
#######################################################
#                                                     #
#                        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   13 (  114),  selected   13 , name T0372TS022_4_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   13 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_4_1-D2.T0372_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:    13       118 - 130         3.94     3.94
  LCS_AVERAGE:      7.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       121 - 128         1.47     5.45
  LCS_AVERAGE:      4.03

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       122 - 128         0.96     6.01
  LCS_AVERAGE:      3.18

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:  172
LCS_GDT     R     118     R     118      4    6   13     3    4    5    5    6    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     A     119     A     119      4    6   13     3    4    5    5    7    7    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     Y     120     Y     120      4    6   13     3    4    5    5    6    7    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     A     121     A     121      4    8   13     3    4    5    6    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     D     122     D     122      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     Y     123     Y     123      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     I     124     I     124      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     Y     125     Y     125      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     L     126     L     126      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     R     127     R     127      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     S     128     S     128      7    8   13     4    5    6    7    8    9    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     D     129     D     129      3    4   13     3    3    4    4    4    4    9   10   11   12   12   12   12   12   12   13   13   13   13   13 
LCS_GDT     L     130     L     130      3    4   13     3    3    4    4    4    4    4    6    7    7    7   11   11   12   12   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   4.92  (   3.18    4.03    7.56 )

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      7      8      9      9     10     11     12     12     12     12     12     12     13     13     13     13     13 
GDT PERCENT_CA   2.33   2.91   3.49   4.07   4.65   5.23   5.23   5.81   6.40   6.98   6.98   6.98   6.98   6.98   6.98   7.56   7.56   7.56   7.56   7.56
GDT RMS_LOCAL    0.31   0.43   0.78   0.96   1.47   1.98   1.98   2.59   2.86   3.19   3.19   3.19   3.19   3.19   3.19   3.94   3.94   3.94   3.94   3.94
GDT RMS_ALL_CA   5.91   6.42   5.95   6.01   5.45   4.87   4.87   4.28   4.25   4.18   4.18   4.18   4.18   4.18   4.18   3.94   3.94   3.94   3.94   3.94

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          7.209
LGA    A     119      A     119          1.317
LGA    Y     120      Y     120          3.871
LGA    A     121      A     121          1.200
LGA    D     122      D     122          2.510
LGA    Y     123      Y     123          4.518
LGA    I     124      I     124          1.847
LGA    Y     125      Y     125          2.483
LGA    L     126      L     126          2.520
LGA    R     127      R     127          3.655
LGA    S     128      S     128          1.653
LGA    D     129      D     129          3.628
LGA    L     130      L     130          9.614

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  172    4.0     10    2.59     5.087     5.030     0.371

LGA_LOCAL      RMSD =  2.594  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.247  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  3.942  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.667861 * X  +  -0.572961 * Y  +  -0.475055 * Z  + 134.272339
  Y_new =   0.572304 * X  +  -0.803395 * Y  +   0.164391 * Z  +  60.009258
  Z_new =  -0.475846 * X  +  -0.162086 * Y  +   0.864464 * Z  +  75.470680 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.185346    2.956246  [ DEG:   -10.6196    169.3804 ]
  Theta =   0.495926    2.645667  [ DEG:    28.4145    151.5855 ]
  Phi   =   2.433095   -0.708498  [ DEG:   139.4061    -40.5940 ]
 
