
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0361AL242_5-D1
# Molecule2: number of CA atoms  158 ( 1268),  selected   25 , name T0361_D1.pdb
# PARAMETERS: T0361AL242_5-D1.T0361_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:    21        43 - 63          4.92     6.77
  LONGEST_CONTINUOUS_SEGMENT:    21        44 - 64          4.81     7.21
  LONGEST_CONTINUOUS_SEGMENT:    21        45 - 65          4.94     7.96
  LCS_AVERAGE:     12.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        47 - 57          1.95     9.76
  LCS_AVERAGE:      5.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        46 - 53          0.97    11.02
  LCS_AVERAGE:      3.34

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:  158
LCS_GDT     L      41     L      41      3    7   13     3    3    3    4    6    6    7    7    8    9   11   11   12   12   12   14   16   16   16   18 
LCS_GDT     F      42     F      42      4    7   16     4    4    4    5    6    6    7    7    8    9   11   11   12   15   16   17   19   21   21   22 
LCS_GDT     V      43     V      43      4    7   21     4    4    4    5    5    6    7    7    8    9   11   14   17   21   21   21   22   22   23   23 
LCS_GDT     D      44     D      44      4    7   21     4    4    4    5    6   10   10   11   12   15   16   17   19   21   21   21   22   22   23   23 
LCS_GDT     N      45     N      45      4    7   21     4    4    4    7    8   10   10   11   13   15   16   17   19   21   21   21   22   22   23   23 
LCS_GDT     D      46     D      46      8   10   21     3    4    7    8   10   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     E      47     E      47      8   11   21     3    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     E      48     E      48      8   11   21     3    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     I      49     I      49      8   11   21     4    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     V      50     V      50      8   11   21     4    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     E      51     E      51      8   11   21     4    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     Y      52     Y      52      8   11   21     4    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     A      53     A      53      8   11   21     4    5    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     V      54     V      54      5   11   21     3    5    6    8   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     K      55     K      55      5   11   21     3    5    6    7   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     P      56     P      56      5   11   21     3    5    6    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     L      57     L      57      5   11   21     3    5    6    8   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     L      58     L      58      4    8   21     2    4    4    4    8    9   12   14   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     A      59     A      59      3    4   21     3    3    4    4   10   11   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     Q      60     Q      60      3    4   21     3    6    7    9   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     S      61     S      61      4    4   21     4    4    4    7   11   13   14   15   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     G      62     G      62      4    4   21     4    4    4    4    6   10   11   13   16   17   17   17   19   21   21   21   22   22   23   23 
LCS_GDT     P      63     P      63      4    4   21     4    4    4    4    4    5    6    8    9   13   14   16   18   21   21   21   22   22   23   23 
LCS_GDT     L      64     L      64      4    4   21     4    4    4    4    4    5    6    6    6    6   13   16   18   20   21   21   22   22   23   23 
LCS_GDT     D      65     D      65      3    4   21     0    3    3    3    4    4    4    4    5    5    9   10   13   18   21   21   22   22   23   23 
LCS_AVERAGE  LCS_A:   7.14  (   3.34    5.11   12.96 )

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      7      9     11     13     14     15     16     17     17     17     19     21     21     21     22     22     23     23 
GDT PERCENT_CA   2.53   3.80   4.43   5.70   6.96   8.23   8.86   9.49  10.13  10.76  10.76  10.76  12.03  13.29  13.29  13.29  13.92  13.92  14.56  14.56
GDT RMS_LOCAL    0.32   0.64   0.76   1.27   1.74   2.02   2.17   2.33   2.57   2.92   2.92   2.92   4.05   4.92   4.81   4.81   5.03   5.03   5.36   5.36
GDT RMS_ALL_CA  10.59  10.48  10.76  10.47  10.22   9.93   9.79  10.01  10.13  10.22  10.22  10.22   8.40   6.77   7.21   7.21   7.37   7.37   6.95   6.95

#      Molecule1      Molecule2       DISTANCE
LGA    L      41      L      41         28.633
LGA    F      42      F      42         21.994
LGA    V      43      V      43         17.256
LGA    D      44      D      44         12.423
LGA    N      45      N      45          9.291
LGA    D      46      D      46          3.451
LGA    E      47      E      47          1.609
LGA    E      48      E      48          1.078
LGA    I      49      I      49          1.139
LGA    V      50      V      50          1.728
LGA    E      51      E      51          1.332
LGA    Y      52      Y      52          1.061
LGA    A      53      A      53          1.604
LGA    V      54      V      54          2.724
LGA    K      55      K      55          2.872
LGA    P      56      P      56          2.450
LGA    L      57      L      57          3.613
LGA    L      58      L      58          4.883
LGA    A      59      A      59          3.263
LGA    Q      60      Q      60          0.577
LGA    S      61      S      61          3.585
LGA    G      62      G      62          7.280
LGA    P      63      P      63         14.117
LGA    L      64      L      64         13.709
LGA    D      65      D      65         13.138

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25  158    4.0     15    2.33     8.070     7.652     0.617

