
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0318AL381_5-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   19 , name T0318_D1.pdb
# PARAMETERS: T0318AL381_5-D1.T0318_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:    13       137 - 149         4.41    14.21
  LCS_AVERAGE:      8.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       138 - 147         1.73    16.67
  LCS_AVERAGE:      4.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       139 - 145         0.80    15.27
  LCS_AVERAGE:      3.14

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:  154
LCS_GDT     K     137     K     137      3    4   13     3    3    4    4    4    4    6    9    9   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     T     138     T     138      3   10   13     3    3    5    6    8   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     S     139     S     139      7   10   13     3    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     G     140     G     140      7   10   13     3    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     I     141     I     141      7   10   13     4    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     R     142     R     142      7   10   13     4    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     E     143     E     143      7   10   13     4    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     L     144     L     144      7   10   13     4    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     N     145     N     145      7   10   13     4    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     V     146     V     146      6   10   13     3    4    6    7    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     N     147     N     147      4   10   13     3    6    8    8    9   10   10   10   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     I     148     I     148      4    6   13     0    4    4    6    6    6    6    8   10   11   12   12   12   12   13   13   13   13   13   13 
LCS_GDT     D     149     D     149      4    6   13     0    4    4    6    6    6    6    8    9   10   10   10   10   11   13   13   13   13   13   13 
LCS_GDT     V     150     V     150      4    6   11     3    4    4    6    6    6    6    8    9   10   10   10   10   10   11   11   11   11   11   11 
LCS_GDT     V     151     V     151      3    6   11     3    3    3    6    6    6    6    8    9   10   10   10   10   10   11   11   11   11   11   11 
LCS_GDT     C     152     C     152      3    4   11     3    3    4    4    4    5    5    7    9   10   10   10   10   10   11   11   11   11   11   11 
LCS_GDT     D     153     D     153      3    4   11     3    3    4    4    4    5    5    8    9   10   10   10   10   10   11   11   11   11   11   11 
LCS_GDT     K     154     K     154      3    4   11     3    3    4    4    4    5    6    8    9   10   10   10   10   10   11   11   11   11   11   11 
LCS_GDT     L     155     L     155      3    4   11     3    3    4    4    5    5    6    8    9   10   10   10   10   10   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   5.37  (   3.14    4.92    8.03 )

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      8      8      9     10     10     10     10     11     12     12     12     12     13     13     13     13     13     13 
GDT PERCENT_CA   2.60   3.90   5.19   5.19   5.84   6.49   6.49   6.49   6.49   7.14   7.79   7.79   7.79   7.79   8.44   8.44   8.44   8.44   8.44   8.44
GDT RMS_LOCAL    0.35   0.57   0.89   0.89   1.37   1.73   1.73   1.73   1.73   2.60   3.43   3.43   3.43   3.43   4.41   4.41   4.41   4.41   4.41   4.41
GDT RMS_ALL_CA  16.17  16.29  15.76  15.76  16.21  16.67  16.67  16.67  16.67  15.38  14.43  14.43  14.43  14.43  14.21  14.21  14.21  14.21  14.21  14.21

#      Molecule1      Molecule2       DISTANCE
LGA    K     137      K     137          9.992
LGA    T     138      T     138          2.882
LGA    S     139      S     139          1.407
LGA    G     140      G     140          2.104
LGA    I     141      I     141          0.858
LGA    R     142      R     142          0.588
LGA    E     143      E     143          1.542
LGA    L     144      L     144          0.732
LGA    N     145      N     145          0.696
LGA    V     146      V     146          2.771
LGA    N     147      N     147          1.741
LGA    I     148      I     148          7.768
LGA    D     149      D     149         12.561
LGA    V     150      V     150         19.016
LGA    V     151      V     151         21.763
LGA    C     152      C     152         25.215
LGA    D     153      D     153         31.922
LGA    K     154      K     154         35.375
LGA    L     155      L     155         34.534

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  154    4.0     10    1.73     6.006     5.992     0.547

