
#######################################################
#                                                     #
#                        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 (  108),  selected   20 , name T0286TS261_1_2
# Molecule2: number of CA atoms  202 ( 1582),  selected   20 , name T0286.pdb
# PARAMETERS: T0286TS261_1_2.T0286.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:    14        46 - 59          3.97    22.30
  LCS_AVERAGE:      5.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        46 - 52          1.74    22.88
  LONGEST_CONTINUOUS_SEGMENT:     7        47 - 53          1.76    29.05
  LCS_AVERAGE:      2.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        46 - 50          0.79    19.56
  LONGEST_CONTINUOUS_SEGMENT:     5        47 - 51          0.87    26.04
  LCS_AVERAGE:      1.73

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:  202
LCS_GDT     S       3     S       3      0    0    9     0    0    1    2    2    4    4    6    7    7    8    8    8    8    9    9   10   11   13   14 
LCS_GDT     K       4     K       4      0    0   10     0    0    0    2    2    4    4    6    7    7    8    8    8    8    9    9   10   11   13   14 
LCS_GDT     G      46     G      46      5    7   14     3    4    5    6    7    8    8    8    9    9   12   13   14   14   14   14   14   14   14   15 
LCS_GDT     S      47     S      47      5    7   14     3    5    6    6    7    8    8    8   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     Q      48     Q      48      5    7   14     3    5    6    6    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     R      49     R      49      5    7   14     3    5    6    6    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     S      50     S      50      5    7   14     4    4    6    6    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     G      51     G      51      5    7   14     2    5    6    6    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     P      52     P      52      3    7   14     1    3    4    4    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     S      53     S      53      4    7   14     3    5    6    6    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     S      54     S      54      4    6   14     4    4    5    6    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     L      55     L      55      4    6   14     3    3    4    4    6    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     P      56     P      56      4    5   14     3    3    4    4    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     D      57     D      57      3    5   14     4    4    5    5    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     K      58     K      58      3    4   14     3    3    3    3    7    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     D      59     D      59      3    4   14     4    4    5    5    6    8   10   11   12   12   13   13   14   14   14   14   14   14   14   15 
LCS_GDT     K     155     K     155      3    3   11     0    3    3    3    3    4    5    6    7    8    8    9   10   11   11   11   13   14   14   15 
LCS_GDT     R     200     R     200      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     A     201     A     201      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     L     202     L     202      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   3.33  (   1.73    2.43    5.82 )

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      5      6      6      7      8     10     11     12     12     13     13     14     14     14     14     14     14     14     15 
GDT PERCENT_CA   1.98   2.48   2.97   2.97   3.47   3.96   4.95   5.45   5.94   5.94   6.44   6.44   6.93   6.93   6.93   6.93   6.93   6.93   6.93   7.43
GDT RMS_LOCAL    0.29   0.74   0.92   0.92   1.52   1.90   2.41   2.69   2.88   2.88   3.38   3.38   3.97   3.97   3.97   3.97   3.97   3.97   3.97   6.13
GDT RMS_ALL_CA  27.78  25.84  28.02  28.02  23.04  20.71  26.31  25.45  24.79  24.79  23.96  23.96  22.30  22.30  22.30  22.30  22.30  22.30  22.30  16.94

#      Molecule1      Molecule2       DISTANCE
LGA    S       3      S       3         51.558
LGA    K       4      K       4         45.701
LGA    G      46      G      46         12.502
LGA    S      47      S      47          9.698
LGA    Q      48      Q      48          3.729
LGA    R      49      R      49          4.737
LGA    S      50      S      50          1.903
LGA    G      51      G      51          3.064
LGA    P      52      P      52          2.023
LGA    S      53      S      53          3.240
LGA    S      54      S      54          2.110
LGA    L      55      L      55          2.988
LGA    P      56      P      56          3.338
LGA    D      57      D      57          1.122
LGA    K      58      K      58          3.549
LGA    D      59      D      59          1.134
LGA    K     155      K     155         34.734
LGA    R     200      R     200         42.601
LGA    A     201      A     201         46.202
LGA    L     202      L     202         45.230

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  202    4.0     11    2.69     4.455     4.150     0.394

LGA_LOCAL      RMSD =  2.692  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 24.802  Number of atoms =   20 
Std_ALL_ATOMS  RMSD = 12.477  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.940882 * X  +   0.090262 * Y  +  -0.326488 * Z  +  82.257263
  Y_new =  -0.287698 * X  +  -0.721717 * Y  +   0.629567 * Z  +  87.788322
  Z_new =  -0.178805 * X  +   0.686278 * Y  +   0.705019 * Z  +  28.441792 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.771929   -2.369664  [ DEG:    44.2283   -135.7717 ]
  Theta =   0.179772    2.961820  [ DEG:    10.3002    169.6998 ]
  Phi   =  -2.844846    0.296746  [ DEG:  -162.9977     17.0023 ]
 