LGA_LOCAL      RMSD =  2.331  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.125  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  6.720  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.583708 * X  +   0.795600 * Y  +   0.162189 * Z  +  19.326271
  Y_new =  -0.757873 * X  +   0.462158 * Y  +   0.460476 * Z  +  10.392402
  Z_new =   0.291398 * X  +  -0.391702 * Y  +   0.872729 * Z  +   1.944884 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.421876    2.719717  [ DEG:   -24.1717    155.8283 ]
  Theta =  -0.295688   -2.845905  [ DEG:   -16.9417   -163.0583 ]
  Phi   =  -0.914497    2.227096  [ DEG:   -52.3968    127.6032 ]
 
# 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: T0361AL242_5-D1                               
REMARK     2: T0361_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0361AL242_5-D1.T0361_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25  158   4.0   15   2.33   7.652     6.72
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL242_5-D1
REMARK Aligment from pdb entry: 2mlp
ATOM      1  N   LEU    41      32.693  27.383  -5.192  1.00  0.00              
ATOM      2  CA  LEU    41      33.352  26.122  -4.718  1.00  0.00              
ATOM      3  C   LEU    41      32.438  25.353  -3.691  1.00  0.00              
ATOM      4  O   LEU    41      32.346  25.731  -2.519  1.00  0.00              
ATOM      5  N   PHE    42      31.712  24.307  -4.141  1.00  0.00              
ATOM      6  CA  PHE    42      30.473  23.797  -3.462  1.00  0.00              
ATOM      7  C   PHE    42      30.075  22.347  -3.941  1.00  0.00              
ATOM      8  O   PHE    42      30.723  21.365  -3.566  1.00  0.00              
ATOM      9  N   VAL    43      29.058  22.214  -4.816  1.00  0.00              
ATOM     10  CA  VAL    43      28.713  20.956  -5.566  1.00  0.00              
ATOM     11  C   VAL    43      28.942  19.627  -4.749  1.00  0.00              
ATOM     12  O   VAL    43      29.386  18.619  -5.309  1.00  0.00              
ATOM     13  N   ASP    44      28.584  19.594  -3.449  1.00  0.00              
ATOM     14  CA  ASP    44      28.257  18.347  -2.675  1.00  0.00              
ATOM     15  C   ASP    44      27.841  17.129  -3.584  1.00  0.00              
ATOM     16  O   ASP    44      26.647  16.898  -3.817  1.00  0.00              
ATOM     17  N   ASN    45      28.804  16.309  -4.051  1.00  0.00              
ATOM     18  CA  ASN    45      28.555  14.943  -4.641  1.00  0.00              
ATOM     19  C   ASN    45      29.281  13.768  -3.889  1.00  0.00              
ATOM     20  O   ASN    45      28.772  12.642  -3.841  1.00  0.00              
ATOM     21  N   ASP    46      30.420  14.040  -3.220  1.00  0.00              
ATOM     22  CA  ASP    46      30.886  13.226  -2.046  1.00  0.00              
ATOM     23  C   ASP    46      29.941  13.378  -0.785  1.00  0.00              
ATOM     24  O   ASP    46      30.206  12.844   0.296  1.00  0.00              
ATOM     25  N   GLU    47      28.792  14.063  -0.951  1.00  0.00              
ATOM     26  CA  GLU    47      27.661  14.162   0.030  1.00  0.00              
ATOM     27  C   GLU    47      26.248  14.116  -0.667  1.00  0.00              
ATOM     28  O   GLU    47      25.214  14.089   0.005  1.00  0.00              
ATOM     29  N   GLU    48      26.208  14.042  -2.018  1.00  0.00              
ATOM     30  CA  GLU    48      24.961  13.770  -2.814  1.00  0.00              
ATOM     31  C   GLU    48      24.472  12.275  -2.727  1.00  0.00              
ATOM     32  O   GLU    48      23.295  11.978  -2.948  1.00  0.00              
ATOM     33  N   ILE    49      25.395  11.323  -2.478  1.00  0.00              
ATOM     34  CA  ILE    49      25.042   9.893  -2.166  1.00  0.00              
ATOM     35  C   ILE    49      24.573   9.697  -0.670  1.00  0.00              
ATOM     36  O   ILE    49      23.646   8.945  -0.364  1.00  0.00              
ATOM     37  N   VAL    50      25.195  10.445   0.268  1.00  0.00              
ATOM     38  CA  VAL    50      24.620  10.793   1.612  1.00  0.00              
ATOM     39  C   VAL    50      23.131  11.310   1.483  1.00  0.00              
ATOM     40  O   VAL    50      22.298  11.071   2.361  1.00  0.00              
ATOM     41  N   GLU    51      22.802  12.011   0.379  1.00  0.00              
ATOM     42  CA  GLU    51      21.478  12.670   0.142  1.00  0.00              
ATOM     43  C   GLU    51      20.386  11.609  -0.250  1.00  0.00              
ATOM     44  O   GLU    51      19.342  11.472   0.392  1.00  0.00              
