
#######################################################
#                                                     #
#                        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   28 (  112),  selected    9 , name T0287AL242_2
# Molecule2: number of CA atoms  161 ( 1345),  selected    9 , name T0287.pdb
# PARAMETERS: T0287AL242_2.T0287.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:     9        21 - 29          1.46     1.46
  LCS_AVERAGE:      5.59

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        21 - 29          1.46     1.46
  LCS_AVERAGE:      5.59

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        22 - 29          0.79     1.72
  LCS_AVERAGE:      4.62

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:  161
LCS_GDT     K      21     K      21      3    9    9     3    3    3    4    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L      22     L      22      8    9    9     4    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     I      23     I      23      8    9    9     4    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E      24     E      24      8    9    9     4    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S      25     S      25      8    9    9     4    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L      26     L      26      8    9    9     4    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Q      27     Q      27      8    9    9     4    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E      28     E      28      8    9    9     3    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     N      29     N      29      8    9    9     3    5    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   5.27  (   4.62    5.59    5.59 )

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      7      8      8      8      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.48   4.35   4.97   4.97   4.97   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59   5.59
GDT RMS_LOCAL    0.16   0.56   0.79   0.79   0.79   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46
GDT RMS_ALL_CA   1.90   1.93   1.72   1.72   1.72   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46

#      Molecule1      Molecule2       DISTANCE
LGA    K      21      K      21          3.083
LGA    L      22      L      22          1.597
LGA    I      23      I      23          0.899
LGA    E      24      E      24          1.114
LGA    S      25      S      25          0.861
LGA    L      26      L      26          0.583
LGA    Q      27      Q      27          0.419
LGA    E      28      E      28          1.796
LGA    N      29      N      29          0.725

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28  161    4.0      9    1.46     5.124     5.361     0.578

LGA_LOCAL      RMSD =  1.457  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.457  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  1.457  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.127087 * X  +  -0.984491 * Y  +  -0.120942 * Z  + 127.284378
  Y_new =  -0.076956 * X  +   0.111776 * Y  +  -0.990749 * Z  + 141.311523
  Z_new =   0.988902 * X  +   0.135218 * Y  +  -0.061557 * Z  +  53.519299 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.998003   -1.143589  [ DEG:   114.4772    -65.5228 ]
  Theta =  -1.421673   -1.719919  [ DEG:   -81.4559    -98.5441 ]
  Phi   =  -0.544484    2.597109  [ DEG:   -31.1966    148.8034 ]
 
