
#######################################################
#                                                     #
#                        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   32 (  128),  selected   28 , name T0320AL044_4-D2
# Molecule2: number of CA atoms   73 (  604),  selected   28 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_4-D2.T0320_D2.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:    11       243 - 263         4.48    23.75
  LCS_AVERAGE:     13.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       228 - 232         1.80    35.46
  LONGEST_CONTINUOUS_SEGMENT:     5       264 - 269         1.54    33.19
  LCS_AVERAGE:      4.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       228 - 230         0.22    38.13
  LONGEST_CONTINUOUS_SEGMENT:     3       229 - 231         0.16    39.95
  LONGEST_CONTINUOUS_SEGMENT:     3       230 - 232         0.90    33.30
  LONGEST_CONTINUOUS_SEGMENT:     3       231 - 233         0.37    34.23
  LONGEST_CONTINUOUS_SEGMENT:     3       232 - 234         0.35    39.29
  LONGEST_CONTINUOUS_SEGMENT:     3       233 - 236         0.63    36.43
  LONGEST_CONTINUOUS_SEGMENT:     3       249 - 251         0.76    30.35
  LONGEST_CONTINUOUS_SEGMENT:     3       250 - 252         0.86    26.64
  LONGEST_CONTINUOUS_SEGMENT:     3       256 - 258         0.25    33.75
  LONGEST_CONTINUOUS_SEGMENT:     3       263 - 265         0.49    33.20
  LONGEST_CONTINUOUS_SEGMENT:     3       264 - 266         0.50    38.08
  LONGEST_CONTINUOUS_SEGMENT:     3       265 - 267         0.04    27.69
  LONGEST_CONTINUOUS_SEGMENT:     3       266 - 269         0.94    28.13
  LCS_AVERAGE:      3.08

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:   73
LCS_GDT     N     228     N     228      3    5   10     3    3    3    4    4    5    6    7    9   10   10   10   12   14   17   17   19   19   19   20 
LCS_GDT     N     229     N     229      3    5   10     3    3    3    4    4    5    6    7    8   10   10   10   11   14   17   17   19   19   19   20 
LCS_GDT     S     230     S     230      3    5   10     3    3    3    4    5    5    6    7    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     L     231     L     231      3    5   10     3    3    3    4    5    5    6    7    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     P     232     P     232      3    5   10     3    3    3    4    5    5    6    7    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     N     233     N     233      3    4   10     3    3    3    4    5    5    6    7    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     P     234     P     234      3    4   10     3    3    3    4    4    4    5    7    8    8    9   10   11   14   17   17   19   19   19   20 
LCS_GDT     L     236     L     236      3    3   10     0    3    3    4    4    4    6    7    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     S     240     S     240      0    3   10     0    0    0    0    3    3    3    4    4    5    7    9   11   12   15   17   19   19   19   20 
LCS_GDT     P     243     P     243      0    3   11     0    1    1    4    6    6    7    8    9    9   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     L     245     L     245      0    3   11     2    3    3    4    6    6    7    8    9    9   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     H     246     H     246      0    4   11     0    1    3    4    4    5    7    8    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     W     249     W     249      3    4   11     0    3    4    4    4    5    7    8    9    9    9   10   13   14   17   17   19   19   19   20 
LCS_GDT     E     250     E     250      3    4   11     2    3    4    4    6    6    7    8    9    9    9   11   13   14   17   17   19   19   19   20 