# 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: T0286TS261_1_2                                
REMARK     2: T0286.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0286TS261_1_2.T0286.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  202   4.0   11   2.69   4.150    12.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0286TS261_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0286
PARENT 1mum_A
ATOM    898  N   MET     1      14.469   4.198 -34.879  1.00  4.88
ATOM    899  CA  MET     1      13.289   5.018 -35.154  1.00  4.88
ATOM    900  C   MET     1      13.398   6.505 -34.813  1.00  4.88
ATOM    901  O   MET     1      12.681   7.329 -35.386  1.00  4.88
ATOM    902  CB  MET     1      12.035   4.430 -34.435  1.00  4.88
ATOM    903  N   ALA     2      14.285   6.847 -33.883  1.00  4.62
ATOM    904  CA  ALA     2      14.456   8.239 -33.462  1.00  4.62
ATOM    905  C   ALA     2      15.805   8.791 -33.916  1.00  4.62
ATOM    906  O   ALA     2      16.843   8.186 -33.655  1.00  4.62
ATOM    907  CB  ALA     2      14.342   8.338 -31.937  1.00  4.62
ATOM    908  N   SER     3      15.786   9.950 -34.574  1.00  4.90
ATOM    909  CA  SER     3      17.012  10.561 -35.088  1.00  4.90
ATOM    910  C   SER     3      17.816  11.394 -34.089  1.00  4.90
ATOM    911  O   SER     3      18.930  11.818 -34.392  1.00  4.90
ATOM    912  CB  SER     3      16.690  11.423 -36.314  1.00  4.90
ATOM    913  N   LYS     4      17.266  11.639 -32.904  1.00  5.09
ATOM    914  CA  LYS     4      17.994  12.426 -31.909  1.00  5.09
ATOM    915  C   LYS     4      19.260  11.705 -31.450  1.00  5.09
ATOM    916  O   LYS     4      19.271  10.481 -31.324  1.00  5.09
ATOM    917  CB  LYS     4      17.111  12.711 -30.692  1.00  5.09
ATOM    918  N   GLY    46      32.774   5.029 -16.403  1.00  6.35
ATOM    919  CA  GLY    46      33.132   5.506 -15.068  1.00  6.35
ATOM    920  C   GLY    46      34.300   4.778 -14.422  1.00  6.35
ATOM    921  O   GLY    46      34.757   3.755 -14.928  1.00  6.35
ATOM    922  N   SER    47      34.777   5.315 -13.297  1.00  5.51
ATOM    923  CA  SER    47      35.915   4.732 -12.599  1.00  5.51
ATOM    924  C   SER    47      35.584   3.738 -11.493  1.00  5.51
ATOM    925  O   SER    47      36.428   3.461 -10.642  1.00  5.51
ATOM    926  CB  SER    47      36.832   5.836 -12.035  1.00  5.51
ATOM    927  N   GLN    48      34.369   3.196 -11.500  1.00  4.04
ATOM    928  CA  GLN    48      33.997   2.218 -10.484  1.00  4.04
ATOM    929  C   GLN    48      34.722   0.894 -10.690  1.00  4.04
ATOM    930  O   GLN    48      35.150   0.570 -11.804  1.00  4.04
ATOM    931  CB  GLN    48      32.483   1.989 -10.470  1.00  4.04
ATOM    932  N   ARG    49      34.864   0.135  -9.609  1.00  5.45
ATOM    933  CA  ARG    49      35.558  -1.149  -9.658  1.00  5.45
ATOM    934  C   ARG    49      34.670  -2.302 -10.102  1.00  5.45
ATOM    935  O   ARG    49      35.125  -3.205 -10.802  1.00  5.45
ATOM    936  CB  ARG    49      36.139  -1.526  -8.274  1.00  5.45
ATOM    937  N   SER    50      33.405  -2.266  -9.696  1.00  4.76
ATOM    938  CA  SER    50      32.500  -3.353 -10.025  1.00  4.76
ATOM    939  C   SER    50      32.784  -4.465  -9.028  1.00  4.76
ATOM    940  O   SER    50      33.222  -4.195  -7.908  1.00  4.76
ATOM    941  CB  SER    50      32.704  -3.804 -11.481  1.00  4.76
ATOM    942  N   GLY    51      32.546  -5.712  -9.416  1.00  5.79
ATOM    943  CA  GLY    51      32.799  -6.839  -8.521  1.00  5.79
ATOM    944  C   GLY    51      34.244  -7.312  -8.675  1.00  5.79
ATOM    945  O   GLY    51      34.693  -7.603  -9.777  1.00  5.79
ATOM    946  N   PRO    52      34.966  -7.377  -7.563  1.00  5.28
ATOM    947  CA  PRO    52      36.361  -7.808  -7.566  1.00  5.28
ATOM    948  C   PRO    52      36.426  -9.259  -7.107  1.00  5.28