# 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: T0372TS022_4_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_4_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  172   4.0   10   2.59   5.030     3.94
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1mk4_A
ATOM    953  N   ARG   118      28.306  38.069  14.298  1.00  0.00
ATOM    954  CA  ARG   118      28.783  37.761  12.988  1.00  0.00
ATOM    955  C   ARG   118      27.695  37.811  11.954  1.00  0.00
ATOM    956  O   ARG   118      27.903  38.372  10.879  1.00  0.00
ATOM    957  CB  ARG   118      29.382  36.353  12.954  1.00  0.00
ATOM    958  CG  ARG   118      30.706  36.224  13.692  1.00  0.00
ATOM    959  CD  ARG   118      31.204  34.787  13.683  1.00  0.00
ATOM    960  NE  ARG   118      32.473  34.646  14.393  1.00  0.00
ATOM    961  CZ  ARG   118      33.086  33.484  14.601  1.00  0.00
ATOM    962  NH1 ARG   118      34.238  33.451  15.257  1.00  0.00
ATOM    963  NH2 ARG   118      32.545  32.359  14.153  1.00  0.00
ATOM    964  N   ALA   119      26.493  37.265  12.250  1.00  0.00
ATOM    965  CA  ALA   119      25.522  37.144  11.194  1.00  0.00
ATOM    966  C   ALA   119      25.170  38.485  10.630  1.00  0.00
ATOM    967  O   ALA   119      25.366  38.727   9.440  1.00  0.00
ATOM    968  CB  ALA   119      24.248  36.499  11.718  1.00  0.00
ATOM    969  N   TYR   120      24.657  39.410  11.462  1.00  0.00
ATOM    970  CA  TYR   120      24.428  40.727  10.942  1.00  0.00
ATOM    971  C   TYR   120      24.953  41.672  11.955  1.00  0.00
ATOM    972  O   TYR   120      24.218  42.043  12.867  1.00  0.00
ATOM    973  CB  TYR   120      22.933  40.960  10.714  1.00  0.00
ATOM    974  CG  TYR   120      22.314  40.024   9.701  1.00  0.00
ATOM    975  CD1 TYR   120      21.625  38.889  10.109  1.00  0.00
ATOM    976  CD2 TYR   120      22.422  40.278   8.340  1.00  0.00
ATOM    977  CE1 TYR   120      21.056  38.028   9.190  1.00  0.00
ATOM    978  CE2 TYR   120      21.860  39.428   7.406  1.00  0.00
ATOM    979  CZ  TYR   120      21.174  38.296   7.843  1.00  0.00
ATOM    980  OH  TYR   120      20.609  37.439   6.926  1.00  0.00
ATOM    981  N   ALA   121      26.213  42.121  11.841  1.00  0.00
ATOM    982  CA  ALA   121      26.550  43.079  12.844  1.00  0.00
ATOM    983  C   ALA   121      27.925  43.592  12.622  1.00  0.00
ATOM    984  O   ALA   121      28.788  42.928  12.050  1.00  0.00
ATOM    985  CB  ALA   121      26.486  42.447  14.225  1.00  0.00
ATOM    986  N   ASP   122      28.135  44.832  13.090  1.00  0.00
ATOM    987  CA  ASP   122      29.398  45.485  13.013  1.00  0.00
ATOM    988  C   ASP   122      29.870  45.601  14.422  1.00  0.00
ATOM    989  O   ASP   122      30.646  44.771  14.895  1.00  0.00
ATOM    990  CB  ASP   122      29.247  46.865  12.369  1.00  0.00
ATOM    991  CG  ASP   122      28.854  46.787  10.907  1.00  0.00
ATOM    992  OD1 ASP   122      29.519  46.047  10.152  1.00  0.00
ATOM    993  OD2 ASP   122      27.880  47.465  10.517  1.00  0.00
ATOM    994  N   TYR   123      29.400  46.642  15.139  1.00  0.00
ATOM    995  CA  TYR   123      29.806  46.822  16.501  1.00  0.00
ATOM    996  C   TYR   123      28.579  46.940  17.354  1.00  0.00
ATOM    997  O   TYR   123      27.574  47.527  16.954  1.00  0.00
ATOM    998  CB  TYR   123      30.650  48.090  16.646  1.00  0.00
ATOM    999  CG  TYR   123      31.951  48.052  15.877  1.00  0.00
ATOM   1000  CD1 TYR   123      32.014  48.500  14.563  1.00  0.00
ATOM   1001  CD2 TYR   123      33.111  47.567  16.466  1.00  0.00
ATOM   1002  CE1 TYR   123      33.199  48.467  13.852  1.00  0.00
ATOM   1003  CE2 TYR   123      34.305  47.528  15.771  1.00  0.00
ATOM   1004  CZ  TYR   123      34.341  47.984  14.454  1.00  0.00
ATOM   1005  OH  TYR   123      35.522  47.952  13.749  1.00  0.00
ATOM   1006  N   ILE   124      28.640  46.351  18.566  1.00  0.00
ATOM   1007  CA  ILE   124      27.543  46.400  19.492  1.00  0.00