# 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: T0287AL242_2                                  
REMARK     2: T0287.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0287AL242_2.T0287.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28  161   4.0    9   1.46   5.361     1.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0287AL242_2
REMARK Aligment from pdb entry: 1fav_C
ATOM      1  N   SER     2     121.912  74.727  53.235  1.00  0.00              
ATOM      2  CA  SER     2     121.336  75.137  54.523  1.00  0.00              
ATOM      3  C   SER     2     120.137  76.066  54.347  1.00  0.00              
ATOM      4  O   SER     2     120.230  77.087  53.663  1.00  0.00              
ATOM      5  N   ASN     3     119.016  75.729  54.980  1.00  0.00              
ATOM      6  CA  ASN     3     117.815  76.542  54.840  1.00  0.00              
ATOM      7  C   ASN     3     117.537  77.563  55.942  1.00  0.00              
ATOM      8  O   ASN     3     118.078  78.667  55.887  1.00  0.00              
ATOM      9  N   ASN     4     116.714  77.239  56.944  1.00  0.00              
ATOM     10  CA  ASN     4     116.449  78.283  57.951  1.00  0.00              
ATOM     11  C   ASN     4     117.487  78.432  59.017  1.00  0.00              
ATOM     12  O   ASN     4     117.669  79.521  59.555  1.00  0.00              
ATOM     13  N   MET     5     118.185  77.352  59.325  1.00  0.00              
ATOM     14  CA  MET     5     119.181  77.435  60.366  1.00  0.00              
ATOM     15  C   MET     5     120.392  78.262  59.991  1.00  0.00              
ATOM     16  O   MET     5     120.951  78.946  60.842  1.00  0.00              
ATOM     17  N   ARG     6     120.814  78.209  58.732  1.00  0.00              
ATOM     18  CA  ARG     6     121.972  78.999  58.347  1.00  0.00              
ATOM     19  C   ARG     6     121.556  80.457  58.151  1.00  0.00              
ATOM     20  O   ARG     6     122.408  81.355  58.128  1.00  0.00              
ATOM     21  N   LYS     7     120.249  80.691  58.014  1.00  0.00              
ATOM     22  CA  LYS     7     119.729  82.048  57.847  1.00  0.00              
ATOM     23  C   LYS     7     119.646  82.729  59.206  1.00  0.00              
ATOM     24  O   LYS     7     119.752  83.952  59.320  1.00  0.00              
ATOM     25  N   LEU     8     119.468  81.927  60.245  1.00  0.00              
ATOM     26  CA  LEU     8     119.372  82.471  61.589  1.00  0.00              
ATOM     27  C   LEU     8     120.746  82.859  62.151  1.00  0.00              
ATOM     28  O   LEU     8     120.885  83.944  62.735  1.00  0.00              
ATOM     29  N   PHE     9     121.752  81.997  61.959  1.00  0.00              
ATOM     30  CA  PHE     9     123.098  82.281  62.461  1.00  0.00              
ATOM     31  C   PHE     9     123.507  83.593  61.843  1.00  0.00              
ATOM     32  O   PHE     9     124.226  84.398  62.434  1.00  0.00              
ATOM     33  N   SER    10     123.023  83.788  60.629  1.00  0.00              
ATOM     34  CA  SER    10     123.299  84.990  59.882  1.00  0.00              
ATOM     35  C   SER    10     122.631  86.163  60.587  1.00  0.00              
ATOM     36  O   SER    10     123.295  87.104  60.995  1.00  0.00              
ATOM     37  N   MET    11     121.317  86.091  60.750  1.00  0.00              
ATOM     38  CA  MET    11     120.584  87.157  61.396  1.00  0.00              
ATOM     39  C   MET    11     121.124  87.490  62.773  1.00  0.00              
ATOM     40  O   MET    11     121.270  88.663  63.123  1.00  0.00              
ATOM     41  N   ILE    12     121.429  86.457  63.554  1.00  0.00              
ATOM     42  CA  ILE    12     121.928  86.651  64.913  1.00  0.00              
ATOM     43  C   ILE    12     123.336  87.220  64.978  1.00  0.00              
ATOM     44  O   ILE    12     123.661  87.985  65.885  1.00  0.00              
ATOM     45  N   ALA    13     124.167  86.834  64.013  1.00  0.00              
ATOM     46  CA  ALA    13     125.535  87.330  63.922  1.00  0.00              
ATOM     47  C   ALA    13     125.383  88.807  63.605  1.00  0.00              
ATOM     48  O   ALA    13     125.885  89.686  64.315  1.00  0.00              
ATOM     49  N   ASP    14     124.657  89.052  62.523  1.00  0.00              
ATOM     50  CA  ASP    14     124.386  90.391  62.046  1.00  0.00              
ATOM     51  C   ASP    14     123.696  91.186  63.143  1.00  0.00              
ATOM     52  O   ASP    14     123.897  92.397  63.263  1.00  0.00              
ATOM     53  N   SER    15     122.889  90.496  63.946  1.00  0.00              
ATOM     54  CA  SER    15     122.162  91.131  65.038  1.00  0.00              