ATOM     45  N   TYR    52      20.591  10.910  -1.391  1.00  0.00              
ATOM     46  CA  TYR    52      19.610   9.930  -1.966  1.00  0.00              
ATOM     47  C   TYR    52      19.475   8.611  -1.126  1.00  0.00              
ATOM     48  O   TYR    52      18.476   7.895  -1.165  1.00  0.00              
ATOM     49  N   ALA    53      20.569   8.227  -0.414  1.00  0.00              
ATOM     50  CA  ALA    53      20.523   7.240   0.715  1.00  0.00              
ATOM     51  C   ALA    53      19.867   7.793   2.042  1.00  0.00              
ATOM     52  O   ALA    53      19.279   7.038   2.822  1.00  0.00              
ATOM     53  N   VAL    54      19.924   9.122   2.247  1.00  0.00              
ATOM     54  CA  VAL    54      19.021   9.834   3.212  1.00  0.00              
ATOM     55  C   VAL    54      17.519   9.740   2.719  1.00  0.00              
ATOM     56  O   VAL    54      16.616   9.635   3.550  1.00  0.00              
ATOM     57  N   LYS    55      17.319   9.698   1.390  1.00  0.00              
ATOM     58  CA  LYS    55      15.975   9.565   0.735  1.00  0.00              
ATOM     59  C   LYS    55      15.356   8.126   0.949  1.00  0.00              
ATOM     60  O   LYS    55      14.155   7.959   1.140  1.00  0.00              
ATOM     61  N   PRO    56      16.218   7.078   0.927  1.00  0.00              
ATOM     62  CA  PRO    56      15.977   5.753   1.585  1.00  0.00              
ATOM     63  C   PRO    56      15.543   5.850   3.108  1.00  0.00              
ATOM     64  O   PRO    56      14.924   4.930   3.639  1.00  0.00              
ATOM     65  N   LEU    57      15.980   6.935   3.775  1.00  0.00              
ATOM     66  CA  LEU    57      15.414   7.392   5.091  1.00  0.00              
ATOM     67  C   LEU    57      14.171   8.347   5.016  1.00  0.00              
ATOM     68  O   LEU    57      13.449   8.539   6.002  1.00  0.00              
ATOM     69  N   LEU    58      12.035   6.939   3.182  1.00  0.00              
ATOM     70  CA  LEU    58      11.491   5.581   3.486  1.00  0.00              
ATOM     71  C   LEU    58      11.666   5.162   4.991  1.00  0.00              
ATOM     72  O   LEU    58      10.827   4.520   5.627  1.00  0.00              
ATOM     73  N   ALA    59      12.816   5.555   5.603  1.00  0.00              
ATOM     74  CA  ALA    59      12.927   5.657   7.110  1.00  0.00              
ATOM     75  C   ALA    59      11.550   6.230   7.680  1.00  0.00              
ATOM     76  O   ALA    59      10.978   5.849   8.702  1.00  0.00              
ATOM     77  N   GLN    60      10.959   7.170   6.907  1.00  0.00              
ATOM     78  CA  GLN    60       9.630   7.861   6.986  1.00  0.00              
ATOM     79  C   GLN    60       8.533   7.135   6.109  1.00  0.00              
ATOM     80  O   GLN    60       7.469   6.661   6.509  1.00  0.00              
ATOM     81  N   SER    61       8.872   6.951   4.802  1.00  0.00              
ATOM     82  CA  SER    61       8.056   6.694   3.558  1.00  0.00              
ATOM     83  C   SER    61       6.882   7.708   3.240  1.00  0.00              
ATOM     84  O   SER    61       6.464   7.881   2.093  1.00  0.00              
ATOM     85  N   GLY    62       6.324   8.322   4.295  1.00  0.00              
ATOM     86  CA  GLY    62       4.966   8.966   4.288  1.00  0.00              
ATOM     87  C   GLY    62       4.456   9.564   5.663  1.00  0.00              
ATOM     88  O   GLY    62       3.900   8.800   6.460  1.00  0.00              
ATOM     89  N   PRO    63       4.537  10.887   5.982  1.00  0.00              
ATOM     90  CA  PRO    63       3.955  11.594   7.173  1.00  0.00              
ATOM     91  C   PRO    63       3.038  10.767   8.142  1.00  0.00              
ATOM     92  O   PRO    63       1.854  11.062   8.326  1.00  0.00              
ATOM     93  N   LEU    64       3.623   9.773   8.838  1.00  0.00              
ATOM     94  CA  LEU    64       2.965   8.854   9.831  1.00  0.00              
ATOM     95  C   LEU    64       1.423   8.595   9.608  1.00  0.00              
ATOM     96  O   LEU    64       0.882   8.659   8.502  1.00  0.00              
ATOM     97  N   ASP    65       0.717   8.189  10.694  1.00  0.00              
ATOM     98  CA  ASP    65      -0.777   8.200  10.784  1.00  0.00              
ATOM     99  C   ASP    65      -1.499   9.311   9.939  1.00  0.00              
ATOM    100  O   ASP    65      -1.753   9.138   8.742  1.00  0.00              
END
