
#######################################################
#                                                     #
#                        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   23 (  112),  selected   23 , name T0316TS102_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   23 , name T0316_D3.pdb
# PARAMETERS: T0316TS102_5-D3.T0316_D3.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:    12       313 - 331         4.84     9.94
  LONGEST_CONTINUOUS_SEGMENT:    12       322 - 360         4.79    14.61
  LCS_AVERAGE:     12.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       313 - 317         0.77    12.97
  LONGEST_CONTINUOUS_SEGMENT:     5       315 - 319         1.95    17.81
  LONGEST_CONTINUOUS_SEGMENT:     5       316 - 320         1.97    13.93
  LONGEST_CONTINUOUS_SEGMENT:     5       349 - 358         1.48    10.76
  LCS_AVERAGE:      4.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       313 - 317         0.77    12.97
  LCS_AVERAGE:      3.77

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:   90
LCS_GDT     S     291     S     291      3    3    3     3    3    3    3    3    3    4    4    4    8    8    8   11   12   12   13   15   16   16   16 
LCS_GDT     Q     292     Q     292      3    3    3     3    3    3    3    3    3    5    5    7    8    8    8   11   12   12   14   15   16   16   16 
LCS_GDT     V     293     V     293      3    3    9     3    3    3    3    4    4    5    5    7    8    8    8   11   12   12   14   15   16   16   16 
LCS_GDT     Y     313     Y     313      5    5   12     4    4    5    5    5    6    7    8    9   10   10   11   13   15   17   17   17   18   18   19 
LCS_GDT     R     314     R     314      5    5   12     4    4    5    5    5    7    7    9   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     Q     315     Q     315      5    5   12     4    4    5    6    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     P     316     P     316      5    5   12     4    4    5    5    5    6    8   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     D     317     D     317      5    5   12     3    4    5    5    5    6    7   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     S     318     S     318      4    5   12     3    3    4    6    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     K     319     K     319      4    5   12     3    3    4    4    5    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     V     320     V     320      3    5   12     3    3    3    3    4    5    7    8    9   11   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     V     322     V     322      0    4   12     3    3    3    4    5    6    6    7    8    9    9   10   11   12   13   16   16   18   18   19 
LCS_GDT     T     329     T     329      3    4   12     0    3    3    4    4    4    5    5    7    8    9   10   11   12   13   14   15   16   17   19 
LCS_GDT     E     330     E     330      3    4   12     3    3    3    4    4    4    5    5    7   10   10   10   11   14   17   17   17   18   18   19 
LCS_GDT     V     331     V     331      3    4   12     3    3    3    4    4    5    7    8    9   10   10   11   11   13   17   17   17   18   18   19 
LCS_GDT     I     332     I     332      3    3   12     3    3    3    3    3    3    5    5    6    6    8   10   11   12   13   14   15   16   16   16 