LGA_LOCAL      RMSD =  1.729  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.673  Number of atoms =   19 
Std_ALL_ATOMS  RMSD = 10.955  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.381253 * X  +  -0.412855 * Y  +   0.827162 * Z  +  37.845940
  Y_new =  -0.625722 * X  +  -0.773884 * Y  +  -0.097858 * Z  +  88.778687
  Z_new =   0.680528 * X  +  -0.480265 * Y  +  -0.553378 * Z  +   4.813432 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.426810    0.714782  [ DEG:  -139.0460     40.9540 ]
  Theta =  -0.748484   -2.393109  [ DEG:   -42.8849   -137.1151 ]
  Phi   =  -1.023566    2.118026  [ DEG:   -58.6460    121.3540 ]
 
# 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: T0318AL381_5-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318AL381_5-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  154   4.0   10   1.73   5.992    10.95
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL381_5-D1
REMARK Aligment from pdb entry: 1t4mA
ATOM      1  N   LYS   137      36.681  72.859   9.037  1.00  0.00              
ATOM      2  CA  LYS   137      36.528  71.425   8.656  1.00  0.00              
ATOM      3  C   LYS   137      35.171  70.897   9.112  1.00  0.00              
ATOM      4  O   LYS   137      34.662  71.304  10.158  1.00  0.00              
ATOM      5  N   THR   138      34.577  70.002   8.327  1.00  0.00              
ATOM      6  CA  THR   138      33.314  69.404   8.734  1.00  0.00              
ATOM      7  C   THR   138      33.710  68.430   9.836  1.00  0.00              
ATOM      8  O   THR   138      34.876  68.032   9.929  1.00  0.00              
ATOM      9  N   SER   139      32.759  68.047  10.699  1.00  0.00              
ATOM     10  CA  SER   139      33.140  67.097  11.744  1.00  0.00              
ATOM     11  C   SER   139      33.477  65.792  11.018  1.00  0.00              
ATOM     12  O   SER   139      32.964  65.534   9.928  1.00  0.00              
ATOM     13  N   GLY   140      34.343  64.985  11.607  1.00  0.00              
ATOM     14  CA  GLY   140      34.720  63.721  10.989  1.00  0.00              
ATOM     15  C   GLY   140      34.100  62.557  11.745  1.00  0.00              
ATOM     16  O   GLY   140      34.201  62.474  12.975  1.00  0.00              
ATOM     17  N   ILE   141      33.431  61.681  11.005  1.00  0.00              
ATOM     18  CA  ILE   141      32.812  60.496  11.580  1.00  0.00              
ATOM     19  C   ILE   141      33.640  59.268  11.165  1.00  0.00              
ATOM     20  O   ILE   141      33.828  59.000   9.971  1.00  0.00              
ATOM     21  N   ARG   142      34.135  58.533  12.154  1.00  0.00              
ATOM     22  CA  ARG   142      34.957  57.357  11.891  1.00  0.00              
ATOM     23  C   ARG   142      34.197  56.065  12.129  1.00  0.00              
ATOM     24  O   ARG   142      33.569  55.883  13.165  1.00  0.00              
ATOM     25  N   GLU   143      34.272  55.173  11.142  1.00  0.00              
ATOM     26  CA  GLU   143      33.541  53.911  11.149  1.00  0.00              
ATOM     27  C   GLU   143      34.418  52.661  11.139  1.00  0.00              
ATOM     28  O   GLU   143      35.112  52.388  10.156  1.00  0.00              
ATOM     29  N   LEU   144      34.349  51.887  12.221  1.00  0.00              
ATOM     30  CA  LEU   144      35.143  50.670  12.353  1.00  0.00              
ATOM     31  C   LEU   144      34.594  49.466  11.599  1.00  0.00              
ATOM     32  O   LEU   144      33.474  49.477  11.093  1.00  0.00              