LCS_GDT     I     251     I     251      3    4   11     1    3    4    4    6    6    7    8    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     I     252     I     252      3    4   11     1    3    4    4    6    6    7    8    9    9   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     G     256     G     256      3    3   11     3    3    3    3    3    4    4    5    6    8    8    9   10   10   15   16   19   19   19   19 
LCS_GDT     K     257     K     257      3    3   11     3    3    3    3    6    6    7    7    9   10   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     D     258     D     258      3    3   11     3    3    3    3    4    5    7    8    9    9   10   11   13   14   17   17   19   19   19   20 
LCS_GDT     R     263     R     263      3    3   11     3    3    3    3    3    4    5    6    6    7    9   10   11   11   14   17   17   18   19   20 
LCS_GDT     S     264     S     264      3    5    8     3    3    3    5    5    5    5    6    6    7    8    9    9   10   10   11   12   12   18   20 
LCS_GDT     S     265     S     265      3    5    8     3    3    3    5    5    5    5    6    6    7    8    9    9   10   10   11   12   12   12   12 
LCS_GDT     A     266     A     266      3    5    8     3    3    3    5    5    5    5    6    6    7    8    9    9   10   10   11   12   12   12   12 
LCS_GDT     I     267     I     267      3    5    8     3    3    3    5    5    5    5    6    6    7    7    9    9   10   10   11   12   12   12   12 
LCS_GDT     T     269     T     269      3    5    8     0    0    3    5    5    5    5    6    6    7    8    9    9   10   10   11   12   12   12   12 
LCS_GDT     V     274     V     274      0    0    8     0    0    0    0    2    3    3    3    3    4    4    4    7   10   10   11   12   12   12   12 
LCS_GDT     K     277     K     277      0    0    8     0    1    1    1    2    3    3    3    4    6    8    9    9   10   10   11   12   12   12   12 
LCS_GDT     S     281     S     281      0    0    4     0    0    0    0    0    3    3    3    4    7    8    9    9   10   10   11   12   12   12   12 
LCS_AVERAGE  LCS_A:   7.11  (   3.08    4.99   13.26 )

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      3      3      4      5      6      6      7      8      9     10     10     11     13     14     17     17     19     19     19     20 
GDT PERCENT_CA   4.11   4.11   5.48   6.85   8.22   8.22   9.59  10.96  12.33  13.70  13.70  15.07  17.81  19.18  23.29  23.29  26.03  26.03  26.03  27.40
GDT RMS_LOCAL    0.04   0.04   1.27   1.54   1.65   1.65   2.34   2.86   3.03   3.68   3.68   4.30   4.82   4.96   5.63   5.63   6.06   6.06   6.06   6.85
GDT RMS_ALL_CA  27.69  27.69  29.03  33.19  24.95  24.95  26.35  23.84  24.36  17.23  17.23  17.79  18.67  17.62  17.69  17.69  18.39  18.39  18.39  16.41

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228         34.663
LGA    N     229      N     229         32.546
LGA    S     230      S     230         30.164
LGA    L     231      L     231         27.776
LGA    P     232      P     232         22.700
LGA    N     233      N     233         17.197
LGA    P     234      P     234         17.876
LGA    L     236      L     236         14.067
LGA    S     240      S     240         12.230
LGA    P     243      P     243          2.592
LGA    L     245      L     245          1.186
LGA    H     246      H     246          3.510
LGA    W     249      W     249          3.951
LGA    E     250      E     250          3.098
LGA    I     251      I     251          2.128
LGA    I     252      I     252          1.368
LGA    G     256      G     256          9.219
LGA    K     257      K     257          4.813
LGA    D     258      D     258          3.681
LGA    R     263      R     263         10.068
LGA    S     264      S     264         14.072
LGA    S     265      S     265         20.267
LGA    A     266      A     266         23.499