LCS_GDT     Y     349     Y     349      3    5   12     0    0    3    5    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     L     355     L     355      3    5   12     3    3    4    6    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     G     356     G     356      3    5   12     3    3    4    6    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     G     357     G     357      3    5   12     3    3    4    6    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     G     358     G     358      3    5   12     3    3    3    6    7    7    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     L     359     L     359      3    4   12     0    3    3    4    5    6    9   11   12   12   14   14   14   15   17   17   17   18   18   19 
LCS_GDT     I     360     I     360      3    4   12     1    3    3    4    5    5    6    7    8   11   14   14   14   15   17   17   17   18   18   19 
LCS_AVERAGE  LCS_A:   6.99  (   3.77    4.88   12.32 )

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      4      5      6      7      7      9     11     12     12     14     14     14     15     17     17     17     18     18     19 
GDT PERCENT_CA   4.44   4.44   5.56   6.67   7.78   7.78  10.00  12.22  13.33  13.33  15.56  15.56  15.56  16.67  18.89  18.89  18.89  20.00  20.00  21.11
GDT RMS_LOCAL    0.32   0.32   0.77   1.56   1.77   1.77   2.48   2.94   3.25   3.25   3.86   3.86   3.86   4.34   5.35   5.35   5.35   5.79   5.79   6.34
GDT RMS_ALL_CA  15.39  15.39  12.97  10.97  11.02  11.02  10.89  11.06  10.80  10.80  10.40  10.40  10.40  10.16   9.62   9.62   9.62   9.45   9.45   9.25

#      Molecule1      Molecule2       DISTANCE
LGA    S     291      S     291         25.964
LGA    Q     292      Q     292         21.214
LGA    V     293      V     293         18.914
LGA    Y     313      Y     313         11.463
LGA    R     314      R     314          6.712
LGA    Q     315      Q     315          3.047
LGA    P     316      P     316          2.764
LGA    D     317      D     317          3.658
LGA    S     318      S     318          2.664
LGA    K     319      K     319          3.575
LGA    V     320      V     320          6.726
LGA    V     322      V     322         12.643
LGA    T     329      T     329         15.046
LGA    E     330      E     330         11.696
LGA    V     331      V     331         11.861
LGA    I     332      I     332         17.284
LGA    Y     349      Y     349          3.808
LGA    L     355      L     355          2.134
LGA    G     356      G     356          1.069
LGA    G     357      G     357          1.502
LGA    G     358      G     358          3.168
LGA    L     359      L     359          3.707
LGA    I     360      I     360          8.713

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   90    4.0     11    2.94    10.556     9.217     0.362

LGA_LOCAL      RMSD =  2.940  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.109  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  8.586  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.496492 * X  +  -0.382442 * Y  +   0.779252 * Z  + -39.937859
  Y_new =  -0.862690 * X  +  -0.117876 * Y  +   0.491803 * Z  +  16.352549
  Z_new =  -0.096231 * X  +  -0.916430 * Y  +  -0.388453 * Z  +  75.025528 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.971715    1.169877  [ DEG:  -112.9710     67.0290 ]
  Theta =   0.096381    3.045212  [ DEG:     5.5222    174.4778 ]
  Phi   =  -1.048574    2.093019  [ DEG:   -60.0789    119.9211 ]
 
# 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: T0316TS102_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_5-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   90   4.0   11   2.94   9.217     8.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_5-D3
PFRMAT TS
TARGET T0316
MODEL 5
PARENT 1jcm_P
ATOM    649  N   SER   291      12.451  23.519   6.310  1.00  1.00
ATOM    650  CA  SER   291      13.267  24.151   5.267  1.00  1.00
