
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0299AL381_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   22 , name T0299_D1.pdb
# PARAMETERS: T0299AL381_1-D1.T0299_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:    22        57 - 78          2.65     2.65
  LCS_AVERAGE:     24.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        57 - 73          1.90     4.10
  LCS_AVERAGE:     16.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        57 - 69          0.90     6.09
  LCS_AVERAGE:     10.94

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:   91
LCS_GDT     V      57     V      57     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     E      58     E      58     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     K      59     K      59     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     L      60     L      60     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     E      61     E      61     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     T      62     T      62     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     F      63     F      63     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     F      64     F      64     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     A      65     A      65     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     V      66     V      66     13   17   22    10   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     H      67     H      67     13   17   22     6   11   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     Y      68     Y      68     13   17   22     4    7   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     P      69     P      69     13   17   22     4    6   13   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     F      70     F      70      4   17   22     3    3    7   13   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     I      71     I      71      4   17   22     1    3    4    6   14   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     Q      72     Q      72      6   17   22     3    5    6   10   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     S      73     S      73      6   17   22     3    5    7   10   15   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     F      74     F      74      6    9   22     3    5    7    8   14   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     S      75     S      75      6    9   22     3    5    7    8   14   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     L      76     L      76      6    9   22     3    5    7    7   11   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     L      77     L      77      6    9   22     3    5    7    7   11   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_GDT     S      78     S      78      6    9   22     3    5    7    7   11   17   20   22   22   22   22   22   22   22   22   22   22   22   22   22 
LCS_AVERAGE  LCS_A:  17.27  (  10.94   16.68   24.18 )

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     10     11     13     13     15     17     20     22     22     22     22     22     22     22     22     22     22     22     22     22 
GDT PERCENT_CA  10.99  12.09  14.29  14.29  16.48  18.68  21.98  24.18  24.18  24.18  24.18  24.18  24.18  24.18  24.18  24.18  24.18  24.18  24.18  24.18
GDT RMS_LOCAL    0.23   0.35   0.90   0.90   1.42   1.90   2.48   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65
GDT RMS_ALL_CA   6.86   6.71   6.09   6.09   5.23   4.10   2.68   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65   2.65

#      Molecule1      Molecule2       DISTANCE
LGA    V      57      V      57          3.913
LGA    E      58      E      58          3.136
LGA    K      59      K      59          1.327
LGA    L      60      L      60          2.176
LGA    E      61      E      61          2.886
LGA    T      62      T      62          1.982
LGA    F      63      F      63          2.117
LGA    F      64      F      64          2.177
LGA    A      65      A      65          1.657
LGA    V      66      V      66          1.962
LGA    H      67      H      67          2.976
LGA    Y      68      Y      68          3.577
LGA    P      69      P      69          2.362
LGA    F      70      F      70          2.035
LGA    I      71      I      71          2.420
LGA    Q      72      Q      72          3.588
LGA    S      73      S      73          1.627
LGA    F      74      F      74          2.338
LGA    S      75      S      75          2.288
LGA    L      76      L      76          3.321
LGA    L      77      L      77          3.258
LGA    S      78      S      78          3.135

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22   91    4.0     22    2.65    18.681    18.948     0.800

LGA_LOCAL      RMSD =  2.651  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.651  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  2.651  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.193571 * X  +   0.296497 * Y  +  -0.935211 * Z  +  -4.638315
  Y_new =  -0.609045 * X  +  -0.783637 * Y  +  -0.122382 * Z  +  81.296967
  Z_new =  -0.769152 * X  +   0.545897 * Y  +   0.332269 * Z  + -13.315965 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.024029   -2.117564  [ DEG:    58.6725   -121.3275 ]
  Theta =   0.877512    2.264080  [ DEG:    50.2778    129.7222 ]
  Phi   =  -1.878526    1.263067  [ DEG:  -107.6316     72.3684 ]
 
