
#######################################################
#                                                     #
#                        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 T0306AL242_5
# Molecule2: number of CA atoms   95 (  694),  selected   24 , name T0306.pdb
# PARAMETERS: T0306AL242_5.T0306.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:    19        45 - 63          4.83    12.34
  LCS_AVERAGE:     18.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        49 - 56          1.99    12.26
  LONGEST_CONTINUOUS_SEGMENT:     8        51 - 58          1.99    12.15
  LONGEST_CONTINUOUS_SEGMENT:     8        52 - 59          2.00    15.42
  LCS_AVERAGE:      6.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        52 - 56          0.80    14.64
  LONGEST_CONTINUOUS_SEGMENT:     5        55 - 59          0.81    17.97
  LCS_AVERAGE:      4.25

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:   95
LCS_GDT     C      40     C      40      3    3   12     0    3    3    3    3    4    4    5    6    7    9   10   11   12   12   12   12   13   14   14 
LCS_GDT     A      41     A      41      3    3   12     0    3    3    3    3    4    6    8    9   10   10   11   11   12   12   13   13   14   16   17 
LCS_GDT     V      42     V      42      3    3   12     1    3    3    3    3    4    7    8    9   10   10   11   11   12   12   13   13   14   16   18 
LCS_GDT     A      43     A      43      3    5   12     3    3    3    4    5    5    6    8    9   10   10   11   11   12   12   13   13   14   16   17 
LCS_GDT     I      44     I      44      3    5   13     3    3    3    4    5    5    7    8    9   10   10   11   11   12   12   13   13   14   16   18 
LCS_GDT     D      45     D      45      3    5   19     3    3    3    4    5    5    7    8    9   10   10   12   12   12   13   15   18   19   19   19 
LCS_GDT     N      46     N      46      4    6   19     3    4    6    6    6    7   11   11   11   12   15   16   18   18   18   18   18   19   19   19 
LCS_GDT     I      47     I      47      4    6   19     3    4    6    6    6    6   11   11   11   14   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     G      48     G      48      4    7   19     3    4    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     A      49     A      49      4    8   19     3    4    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     G      50     G      50      4    8   19     4    6    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     T      51     T      51      4    8   19     3    3    5    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     G      52     G      52      5    8   19     4    6    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     E      53     E      53      5    8   19     3    5    6    6    7   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     W      54     W      54      5    8   19     3    5    5    5    8   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     V      55     V      55      5    8   19     3    6    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     L      56     L      56      5    8   19     3    5    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     L      57     L      57      5    8   19     3    6    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     V      58     V      58      5    8   19     4    6    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     S      59     S      59      5    8   19     4    6    6    8   10   10   12   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     G      60     G      60      4    6   19     3    3    4    5    5    7   11   11   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     S      61     S      61      4    6   19     3    3    4    5    5    6    6    9   11   13   14   17   18   18   18   18   18   19   19   19 
LCS_GDT     S      62     S      62      4    6   19     0    3    4    5    5    7    8   11   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_GDT     A      63     A      63      3    3   19     0    3    3    6    8   10   10   12   14   15   16   17   18   18   18   18   18   19   19   19 
LCS_AVERAGE  LCS_A:   9.81  (   4.25    6.67   18.51 )

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      4      6      6      8     10     10     12     12     14     15     16     17     18     18     18     18     18     19     19     19 
GDT PERCENT_CA   4.21   6.32   6.32   8.42  10.53  10.53  12.63  12.63  14.74  15.79  16.84  17.89  18.95  18.95  18.95  18.95  18.95  20.00  20.00  20.00
GDT RMS_LOCAL    0.26   0.76   0.76   1.36   1.74   1.74   2.30   2.30   2.97   3.20   3.46   3.72   4.09   4.09   4.09   4.09   4.09   4.83   4.83   4.83
GDT RMS_ALL_CA  14.85  14.65  14.65  14.43  14.01  14.01  13.83  13.83  13.56  13.51  13.34  13.34  12.84  12.84  12.84  12.84  12.84  12.34  12.34  12.34

#      Molecule1      Molecule2       DISTANCE
LGA    C      40      C      40         35.866
LGA    A      41      A      41         30.999
LGA    V      42      V      42         25.044
LGA    A      43      A      43         25.106
LGA    I      44      I      44         21.150
LGA    D      45      D      45         14.149
LGA    N      46      N      46          9.711
LGA    I      47      I      47          7.779
LGA    G      48      G      48          2.704
LGA    A      49      A      49          2.558
LGA    G      50      G      50          1.034
LGA    T      51      T      51          3.010
LGA    G      52      G      52          1.973
LGA    E      53      E      53          3.200
LGA    W      54      W      54          3.691
LGA    V      55      V      55          0.515
LGA    L      56      L      56          1.992
LGA    L      57      L      57          1.599
LGA    V      58      V      58          0.638
LGA    S      59      S      59          2.110
LGA    G      60      G      60          5.075
LGA    S      61      S      61          9.139
LGA    S      62      S      62          7.772
LGA    A      63      A      63          7.233