LGA    I     267      I     267         28.266
LGA    T     269      T     269         35.299
LGA    V     274      V     274         45.038
LGA    K     277      K     277         46.703
LGA    S     281      S     281         52.968

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   73    4.0      8    2.86    11.301     9.551     0.270

LGA_LOCAL      RMSD =  2.864  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.842  Number of atoms =   28 
Std_ALL_ATOMS  RMSD = 13.979  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.622849 * X  +   0.626563 * Y  +  -0.468485 * Z  +   0.457447
  Y_new =  -0.733886 * X  +  -0.260460 * Y  +   0.627353 * Z  +  14.496953
  Z_new =   0.271055 * X  +   0.734560 * Y  +   0.622054 * Z  + -105.970551 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.868141   -2.273452  [ DEG:    49.7408   -130.2592 ]
  Theta =  -0.274489   -2.867104  [ DEG:   -15.7270   -164.2730 ]
  Phi   =  -2.274535    0.867058  [ DEG:  -130.3212     49.6788 ]
 
# 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: T0320AL044_4-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_4-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   73   4.0    8   2.86   9.551    13.98
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_4-D2
REMARK Aligment from pdb entry: 2c5s_A
ATOM    753  N   ASN   228       3.446  13.797 -12.204  1.00  0.00              
ATOM    754  CA  ASN   228       2.160  13.135 -11.957  1.00  0.00              
ATOM    755  C   ASN   228       2.111  12.584 -10.528  1.00  0.00              
ATOM    756  O   ASN   228       2.592  11.475 -10.267  1.00  0.00              
ATOM    757  N   ASN   229       1.550  13.364  -9.592  1.00  0.00              
ATOM    758  CA  ASN   229       1.481  12.927  -8.200  1.00  0.00              
ATOM    759  C   ASN   229       0.582  11.707  -7.999  1.00  0.00              
ATOM    760  O   ASN   229      -0.504  11.631  -8.579  1.00  0.00              
ATOM    761  N   SER   230       1.052  10.766  -7.186  1.00  0.00              
ATOM    762  CA  SER   230       0.288   9.582  -6.828  1.00  0.00              
ATOM    763  C   SER   230      -0.202   9.696  -5.380  1.00  0.00              
ATOM    764  O   SER   230       0.456  10.320  -4.545  1.00  0.00              
ATOM    765  N   LEU   231      -1.352   9.083  -5.094  1.00  0.00              
ATOM    766  CA  LEU   231      -1.920   9.018  -3.737  1.00  0.00              
ATOM    767  C   LEU   231      -1.027   8.280  -2.701  1.00  0.00              
ATOM    768  O   LEU   231      -0.870   8.735  -1.567  1.00  0.00              
ATOM    769  N   PRO   232      -0.424   7.170  -3.117  1.00  0.00              
ATOM    770  CA  PRO   232       0.498   6.402  -2.286  1.00  0.00              
ATOM    771  C   PRO   232       1.648   7.243  -1.715  1.00  0.00              
ATOM    772  O   PRO   232       1.949   7.158  -0.525  1.00  0.00              
ATOM    773  N   ASN   233       2.282   8.050  -2.561  1.00  0.00              
ATOM    774  CA  ASN   233       3.393   8.880  -2.113  1.00  0.00              
ATOM    775  C   ASN   233       2.892  10.060  -1.293  1.00  0.00              
ATOM    776  O   ASN   233       3.507  10.412  -0.284  1.00  0.00              
ATOM    777  N   PRO   234       1.779  10.663  -1.705  1.00  0.00              
ATOM    778  CA  PRO   234       1.215  11.767  -0.942  1.00  0.00              
ATOM    779  C   PRO   234       0.913  11.327   0.494  1.00  0.00              
ATOM    780  O   PRO   234       1.182  12.059   1.448  1.00  0.00              
ATOM    781  N   LEU   236       0.368  10.122   0.642  1.00  0.00              
ATOM    782  CA  LEU   236       0.019   9.598   1.959  1.00  0.00              
ATOM    783  C   LEU   236       1.252   9.237   2.779  1.00  0.00              
ATOM    784  O   LEU   236       1.345   9.590   3.956  1.00  0.00              