ATOM     55  C   SER    15     123.007  91.201  66.284  1.00  0.00              
ATOM     56  O   SER    15     122.506  91.439  67.372  1.00  0.00              
ATOM     57  N   LYS    16     124.296  90.980  66.133  1.00  0.00              
ATOM     58  CA  LYS    16     125.164  91.030  67.280  1.00  0.00              
ATOM     59  C   LYS    16     126.030  92.268  67.140  1.00  0.00              
ATOM     60  O   LYS    16     126.220  93.016  68.096  1.00  0.00              
ATOM     61  N   ASP    17     126.528  92.495  65.929  1.00  0.00              
ATOM     62  CA  ASP    17     127.369  93.647  65.656  1.00  0.00              
ATOM     63  C   ASP    17     126.598  94.926  65.908  1.00  0.00              
ATOM     64  O   ASP    17     127.079  95.810  66.604  1.00  0.00              
ATOM     65  N   LYS    18     125.391  95.009  65.361  1.00  0.00              
ATOM     66  CA  LYS    18     124.546  96.187  65.538  1.00  0.00              
ATOM     67  C   LYS    18     124.341  96.479  67.012  1.00  0.00              
ATOM     68  O   LYS    18     124.521  97.615  67.445  1.00  0.00              
ATOM     69  N   LYS    19     123.967  95.461  67.786  1.00  0.00              
ATOM     70  CA  LYS    19     123.755  95.661  69.214  1.00  0.00              
ATOM     71  C   LYS    19     125.049  96.109  69.873  1.00  0.00              
ATOM     72  O   LYS    19     125.041  96.853  70.858  1.00  0.00              
ATOM     73  N   GLU    20     126.159  95.646  69.311  1.00  0.00              
ATOM     74  CA  GLU    20     127.495  95.978  69.794  1.00  0.00              
ATOM     75  C   GLU    20     127.820  97.426  69.447  1.00  0.00              
ATOM     76  O   GLU    20     128.497  98.126  70.195  1.00  0.00              
ATOM     77  N   LYS    21     127.322  97.860  68.295  1.00  0.00              
ATOM     78  CA  LYS    21     127.539  99.210  67.792  1.00  0.00              
ATOM     79  C   LYS    21     126.635 100.247  68.464  1.00  0.00              
ATOM     80  O   LYS    21     127.119 101.267  68.958  1.00  0.00              
ATOM     81  N   LEU    22     125.328  99.971  68.471  1.00  0.00              
ATOM     82  CA  LEU    22     124.292 100.839  69.056  1.00  0.00              
ATOM     83  C   LEU    22     124.654 101.298  70.468  1.00  0.00              
ATOM     84  O   LEU    22     124.358 102.420  70.864  1.00  0.00              
ATOM     85  N   ILE    23     125.293 100.418  71.224  1.00  0.00              
ATOM     86  CA  ILE    23     125.677 100.727  72.586  1.00  0.00              
ATOM     87  C   ILE    23     126.861 101.672  72.602  1.00  0.00              
ATOM     88  O   ILE    23     126.954 102.546  73.458  1.00  0.00              
ATOM     89  N   GLU    24     127.770 101.480  71.656  1.00  0.00              
ATOM     90  CA  GLU    24     128.952 102.312  71.547  1.00  0.00              
ATOM     91  C   GLU    24     128.449 103.724  71.420  1.00  0.00              
ATOM     92  O   GLU    24     128.686 104.561  72.284  1.00  0.00              
ATOM     93  N   SER    25     127.733 103.967  70.328  1.00  0.00              
ATOM     94  CA  SER    25     127.169 105.275  70.037  1.00  0.00              
ATOM     95  C   SER    25     126.389 105.869  71.207  1.00  0.00              
ATOM     96  O   SER    25     126.522 107.052  71.519  1.00  0.00              
ATOM     97  N   LEU    26     125.573 105.040  71.846  1.00  0.00              
ATOM     98  CA  LEU    26     124.761 105.466  72.974  1.00  0.00              
ATOM     99  C   LEU    26     125.628 106.070  74.070  1.00  0.00              
ATOM    100  O   LEU    26     125.208 106.991  74.771  1.00  0.00              
ATOM    101  N   GLN    27     126.842 105.541  74.209  1.00  0.00              
ATOM    102  CA  GLN    27     127.793 106.030  75.204  1.00  0.00              
ATOM    103  C   GLN    27     128.327 107.376  74.731  1.00  0.00              
ATOM    104  O   GLN    27     128.376 108.356  75.484  1.00  0.00              
ATOM    105  N   GLU    28     128.718 107.424  73.464  1.00  0.00              
ATOM    106  CA  GLU    28     129.245 108.655  72.890  1.00  0.00              
ATOM    107  C   GLU    28     128.070 109.629  72.692  1.00  0.00              
ATOM    108  O   GLU    28     127.876 110.232  71.651  1.00  0.00              
ATOM    109  N   ASN    29     127.283 109.785  73.748  1.00  0.00              
ATOM    110  CA  ASN    29     126.119 110.656  73.724  1.00  0.00              
ATOM    111  C   ASN    29     126.295 111.606  74.882  1.00  0.00              
ATOM    112  O   ASN    29     126.836 111.088  75.885  1.00  0.00              
END