# 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: T0299AL381_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_1-D1.T0299_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22   91   4.0   22   2.65  18.948     2.65
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_1-D1
REMARK Aligment from pdb entry: 1atg
ATOM      1  N   VAL    57     -11.567  45.739   5.283  1.00  0.00              
ATOM      2  CA  VAL    57     -10.327  45.067   4.901  1.00  0.00              
ATOM      3  C   VAL    57      -9.522  44.695   6.143  1.00  0.00              
ATOM      4  O   VAL    57      -8.867  43.640   6.130  1.00  0.00              
ATOM      5  N   GLU    58      -9.565  45.493   7.211  1.00  0.00              
ATOM      6  CA  GLU    58      -8.877  45.114   8.449  1.00  0.00              
ATOM      7  C   GLU    58      -9.486  43.833   8.991  1.00  0.00              
ATOM      8  O   GLU    58      -8.765  42.922   9.434  1.00  0.00              
ATOM      9  N   LYS    59     -10.808  43.716   8.981  1.00  0.00              
ATOM     10  CA  LYS    59     -11.467  42.488   9.412  1.00  0.00              
ATOM     11  C   LYS    59     -11.065  41.325   8.512  1.00  0.00              
ATOM     12  O   LYS    59     -10.752  40.221   9.003  1.00  0.00              
ATOM     13  N   LEU    60     -11.087  41.524   7.204  1.00  0.00              
ATOM     14  CA  LEU    60     -10.722  40.477   6.256  1.00  0.00              
ATOM     15  C   LEU    60      -9.279  40.034   6.425  1.00  0.00              
ATOM     16  O   LEU    60      -9.016  38.823   6.454  1.00  0.00              
ATOM     17  N   GLU    61      -8.352  40.976   6.503  1.00  0.00              
ATOM     18  CA  GLU    61      -6.941  40.664   6.705  1.00  0.00              
ATOM     19  C   GLU    61      -6.746  39.875   7.988  1.00  0.00              
ATOM     20  O   GLU    61      -5.989  38.877   8.009  1.00  0.00              
ATOM     21  N   THR    62      -7.414  40.195   9.079  1.00  0.00              
ATOM     22  CA  THR    62      -7.336  39.480  10.340  1.00  0.00              
ATOM     23  C   THR    62      -7.775  38.030  10.155  1.00  0.00              
ATOM     24  O   THR    62      -7.114  37.094  10.641  1.00  0.00              
ATOM     25  N   PHE    63      -8.888  37.813   9.458  1.00  0.00              
ATOM     26  CA  PHE    63      -9.357  36.452   9.221  1.00  0.00              
ATOM     27  C   PHE    63      -8.417  35.701   8.296  1.00  0.00              
ATOM     28  O   PHE    63      -8.140  34.502   8.542  1.00  0.00              
ATOM     29  N   PHE    64      -7.889  36.314   7.256  1.00  0.00              
ATOM     30  CA  PHE    64      -6.988  35.655   6.321  1.00  0.00              
ATOM     31  C   PHE    64      -5.721  35.231   7.044  1.00  0.00              
ATOM     32  O   PHE    64      -5.163  34.151   6.789  1.00  0.00              
ATOM     33  N   ALA    65      -5.243  36.073   7.961  1.00  0.00              
ATOM     34  CA  ALA    65      -4.064  35.756   8.770  1.00  0.00              
ATOM     35  C   ALA    65      -4.344  34.602   9.710  1.00  0.00              
ATOM     36  O   ALA    65      -3.506  33.677   9.816  1.00  0.00              
ATOM     37  N   VAL    66      -5.479  34.563  10.373  1.00  0.00              
ATOM     38  CA  VAL    66      -5.831  33.455  11.250  1.00  0.00              
ATOM     39  C   VAL    66      -5.855  32.156  10.449  1.00  0.00              
ATOM     40  O   VAL    66      -5.347  31.117  10.902  1.00  0.00              
ATOM     41  N   HIS    67      -6.476  32.171   9.272  1.00  0.00              
ATOM     42  CA  HIS    67      -6.596  30.959   8.482  1.00  0.00              