ATOM    785  N   SER   240       2.201   8.564   2.129  1.00  0.00              
ATOM    786  CA  SER   240       3.452   8.122   2.748  1.00  0.00              
ATOM    787  C   SER   240       4.278   9.287   3.289  1.00  0.00              
ATOM    788  O   SER   240       4.883   9.178   4.358  1.00  0.00              
ATOM    789  N   PRO   243       4.306  10.397   2.552  1.00  0.00              
ATOM    790  CA  PRO   243       5.023  11.585   3.014  1.00  0.00              
ATOM    791  C   PRO   243       4.277  12.266   4.171  1.00  0.00              
ATOM    792  O   PRO   243       4.888  12.627   5.172  1.00  0.00              
ATOM    793  N   LEU   245       2.960  12.418   4.039  1.00  0.00              
ATOM    794  CA  LEU   245       2.149  13.038   5.093  1.00  0.00              
ATOM    795  C   LEU   245       2.156  12.236   6.401  1.00  0.00              
ATOM    796  O   LEU   245       1.970  12.796   7.487  1.00  0.00              
ATOM    797  N   HIS   246       2.319  15.085  11.854  1.00  0.00              
ATOM    798  CA  HIS   246       0.898  15.305  12.137  1.00  0.00              
ATOM    799  C   HIS   246       0.487  16.777  11.913  1.00  0.00              
ATOM    800  O   HIS   246       0.806  17.663  12.713  1.00  0.00              
ATOM    801  N   TRP   249      -0.234  17.011  10.818  1.00  0.00              
ATOM    802  CA  TRP   249      -0.637  18.349  10.389  1.00  0.00              
ATOM    803  C   TRP   249      -1.943  18.796  11.030  1.00  0.00              
ATOM    804  O   TRP   249      -2.392  19.929  10.819  1.00  0.00              
ATOM    805  N   GLU   250      -2.549  17.911  11.818  1.00  0.00              
ATOM    806  CA  GLU   250      -3.837  18.201  12.460  1.00  0.00              
ATOM    807  C   GLU   250      -3.848  19.475  13.324  1.00  0.00              
ATOM    808  O   GLU   250      -4.783  20.274  13.210  1.00  0.00              
ATOM    809  N   ILE   251      -1.875  22.108  13.022  1.00  0.00              
ATOM    810  CA  ILE   251      -1.774  23.165  12.022  1.00  0.00              
ATOM    811  C   ILE   251      -3.107  23.418  11.302  1.00  0.00              
ATOM    812  O   ILE   251      -3.518  24.565  11.149  1.00  0.00              
ATOM    813  N   ILE   252      -3.766  22.346  10.868  1.00  0.00              
ATOM    814  CA  ILE   252      -5.069  22.433  10.210  1.00  0.00              
ATOM    815  C   ILE   252      -6.095  23.119  11.116  1.00  0.00              
ATOM    816  O   ILE   252      -6.788  24.049  10.685  1.00  0.00              
ATOM    817  N   GLY   256      -6.171  22.676  12.371  1.00  0.00              
ATOM    818  CA  GLY   256      -7.145  23.207  13.327  1.00  0.00              
ATOM    819  C   GLY   256      -6.887  24.679  13.688  1.00  0.00              
ATOM    820  O   GLY   256      -7.837  25.450  13.862  1.00  0.00              
ATOM    821  N   LYS   257      -5.610  25.064  13.780  1.00  0.00              
ATOM    822  CA  LYS   257      -5.255  26.437  14.133  1.00  0.00              
ATOM    823  C   LYS   257      -5.568  27.390  12.984  1.00  0.00              
ATOM    824  O   LYS   257      -6.046  28.503  13.202  1.00  0.00              
ATOM    825  N   ASP   258      -5.318  26.937  11.759  1.00  0.00              
ATOM    826  CA  ASP   258      -5.614  27.722  10.566  1.00  0.00              
ATOM    827  C   ASP   258      -7.108  28.027  10.474  1.00  0.00              
ATOM    828  O   ASP   258      -7.503  29.148  10.172  1.00  0.00              
ATOM    829  N   ALA   259      -7.935  27.023  10.738  1.00  0.00              
ATOM    830  CA  ALA   259      -9.380  27.221  10.820  1.00  0.00              
ATOM    831  C   ALA   259      -9.707  28.245  11.918  1.00  0.00              
ATOM    832  O   ALA   259     -10.458  29.187  11.679  1.00  0.00              