ATOM     33  N   ASN   145      35.407  48.420  11.531  1.00  0.00              
ATOM     34  CA  ASN   145      34.994  47.218  10.838  1.00  0.00              
ATOM     35  C   ASN   145      34.537  46.135  11.792  1.00  0.00              
ATOM     36  O   ASN   145      34.263  46.391  12.970  1.00  0.00              
ATOM     37  N   VAL   146      34.460  44.919  11.264  1.00  0.00              
ATOM     38  CA  VAL   146      34.031  43.749  12.015  1.00  0.00              
ATOM     39  C   VAL   146      34.914  43.507  13.234  1.00  0.00              
ATOM     40  O   VAL   146      36.145  43.486  13.136  1.00  0.00              
ATOM     41  N   ASN   147      34.264  43.329  14.380  1.00  0.00              
ATOM     42  CA  ASN   147      34.973  43.088  15.625  1.00  0.00              
ATOM     43  C   ASN   147      35.771  44.284  16.107  1.00  0.00              
ATOM     44  O   ASN   147      36.552  44.172  17.051  1.00  0.00              
ATOM     45  N   ILE   148      35.566  45.432  15.466  1.00  0.00              
ATOM     46  CA  ILE   148      36.285  46.637  15.843  1.00  0.00              
ATOM     47  C   ILE   148      35.573  47.517  16.859  1.00  0.00              
ATOM     48  O   ILE   148      34.520  47.172  17.396  1.00  0.00              
ATOM     49  N   ASP   149      36.152  48.678  17.118  1.00  0.00              
ATOM     50  CA  ASP   149      35.580  49.602  18.086  1.00  0.00              
ATOM     51  C   ASP   149      36.010  51.016  17.764  1.00  0.00              
ATOM     52  O   ASP   149      36.938  51.234  16.971  1.00  0.00              
ATOM     53  N   VAL   150      35.337  51.977  18.383  1.00  0.00              
ATOM     54  CA  VAL   150      35.668  53.379  18.167  1.00  0.00              
ATOM     55  C   VAL   150      37.143  53.598  18.523  1.00  0.00              
ATOM     56  O   VAL   150      37.820  54.421  17.908  1.00  0.00              
ATOM     57  N   VAL   151      37.622  52.844  19.514  1.00  0.00              
ATOM     58  CA  VAL   151      39.007  52.919  19.988  1.00  0.00              
ATOM     59  C   VAL   151      40.038  52.713  18.888  1.00  0.00              
ATOM     60  O   VAL   151      41.164  53.200  18.987  1.00  0.00              
ATOM     61  N   CYS   152      39.648  51.988  17.846  1.00  0.00              
ATOM     62  CA  CYS   152      40.537  51.698  16.726  1.00  0.00              
ATOM     63  C   CYS   152      41.053  52.958  16.055  1.00  0.00              
ATOM     64  O   CYS   152      42.075  52.934  15.357  1.00  0.00              
ATOM     65  N   ASP   153      40.349  54.061  16.274  1.00  0.00              
ATOM     66  CA  ASP   153      40.722  55.313  15.643  1.00  0.00              
ATOM     67  C   ASP   153      41.566  56.283  16.448  1.00  0.00              
ATOM     68  O   ASP   153      41.666  57.454  16.090  1.00  0.00              
ATOM     69  N   LYS   154      42.190  55.799  17.518  1.00  0.00              
ATOM     70  CA  LYS   154      43.030  56.660  18.354  1.00  0.00              
ATOM     71  C   LYS   154      44.140  57.313  17.532  1.00  0.00              
ATOM     72  O   LYS   154      44.369  58.520  17.624  1.00  0.00              
ATOM     73  N   LEU   155      44.826  56.513  16.728  1.00  0.00              
ATOM     74  CA  LEU   155      45.901  57.044  15.908  1.00  0.00              
ATOM     75  C   LEU   155      45.448  58.116  14.928  1.00  0.00              
ATOM     76  O   LEU   155      46.032  59.193  14.862  1.00  0.00              
END