ATOM     43  C   HIS    67      -5.309  30.471   7.859  1.00  0.00              
ATOM     44  O   HIS    67      -5.101  29.243   7.824  1.00  0.00              
ATOM     45  N   TYR    68      -4.472  31.338   7.331  1.00  0.00              
ATOM     46  CA  TYR    68      -3.324  30.994   6.535  1.00  0.00              
ATOM     47  C   TYR    68      -1.966  31.324   7.120  1.00  0.00              
ATOM     48  O   TYR    68      -0.961  30.869   6.577  1.00  0.00              
ATOM     49  N   PRO    69      -1.937  32.177   8.135  1.00  0.00              
ATOM     50  CA  PRO    69      -0.673  32.598   8.725  1.00  0.00              
ATOM     51  C   PRO    69      -0.052  33.768   7.977  1.00  0.00              
ATOM     52  O   PRO    69       0.992  34.281   8.396  1.00  0.00              
ATOM     53  N   PHE    70      -0.657  34.199   6.876  1.00  0.00              
ATOM     54  CA  PHE    70      -0.140  35.301   6.087  1.00  0.00              
ATOM     55  C   PHE    70      -0.632  36.641   6.637  1.00  0.00              
ATOM     56  O   PHE    70      -1.826  36.831   6.873  1.00  0.00              
ATOM     57  N   ILE    71       0.304  37.570   6.773  1.00  0.00              
ATOM     58  CA  ILE    71      -0.007  38.916   7.237  1.00  0.00              
ATOM     59  C   ILE    71      -0.022  39.861   6.039  1.00  0.00              
ATOM     60  O   ILE    71       0.714  39.717   5.066  1.00  0.00              
ATOM     61  N   GLN    72      -0.945  40.814   6.074  1.00  0.00              
ATOM     62  CA  GLN    72      -1.082  41.792   4.997  1.00  0.00              
ATOM     63  C   GLN    72      -0.741  43.173   5.550  1.00  0.00              
ATOM     64  O   GLN    72      -1.047  43.427   6.711  1.00  0.00              
ATOM     65  N   SER    73      -0.133  44.017   4.737  1.00  0.00              
ATOM     66  CA  SER    73       0.151  45.397   5.106  1.00  0.00              
ATOM     67  C   SER    73      -0.861  46.255   4.347  1.00  0.00              
ATOM     68  O   SER    73      -0.855  46.237   3.124  1.00  0.00              
ATOM     69  N   PHE    74      -1.724  46.949   5.073  1.00  0.00              
ATOM     70  CA  PHE    74      -2.775  47.756   4.474  1.00  0.00              
ATOM     71  C   PHE    74      -2.398  49.232   4.379  1.00  0.00              
ATOM     72  O   PHE    74      -1.928  49.810   5.356  1.00  0.00              
ATOM     73  N   SER    75      -2.697  49.819   3.239  1.00  0.00              
ATOM     74  CA  SER    75      -2.607  51.252   3.030  1.00  0.00              
ATOM     75  C   SER    75      -3.977  51.713   2.498  1.00  0.00              
ATOM     76  O   SER    75      -4.720  50.880   1.950  1.00  0.00              
ATOM     77  N   LEU    76      -4.276  53.001   2.611  1.00  0.00              
ATOM     78  CA  LEU    76      -5.580  53.458   2.121  1.00  0.00              
ATOM     79  C   LEU    76      -5.553  54.897   1.637  1.00  0.00              
ATOM     80  O   LEU    76      -4.668  55.670   2.063  1.00  0.00              
ATOM     81  N   LEU    77      -6.483  55.221   0.768  1.00  0.00              
ATOM     82  CA  LEU    77      -6.623  56.594   0.277  1.00  0.00              
ATOM     83  C   LEU    77      -7.849  56.626  -0.622  1.00  0.00              
ATOM     84  O   LEU    77      -8.514  55.580  -0.783  1.00  0.00              
ATOM     85  N   SER    78      -8.218  57.772  -1.169  1.00  0.00              
ATOM     86  CA ASER    78      -9.323  57.869  -2.102  1.00  0.00              
ATOM     87  C   SER    78      -8.946  57.104  -3.367  1.00  0.00              
ATOM     88  O   SER    78      -7.754  57.054  -3.733  1.00  0.00              
END