ATOM    833  N   GLU   260      -9.118  28.064  13.099  1.00  0.00              
ATOM    834  CA  GLU   260      -9.344  28.965  14.244  1.00  0.00              
ATOM    835  C   GLU   260      -8.865  30.389  14.009  1.00  0.00              
ATOM    836  O   GLU   260      -9.357  31.309  14.664  1.00  0.00              
ATOM    837  N   GLY   261      -7.911  30.555  13.084  1.00  0.00              
ATOM    838  CA  GLY   261      -7.228  31.830  12.846  1.00  0.00              
ATOM    839  C   GLY   261      -7.774  32.618  11.647  1.00  0.00              
ATOM    840  O   GLY   261      -7.391  33.772  11.425  1.00  0.00              
ATOM    841  N   GLU   262      -8.678  32.010  10.886  1.00  0.00              
ATOM    842  CA  GLU   262      -9.268  32.696   9.732  1.00  0.00              
ATOM    843  C   GLU   262      -9.916  34.025  10.125  1.00  0.00              
ATOM    844  O   GLU   262     -10.524  34.154  11.186  1.00  0.00              
ATOM    845  N   ARG   263      -9.765  35.016   9.265  1.00  0.00              
ATOM    846  CA  ARG   263     -10.411  36.289   9.473  1.00  0.00              
ATOM    847  C   ARG   263     -11.540  36.404   8.473  1.00  0.00              
ATOM    848  O   ARG   263     -11.464  35.836   7.380  1.00  0.00              
ATOM    849  N   SER   264     -12.598  37.108   8.858  1.00  0.00              
ATOM    850  CA  SER   264     -13.767  37.219   8.012  1.00  0.00              
ATOM    851  C   SER   264     -14.094  38.677   7.732  1.00  0.00              
ATOM    852  O   SER   264     -14.300  39.459   8.647  1.00  0.00              
ATOM    853  N   SER   265     -14.124  39.018   6.446  1.00  0.00              
ATOM    854  CA  SER   265     -14.617  40.312   5.978  1.00  0.00              
ATOM    855  C   SER   265     -15.964  40.085   5.328  1.00  0.00              
ATOM    856  O   SER   265     -16.197  39.032   4.744  1.00  0.00              
ATOM    857  N   ALA   266     -16.846  41.071   5.425  1.00  0.00              
ATOM    858  CA  ALA   266     -18.150  41.012   4.776  1.00  0.00              
ATOM    859  C   ALA   266     -18.299  42.210   3.858  1.00  0.00              
ATOM    860  O   ALA   266     -18.319  43.338   4.314  1.00  0.00              
ATOM    861  N   ILE   267     -18.388  41.945   2.557  1.00  0.00              
ATOM    862  CA  ILE   267     -18.420  42.999   1.555  1.00  0.00              
ATOM    863  C   ILE   267     -19.806  43.200   0.933  1.00  0.00              
ATOM    864  O   ILE   267     -20.561  42.254   0.731  1.00  0.00              
ATOM    865  N   THR   269     -20.119  44.452   0.635  1.00  0.00              
ATOM    866  CA  THR   269     -21.401  44.862   0.085  1.00  0.00              
ATOM    867  C   THR   269     -21.102  45.806  -1.036  1.00  0.00              
ATOM    868  O   THR   269     -20.027  46.387  -1.063  1.00  0.00              
ATOM    869  N   VAL   274     -22.052  45.986  -1.946  1.00  0.00              
ATOM    870  CA  VAL   274     -21.923  47.030  -2.944  1.00  0.00              
ATOM    871  C   VAL   274     -22.247  48.358  -2.291  1.00  0.00              
ATOM    872  O   VAL   274     -23.333  48.557  -1.733  1.00  0.00              
ATOM    873  N   LYS   277     -21.268  49.253  -2.370  1.00  0.00              
ATOM    874  CA  LYS   277     -21.283  50.515  -1.659  1.00  0.00              
ATOM    875  C   LYS   277     -21.818  51.638  -2.571  1.00  0.00              
ATOM    876  O   LYS   277     -21.089  52.569  -2.952  1.00  0.00              
ATOM    877  N   SER   281     -23.104  51.515  -2.911  1.00  0.00              
ATOM    878  CA  SER   281     -23.868  52.495  -3.699  1.00  0.00              
ATOM    879  C   SER   281     -23.158  53.829  -4.012  1.00  0.00              
ATOM    880  O   SER   281     -23.324  54.834  -3.312  1.00  0.00              
END
