3.004  1.00  0.00              
ATOM     55  C   SER    57      36.063  11.424  -3.385  1.00  0.00              
ATOM     56  O   SER    57      35.560  10.583  -4.144  1.00  0.00              
ATOM     57  N   THR    58      20.338  18.132   0.829  1.00  0.00              
ATOM     58  CA  THR    58      19.852  18.148   2.210  1.00  0.00              
ATOM     59  C   THR    58      18.372  18.475   2.160  1.00  0.00              
ATOM     60  O   THR    58      17.967  19.546   1.689  1.00  0.00              
ATOM     61  N   LYS    60      17.572  17.527   2.621  1.00  0.00              
ATOM     62  CA  LYS    60      16.128  17.587   2.523  1.00  0.00              
ATOM     63  C   LYS    60      15.569  17.601   3.910  1.00  0.00              
ATOM     64  O   LYS    60      15.852  16.725   4.722  1.00  0.00              
ATOM     65  N   ILE    63      14.775  18.623   4.195  1.00  0.00              
ATOM     66  CA  ILE    63      14.248  18.845   5.536  1.00  0.00              
ATOM     67  C   ILE    63      12.739  18.765   5.472  1.00  0.00              
ATOM     68  O   ILE    63      12.128  19.266   4.520  1.00  0.00              
ATOM     69  N   PHE    64       8.979  18.860   7.951  1.00  0.00              
ATOM     70  CA  PHE    64       8.323  19.440   9.117  1.00  0.00              
ATOM     71  C   PHE    64       7.135  18.597   9.623  1.00  0.00              
ATOM     72  O   PHE    64       6.966  18.454  10.836  1.00  0.00              
ATOM     73  N   SER    65       6.350  17.991   8.735  1.00  0.00              
ATOM     74  CA  SER    65       5.266  17.101   9.201  1.00  0.00              
ATOM     75  C   SER    65       5.620  16.630  10.607  1.00  0.00              
ATOM     76  O   SER    65       5.325  17.334  11.580  1.00  0.00              
ATOM     77  N   ARG    66       9.504  16.270  12.270  1.00  0.00              
ATOM     78  CA  ARG    66      10.812  16.811  11.836  1.00  0.00              
ATOM     79  C   ARG    66      11.789  15.726  11.353  1.00  0.00              
ATOM     80  O   ARG    66      11.849  14.626  11.898  1.00  0.00              
ATOM     81  N   PRO    67      12.575  16.051  10.336  1.00  0.00              
ATOM     82  CA  PRO    67      13.605  15.133   9.858  1.00  0.00              
ATOM     83  C   PRO    67      14.589  15.928   9.019  1.00  0.00              
ATOM     84  O   PRO    67      14.218  16.899   8.358  1.00  0.00              
ATOM     85  N   ILE    68      15.835  15.518   9.088  1.00  0.00              
ATOM     86  CA  ILE    68      16.819  15.972   8.128  1.00  0.00              
ATOM     87  C   ILE    68      17.367  14.773   7.359  1.00  0.00              
ATOM     88  O   ILE    68      17.771  13.793   7.945  1.00  0.00              
ATOM     89  N   THR    71      17.382  14.880   6.042  1.00  0.00              
ATOM     90  CA  THR    71      17.748  13.773   5.164  1.00  0.00              
ATOM     91  C   THR    71      18.885  14.231   4.229  1.00  0.00              
ATOM     92  O   THR    71      18.942  15.400   3.802  1.00  0.00              
ATOM     93  N   ASP    72      22.330   7.839  -5.139  1.00  0.00              
ATOM     94  CA  ASP    72      21.066   7.348  -4.625  1.00  0.00              
ATOM     95  C   ASP    72      21.093   6.915  -3.173  1.00  0.00              
ATOM     96  O   ASP    72      20.063   6.565  -2.642  1.00  0.00              
END