ATOM   1008  C   ILE   124      28.039  47.172  20.667  1.00  0.00
ATOM   1009  O   ILE   124      29.135  46.918  21.168  1.00  0.00
ATOM   1010  CB  ILE   124      27.105  44.988  19.923  1.00  0.00
ATOM   1011  CG1 ILE   124      26.639  44.180  18.710  1.00  0.00
ATOM   1012  CG2 ILE   124      25.959  45.067  20.919  1.00  0.00
ATOM   1013  CD1 ILE   124      26.408  42.714  19.006  1.00  0.00
ATOM   1014  N   TYR   125      27.252  48.158  21.133  1.00  0.00
ATOM   1015  CA  TYR   125      27.713  48.959  22.226  1.00  0.00
ATOM   1016  C   TYR   125      26.696  48.901  23.316  1.00  0.00
ATOM   1017  O   TYR   125      25.495  49.008  23.074  1.00  0.00
ATOM   1018  CB  TYR   125      27.904  50.411  21.784  1.00  0.00
ATOM   1019  CG  TYR   125      29.000  50.601  20.760  1.00  0.00
ATOM   1020  CD1 TYR   125      28.721  50.549  19.401  1.00  0.00
ATOM   1021  CD2 TYR   125      30.312  50.832  21.157  1.00  0.00
ATOM   1022  CE1 TYR   125      29.717  50.721  18.458  1.00  0.00
ATOM   1023  CE2 TYR   125      31.320  51.006  20.228  1.00  0.00
ATOM   1024  CZ  TYR   125      31.012  50.950  18.870  1.00  0.00
ATOM   1025  OH  TYR   125      32.006  51.121  17.933  1.00  0.00
ATOM   1026  N   LEU   126      27.161  48.701  24.562  1.00  0.00
ATOM   1027  CA  LEU   126      26.244  48.680  25.655  1.00  0.00
ATOM   1028  C   LEU   126      26.512  49.862  26.511  1.00  0.00
ATOM   1029  O   LEU   126      27.654  50.197  26.819  1.00  0.00
ATOM   1030  CB  LEU   126      26.419  47.402  26.478  1.00  0.00
ATOM   1031  CG  LEU   126      25.725  46.149  25.939  1.00  0.00
ATOM   1032  CD1 LEU   126      26.247  45.798  24.554  1.00  0.00
ATOM   1033  CD2 LEU   126      25.974  44.962  26.855  1.00  0.00
ATOM   1034  N   ARG   127      25.422  50.546  26.889  1.00  0.00
ATOM   1035  CA  ARG   127      25.532  51.602  27.830  1.00  0.00
ATOM   1036  C   ARG   127      25.640  50.858  29.109  1.00  0.00
ATOM   1037  O   ARG   127      24.869  49.927  29.347  1.00  0.00
ATOM   1038  CB  ARG   127      24.297  52.503  27.773  1.00  0.00
ATOM   1039  CG  ARG   127      24.147  53.266  26.467  1.00  0.00
ATOM   1040  CD  ARG   127      22.893  54.125  26.470  1.00  0.00
ATOM   1041  NE  ARG   127      22.730  54.862  25.218  1.00  0.00
ATOM   1042  CZ  ARG   127      21.692  55.644  24.942  1.00  0.00
ATOM   1043  NH1 ARG   127      21.629  56.275  23.778  1.00  0.00
ATOM   1044  NH2 ARG   127      20.719  55.793  25.830  1.00  0.00
ATOM   1045  N   SER   128      26.573  51.258  29.990  1.00  0.00
ATOM   1046  CA  SER   128      26.715  50.491  31.189  1.00  0.00
ATOM   1047  C   SER   128      25.494  50.728  32.014  1.00  0.00
ATOM   1048  O   SER   128      24.534  51.346  31.553  1.00  0.00
ATOM   1049  CB  SER   128      27.962  50.929  31.960  1.00  0.00
ATOM   1050  OG  SER   128      27.813  52.242  32.470  1.00  0.00
ATOM   1051  N   ASP   129      25.492  50.208  33.255  1.00  0.00
ATOM   1052  CA  ASP   129      24.359  50.300  34.127  1.00  0.00
ATOM   1053  C   ASP   129      23.926  51.729  34.176  1.00  0.00
ATOM   1054  O   ASP   129      24.718  52.623  34.465  1.00  0.00
ATOM   1055  CB  ASP   129      24.726  49.824  35.535  1.00  0.00
ATOM   1056  CG  ASP   129      23.527  49.761  36.460  1.00  0.00
ATOM   1057  OD1 ASP   129      22.435  50.208  36.049  1.00  0.00
ATOM   1058  OD2 ASP   129      23.679  49.266  37.596  1.00  0.00
ATOM   1059  N   LEU   130      22.645  51.976  33.842  1.00  0.00
ATOM   1060  CA  LEU   130      22.131  53.314  33.882  1.00  0.00
ATOM   1061  C   LEU   130      21.327  53.395  35.175  1.00  0.00
ATOM   1062  O   LEU   130      21.052  52.304  35.742  1.00  0.00
ATOM   1063  CB  LEU   130      21.246  53.585  32.664  1.00  0.00
ATOM   1064  CG  LEU   130      21.908  53.424  31.295  1.00  0.00
ATOM   1065  CD1 LEU   130      20.901  53.660  30.179  1.00  0.00
ATOM   1066  CD2 LEU   130      23.046  54.420  31.128  1.00  0.00
TER
END