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   95    4.0     12    2.30    11.579    10.988     0.500

LGA_LOCAL      RMSD =  2.298  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.833  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  9.782  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.159654 * X  +  -0.939970 * Y  +  -0.301608 * Z  +  55.438984
  Y_new =  -0.518787 * X  +  -0.180044 * Y  +   0.835730 * Z  + -54.935970
  Z_new =  -0.839863 * X  +   0.289898 * Y  +  -0.458899 * Z  + 133.729660 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.578172   -0.563420  [ DEG:   147.7184    -32.2816 ]
  Theta =   0.997031    2.144561  [ DEG:    57.1257    122.8743 ]
  Phi   =  -1.869344    1.272249  [ DEG:  -107.1055     72.8945 ]
 
# 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: T0306AL242_5                                  
REMARK     2: T0306.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0306AL242_5.T0306.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   95   4.0   12   2.30  10.988     9.78
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL242_5
REMARK Aligment from pdb entry: 1m06_J
ATOM      1  N   CYS    40      36.679   2.348  51.675  1.00  0.00              
ATOM      2  CA  CYS    40      35.893   3.342  50.879  1.00  0.00              
ATOM      3  C   CYS    40      34.825   4.003  51.749  1.00  0.00              
ATOM      4  O   CYS    40      33.747   4.369  51.279  1.00  0.00              
ATOM      5  N   ALA    41      35.127   4.145  53.033  1.00  0.00              
ATOM      6  CA  ALA    41      34.198   4.775  53.964  1.00  0.00              
ATOM      7  C   ALA    41      34.705   6.204  54.114  1.00  0.00              
ATOM      8  O   ALA    41      33.968   7.167  53.893  1.00  0.00              
ATOM      9  N   VAL    42      35.987   6.317  54.466  1.00  0.00              
ATOM     10  CA  VAL    42      36.650   7.601  54.655  1.00  0.00              
ATOM     11  C   VAL    42      36.790   8.352  53.336  1.00  0.00              
ATOM     12  O   VAL    42      36.668   9.579  53.291  1.00  0.00              
ATOM     13  N   ALA    43      37.047   7.605  52.269  1.00  0.00              
ATOM     14  CA  ALA    43      37.240   8.174  50.938  1.00  0.00              
ATOM     15  C   ALA    43      36.095   9.056  50.453  1.00  0.00              
ATOM     16  O   ALA    43      36.279   9.840  49.527  1.00  0.00              
ATOM     17  N   ILE    44      34.916   8.931  51.056  1.00  0.00              
ATOM     18  CA  ILE    44      33.780   9.755  50.640  1.00  0.00              
ATOM     19  C   ILE    44      33.745  11.071  51.433  1.00  0.00              
ATOM     20  O   ILE    44      33.234  12.095  50.956  1.00  0.00              
ATOM     21  N   ASP    45      34.286  11.037  52.648  1.00  0.00              
ATOM     22  CA  ASP    45      34.275  12.213  53.508  1.00  0.00              
ATOM     23  C   ASP    45      35.623  12.905  53.689  1.00  0.00              
ATOM     24  O   ASP    45      36.605  12.292  54.118  1.00  0.00              
ATOM     25  N   ASN    46      35.658  14.195  53.354  1.00  0.00              
ATOM     26  CA  ASN    46      36.879  14.985  53.482  1.00  0.00              
ATOM     27  C   ASN    46      37.335  14.982  54.931  1.00  0.00              
ATOM     28  O   ASN    46      36.564  15.319  55.831  1.00  0.00              
ATOM     29  N   ILE    47      38.600  14.624  55.174  1.00  0.00              
ATOM     30  CA  ILE    47      39.166  14.577  56.520  1.00  0.00              
ATOM     31  C   ILE    47      38.784  15.746  57.432  1.00  0.00              
ATOM     32  O   ILE    47      38.259  16.774  56.984  1.00  0.00              
ATOM     33  N   GLY    48      39.066  15.567  58.715  1.00  0.00              
ATOM     34  CA  GLY    48      38.730  16.541  59.734  1.00  0.00              
ATOM     35  C   GLY    48      39.856  17.497  60.100  1.00  0.00              
ATOM     36  O   GLY    48      39.592  18.600  60.580  1.00  0.00              
ATOM     37  N   ALA    49      41.103  17.089  59.880  1.00  0.00              
ATOM     38  CA  ALA    49      42.246  17.928  60.241  1.00  0.00              
ATOM     39  C   ALA    49      42.115  18.307  61.721  1.00  0.00              
ATOM     40  O   ALA    49      42.364  19.454  62.105  1.00  0.00              
ATOM     41  N   GLY    50      41.715  17.339  62.543  1.00  0.00              