ATOM    949  O   PRO    52      37.428  -9.943  -7.306  1.00  5.28
ATOM    950  CB  PRO    52      37.172  -6.920  -6.610  1.00  5.28
ATOM    951  N   SER    53      35.336  -9.722  -6.510  1.00  5.80
ATOM    952  CA  SER    53      35.257 -11.077  -5.984  1.00  5.80
ATOM    953  C   SER    53      33.842 -11.623  -6.159  1.00  5.80
ATOM    954  O   SER    53      32.880 -10.858  -6.213  1.00  5.80
ATOM    955  CB  SER    53      35.638 -11.038  -4.502  1.00  5.80
ATOM    956  N   SER    54      33.713 -12.944  -6.242  1.00  5.21
ATOM    957  CA  SER    54      32.404 -13.564  -6.413  1.00  5.21
ATOM    958  C   SER    54      31.423 -13.109  -5.324  1.00  5.21
ATOM    959  O   SER    54      30.262 -12.806  -5.608  1.00  5.21
ATOM    960  CB  SER    54      32.537 -15.095  -6.400  1.00  5.21
ATOM    961  N   LEU    55      31.897 -13.044  -4.081  1.00  4.97
ATOM    962  CA  LEU    55      31.031 -12.627  -2.989  1.00  4.97
ATOM    963  C   LEU    55      31.048 -11.136  -2.695  1.00  4.97
ATOM    964  O   LEU    55      30.534 -10.699  -1.660  1.00  4.97
ATOM    965  CB  LEU    55      31.426 -13.423  -1.734  1.00  4.97
ATOM    966  N   PRO    56      31.626 -10.352  -3.601  1.00  6.07
ATOM    967  CA  PRO    56      31.716  -8.902  -3.429  1.00  6.07
ATOM    968  C   PRO    56      30.330  -8.254  -3.400  1.00  6.07
ATOM    969  O   PRO    56      29.589  -8.309  -4.381  1.00  6.07
ATOM    970  CB  PRO    56      32.538  -8.296  -4.569  1.00  6.07
ATOM    971  N   ASP    57      29.983  -7.639  -2.272  1.00  5.76
ATOM    972  CA  ASP    57      28.688  -6.983  -2.129  1.00  5.76
ATOM    973  C   ASP    57      28.590  -5.777  -3.057  1.00  5.76
ATOM    974  O   ASP    57      29.606  -5.265  -3.524  1.00  5.76
ATOM    975  CB  ASP    57      28.486  -6.502  -0.684  1.00  5.76
ATOM    976  N   LYS    58      27.362  -5.316  -3.343  1.00  5.65
ATOM    977  CA  LYS    58      27.192  -4.150  -4.218  1.00  5.65
ATOM    978  C   LYS    58      28.005  -3.018  -3.585  1.00  5.65
ATOM    979  O   LYS    58      27.925  -2.807  -2.373  1.00  5.65
ATOM    980  CB  LYS    58      25.692  -3.898  -4.153  1.00  5.65
ATOM    981  N   ASP    59      28.779  -2.288  -4.384  1.00  5.12
ATOM    982  CA  ASP    59      29.624  -1.243  -3.813  1.00  5.12
ATOM    983  C   ASP    59      29.878  -0.030  -4.700  1.00  5.12
ATOM    984  O   ASP    59      29.587  -0.046  -5.899  1.00  5.12
ATOM    985  CB  ASP    59      30.965  -1.858  -3.424  1.00  5.12
ATOM    986  N   LYS   155      30.879  19.919 -19.087  1.00  4.96
ATOM    987  CA  LYS   155      30.543  19.245 -17.837  1.00  4.96
ATOM    988  C   LYS   155      29.069  18.828 -17.848  1.00  4.96
ATOM    989  O   LYS   155      28.193  19.611 -18.228  1.00  4.96
ATOM    990  CB  LYS   155      30.765  20.184 -16.615  1.00  4.96
ATOM    991  N   ARG   200      -8.222  -4.082  -7.838  1.00  5.20
ATOM    992  CA  ARG   200      -9.159  -3.742  -6.768  1.00  5.20
ATOM    993  C   ARG   200     -10.618  -3.667  -7.227  1.00  5.20
ATOM    994  O   ARG   200     -11.513  -4.222  -6.581  1.00  5.20
ATOM    995  CB  ARG   200      -8.781  -2.392  -6.145  1.00  5.20
ATOM    996  N   ALA   201     -10.858  -2.998  -8.351  1.00  3.50
ATOM    997  CA  ALA   201     -12.226  -2.799  -8.820  1.00  3.50
ATOM    998  C   ALA   201     -12.749  -3.661  -9.960  1.00  3.50
ATOM    999  O   ALA   201     -13.933  -3.584 -10.287  1.00  3.50
ATOM   1000  CB  ALA   201     -12.415  -1.323  -9.171  1.00  3.50
ATOM   1001  N   LEU   202     -11.891  -4.475 -10.565  1.00  4.20
ATOM   1002  CA  LEU   202     -12.342  -5.325 -11.656  1.00  4.20
ATOM   1003  C   LEU   202     -12.714  -4.568 -12.922  1.00  4.20
ATOM   1004  O   LEU   202     -13.499  -5.058 -13.737  1.00  4.20
ATOM   1005  CB  LEU   202     -13.535  -6.159 -11.158  1.00  4.20
TER
END