ATOM    651  C   SER   291      14.621  23.535   4.912  1.00  1.00
ATOM    652  O   SER   291      14.985  23.479   3.734  1.00  1.00
ATOM    653  CB  SER   291      13.497  25.626   5.609  1.00  1.00
ATOM    654  N   GLN   292      15.383  23.106   5.916  1.00  1.00
ATOM    655  CA  GLN   292      16.704  22.517   5.668  1.00  1.00
ATOM    656  C   GLN   292      16.603  21.379   4.661  1.00  1.00
ATOM    657  O   GLN   292      17.587  21.044   3.991  1.00  1.00
ATOM    658  CB  GLN   292      17.316  22.018   6.973  1.00  1.00
ATOM    659  N   VAL   293      15.402  20.803   4.567  1.00  1.00
ATOM    660  CA  VAL   293      15.105  19.710   3.641  1.00  1.00
ATOM    661  C   VAL   293      14.331  20.148   2.374  1.00  1.00
ATOM    662  O   VAL   293      14.756  19.852   1.246  1.00  1.00
ATOM    663  CB  VAL   293      14.331  18.616   4.379  1.00  1.00
ATOM    664  N   TYR   313      13.212  20.853   2.570  1.00  1.00
ATOM    665  CA  TYR   313      12.356  21.342   1.477  1.00  1.00
ATOM    666  C   TYR   313      13.080  22.278   0.502  1.00  1.00
ATOM    667  O   TYR   313      12.637  22.460  -0.633  1.00  1.00
ATOM    668  CB  TYR   313      11.136  22.092   2.036  1.00  1.00
ATOM    669  N   ARG   314      14.188  22.873   0.938  1.00  1.00
ATOM    670  CA  ARG   314      14.936  23.802   0.095  1.00  1.00
ATOM    671  C   ARG   314      15.863  23.102  -0.892  1.00  1.00
ATOM    672  O   ARG   314      16.601  23.753  -1.631  1.00  1.00
ATOM    673  CB  ARG   314      15.729  24.758   0.968  1.00  1.00
ATOM    674  N   GLN   315      15.833  21.776  -0.913  1.00  1.00
ATOM    675  CA  GLN   315      16.699  21.049  -1.829  1.00  1.00
ATOM    676  C   GLN   315      15.943  20.122  -2.756  1.00  1.00
ATOM    677  O   GLN   315      14.999  19.441  -2.347  1.00  1.00
ATOM    678  CB  GLN   315      17.750  20.249  -1.061  1.00  1.00
ATOM    679  N   PRO   316      16.380  20.101  -4.014  1.00  1.00
ATOM    680  CA  PRO   316      15.769  19.261  -5.031  1.00  1.00
ATOM    681  C   PRO   316      15.993  17.788  -4.698  1.00  1.00
ATOM    682  O   PRO   316      15.037  17.028  -4.528  1.00  1.00
ATOM    683  CB  PRO   316      16.366  19.584  -6.396  1.00  1.00
ATOM    684  N   ASP   317      17.258  17.380  -4.616  1.00  1.00
ATOM    685  CA  ASP   317      17.561  16.000  -4.269  1.00  1.00
ATOM    686  C   ASP   317      17.203  15.911  -2.797  1.00  1.00
ATOM    687  O   ASP   317      18.021  16.205  -1.928  1.00  1.00
ATOM    688  CB  ASP   317      19.047  15.702  -4.460  1.00  1.00
ATOM    689  N   SER   318      15.968  15.523  -2.525  1.00  1.00
ATOM    690  CA  SER   318      15.492  15.425  -1.157  1.00  1.00
ATOM    691  C   SER   318      16.158  14.328  -0.329  1.00  1.00
ATOM    692  O   SER   318      16.302  14.478   0.880  1.00  1.00
ATOM    693  CB  SER   318      13.976  15.223  -1.148  1.00  1.00
ATOM    694  N   LYS   319      16.562  13.232  -0.966  1.00  1.00
ATOM    695  CA  LYS   319      17.201  12.139  -0.236  1.00  1.00
ATOM    696  C   LYS   319      18.617  12.531   0.196  1.00  1.00
ATOM    697  O   LYS   319      19.047  12.228   1.314  1.00  1.00
ATOM    698  CB  LYS   319      17.234  10.864  -1.097  1.00  1.00
ATOM    699  N   VAL   320      19.330  13.211  -0.699  1.00  1.00
ATOM    700  CA  VAL   320      20.687  13.658  -0.420  1.00  1.00
ATOM    701  C   VAL   320      20.646  14.681   0.719  1.00  1.00
ATOM    702  O   VAL   320      21.583  14.788   1.513  1.00  1.00
ATOM    703  CB  VAL   320      21.300  14.279  -1.681  1.00  1.00
ATOM    704  N   VAL   322      19.543  15.419   0.806  1.00  1.00
ATOM    705  CA  VAL   322      19.379  16.436   1.842  1.00  1.00