ATOM     42  CA  GLY    50      41.528  17.557  63.977  1.00  0.00              
ATOM     43  C   GLY    50      42.866  17.476  64.738  1.00  0.00              
ATOM     44  O   GLY    50      43.027  18.096  65.800  1.00  0.00              
ATOM     45  N   THR    51      43.821  16.723  64.186  1.00  0.00              
ATOM     46  CA  THR    51      45.148  16.583  64.800  1.00  0.00              
ATOM     47  C   THR    51      45.910  17.900  64.669  1.00  0.00              
ATOM     48  O   THR    51      45.729  18.629  63.700  1.00  0.00              
ATOM     49  N   GLY    52      46.756  18.211  65.644  1.00  0.00              
ATOM     50  CA  GLY    52      47.509  19.451  65.569  1.00  0.00              
ATOM     51  C   GLY    52      46.857  20.602  66.307  1.00  0.00              
ATOM     52  O   GLY    52      45.857  20.420  67.012  1.00  0.00              
ATOM     53  N   GLU    53      47.415  21.794  66.135  1.00  0.00              
ATOM     54  CA  GLU    53      46.901  22.979  66.813  1.00  0.00              
ATOM     55  C   GLU    53      45.824  23.710  66.037  1.00  0.00              
ATOM     56  O   GLU    53      45.365  23.228  65.005  1.00  0.00              
ATOM     57  N   TRP    54      45.432  24.879  66.548  1.00  0.00              
ATOM     58  CA  TRP    54      44.396  25.705  65.932  1.00  0.00              
ATOM     59  C   TRP    54      44.963  26.466  64.753  1.00  0.00              
ATOM     60  O   TRP    54      46.069  27.019  64.842  1.00  0.00              
ATOM     61  N   VAL    55      44.198  26.500  63.659  1.00  0.00              
ATOM     62  CA  VAL    55      44.611  27.181  62.430  1.00  0.00              
ATOM     63  C   VAL    55      43.770  28.399  62.089  1.00  0.00              
ATOM     64  O   VAL    55      44.274  29.404  61.595  1.00  0.00              
ATOM     65  N   LEU    56      42.482  28.302  62.362  1.00  0.00              
ATOM     66  CA  LEU    56      41.562  29.379  61.964  1.00  0.00              
ATOM     67  C   LEU    56      41.144  30.345  63.035  1.00  0.00              
ATOM     68  O   LEU    56      40.391  30.016  63.951  1.00  0.00              
ATOM     69  N   LEU    57      41.666  31.550  62.910  1.00  0.00              
ATOM     70  CA  LEU    57      41.243  32.613  63.780  1.00  0.00              
ATOM     71  C   LEU    57      40.403  33.488  62.873  1.00  0.00              
ATOM     72  O   LEU    57      40.878  33.958  61.846  1.00  0.00              
ATOM     73  N   VAL    58      39.156  33.711  63.249  1.00  0.00              
ATOM     74  CA  VAL    58      38.262  34.457  62.411  1.00  0.00              
ATOM     75  C   VAL    58      37.494  35.510  63.202  1.00  0.00              
ATOM     76  O   VAL    58      36.535  36.090  62.713  1.00  0.00              
ATOM     77  N   SER    59      37.926  35.754  64.430  1.00  0.00              
ATOM     78  CA  SER    59      37.268  36.749  65.258  1.00  0.00              
ATOM     79  C   SER    59      36.488  36.177  66.426  1.00  0.00              
ATOM     80  O   SER    59      36.189  36.878  67.403  1.00  0.00              
ATOM     81  N   GLY    60      36.153  34.892  66.338  1.00  0.00              
ATOM     82  CA  GLY    60      35.399  34.254  67.402  1.00  0.00              
ATOM     83  C   GLY    60      34.880  32.913  66.942  1.00  0.00              
ATOM     84  O   GLY    60      35.443  32.325  66.021  1.00  0.00              
ATOM     85  N   SER    61      33.814  32.427  67.574  1.00  0.00              
ATOM     86  CA  SER    61      33.241  31.137  67.210  1.00  0.00              
ATOM     87  C   SER    61      32.369  31.244  65.974  1.00  0.00              
ATOM     88  O   SER    61      31.515  32.124  65.865  1.00  0.00              
ATOM     89  N   SER    62      32.614  30.350  65.027  1.00  0.00              
ATOM     90  CA  SER    62      31.860  30.317  63.782  1.00  0.00              
ATOM     91  C   SER    62      31.605  28.860  63.492  1.00  0.00              
ATOM     92  O   SER    62      32.544  28.075  63.421  1.00  0.00              
ATOM     93  N   ALA    63      30.341  28.490  63.338  1.00  0.00              
ATOM     94  CA  ALA    63      30.008  27.105  63.056  1.00  0.00              
ATOM     95  C   ALA    63      30.280  26.693  61.605  1.00  0.00              
ATOM     96  O   ALA    63      30.554  27.580  60.754  1.00  0.00              
END