ATOM    706  C   VAL   322      19.227  15.800   3.216  1.00  1.00
ATOM    707  O   VAL   322      19.756  16.306   4.198  1.00  1.00
ATOM    708  CB  VAL   322      18.162  17.320   1.535  1.00  1.00
ATOM    709  N   THR   329      18.497  14.692   3.279  1.00  1.00
ATOM    710  CA  THR   329      18.276  14.003   4.540  1.00  1.00
ATOM    711  C   THR   329      19.561  13.359   5.011  1.00  1.00
ATOM    712  O   THR   329      19.808  13.253   6.214  1.00  1.00
ATOM    713  CB  THR   329      17.171  12.942   4.414  1.00  1.00
ATOM    714  N   GLU   330      20.385  12.939   4.060  1.00  1.00
ATOM    715  CA  GLU   330      21.659  12.330   4.405  1.00  1.00
ATOM    716  C   GLU   330      22.614  13.363   5.006  1.00  1.00
ATOM    717  O   GLU   330      23.283  13.084   6.001  1.00  1.00
ATOM    718  CB  GLU   330      22.271  11.652   3.169  1.00  1.00
ATOM    719  N   VAL   331      22.665  14.557   4.415  1.00  1.00
ATOM    720  CA  VAL   331      23.538  15.618   4.912  1.00  1.00
ATOM    721  C   VAL   331      23.127  16.159   6.284  1.00  1.00
ATOM    722  O   VAL   331      23.934  16.206   7.211  1.00  1.00
ATOM    723  CB  VAL   331      23.561  16.815   3.945  1.00  1.00
ATOM    724  N   ILE   332      21.864  16.569   6.386  1.00  1.00
ATOM    725  CA  ILE   332      21.309  17.186   7.589  1.00  1.00
ATOM    726  C   ILE   332      20.941  16.279   8.752  1.00  1.00
ATOM    727  O   ILE   332      21.176  16.623   9.906  1.00  1.00
ATOM    728  CB  ILE   332      20.084  18.052   7.210  1.00  1.00
ATOM    729  N   TYR   349      20.359  15.128   8.461  1.00  1.00
ATOM    730  CA  TYR   349      19.980  14.217   9.524  1.00  1.00
ATOM    731  C   TYR   349      21.061  13.198   9.858  1.00  1.00
ATOM    732  O   TYR   349      21.258  12.850  11.022  1.00  1.00
ATOM    733  CB  TYR   349      18.691  13.494   9.151  1.00  1.00
ATOM    734  N   LEU   355      21.777  12.731   8.842  1.00  1.00
ATOM    735  CA  LEU   355      22.801  11.730   9.066  1.00  1.00
ATOM    736  C   LEU   355      24.227  12.246   9.112  1.00  1.00
ATOM    737  O   LEU   355      25.145  11.490   9.415  1.00  1.00
ATOM    738  CB  LEU   355      22.704  10.654   7.990  1.00  1.00
ATOM    739  N   GLY   356      24.423  13.524   8.821  1.00  1.00
ATOM    740  CA  GLY   356      25.775  14.050   8.818  1.00  1.00
ATOM    741  C   GLY   356      26.550  13.203   7.836  1.00  1.00
ATOM    742  O   GLY   356      27.741  12.936   8.005  1.00  1.00
ATOM    743  N   GLY   357      25.839  12.774   6.802  1.00  1.00
ATOM    744  CA  GLY   357      26.402  11.938   5.762  1.00  1.00
ATOM    745  C   GLY   357      26.978  12.783   4.645  1.00  1.00
ATOM    746  O   GLY   357      27.303  13.949   4.859  1.00  1.00
ATOM    747  N   GLY   358      27.085  12.194   3.453  1.00  1.00
ATOM    748  CA  GLY   358      27.669  12.866   2.289  1.00  1.00
ATOM    749  C   GLY   358      28.955  13.525   2.776  1.00  1.00
ATOM    750  O   GLY   358      29.464  14.470   2.170  1.00  1.00
ATOM    751  N   LEU   359      29.472  12.985   3.881  1.00  1.00
ATOM    752  CA  LEU   359      30.683  13.474   4.518  1.00  1.00
ATOM    753  C   LEU   359      30.654  14.994   4.496  1.00  1.00
ATOM    754  O   LEU   359      31.656  15.644   4.202  1.00  1.00
ATOM    755  CB  LEU   359      31.921  12.930   3.790  1.00  1.00
ATOM    756  N   ILE   360      29.474  15.535   4.808  1.00  1.00
ATOM    757  CA  ILE   360      29.193  16.971   4.852  1.00  1.00
ATOM    758  C   ILE   360      28.663  17.492   3.510  1.00  1.00
ATOM    759  O   ILE   360      27.670  18.252   3.523  1.00  1.00
ATOM    760  CB  ILE   360      30.443  17.801   5.286  1.00  1.00
TER
END
