
#######################################################
#                                                     #
#                        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   12 (  106),  selected   12 , name T0372TS022_2_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   12 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_2_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:    12       118 - 129         4.84     4.84
  LCS_AVERAGE:      6.98

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       118 - 123         1.91    11.05
  LONGEST_CONTINUOUS_SEGMENT:     6       123 - 128         1.54     9.27
  LCS_AVERAGE:      3.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       124 - 128         0.78    11.01
  LCS_AVERAGE:      2.42

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   12     4    4    4    5    5    6    7    8    8    8    8    9   10   11   12   12   12   12   12   12 
LCS_GDT     A     119     A     119      4    6   12     4    4    4    5    5    6    7    8    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     Y     120     Y     120      4    6   12     4    4    4    5    5    6    7    8    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     A     121     A     121      4    6   12     4    4    4    5    5    6    7    8    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     D     122     D     122      3    6   12     3    3    3    5    5    5    6    8    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     Y     123     Y     123      3    6   12     3    3    4    5    6    6    7    8    8    8   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     I     124     I     124      5    6   12     3    5    5    5    6    6    7    8    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     Y     125     Y     125      5    6   12     4    5    5    5    6    6    7    8    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     L     126     L     126      5    6   12     4    5    5    5    6    6    6    7    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     R     127     R     127      5    6   12     4    5    5    5    6    6    6    7    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_GDT     S     128     S     128      5    6   12     4    5    5    5    6    6    6    7    8    8    9   11   11   11   12   12   12   12   12   12 
LCS_GDT     D     129     D     129      3    3   12     3    3    3    3    4    4    6    7    8    9   10   11   11   11   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   4.25  (   2.42    3.34    6.98 )

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      5      5      6      6      7      8      8      9     10     11     11     11     12     12     12     12     12     12 
GDT PERCENT_CA   2.33   2.91   2.91   2.91   3.49   3.49   4.07   4.65   4.65   5.23   5.81   6.40   6.40   6.40   6.98   6.98   6.98   6.98   6.98   6.98
GDT RMS_LOCAL    0.26   0.78   0.78   0.78   1.54   1.54   2.51   2.72   2.72   3.97   4.14   4.40   4.40   4.40   4.84   4.84   4.84   4.84   4.84   4.84
GDT RMS_ALL_CA  12.50  11.01  11.01  11.01   9.27   9.27   8.69   8.44   8.44   4.92   4.94   5.01   5.01   5.01   4.84   4.84   4.84   4.84   4.84   4.84

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          2.093
LGA    A     119      A     119          1.959
LGA    Y     120      Y     120          2.125
LGA    A     121      A     121          1.759
LGA    D     122      D     122          3.564
LGA    Y     123      Y     123          2.951
LGA    I     124      I     124          2.782
LGA    Y     125      Y     125          3.797
LGA    L     126      L     126          9.666
LGA    R     127      R     127         13.683
LGA    S     128      S     128         16.630
LGA    D     129      D     129         15.465

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  172    4.0      8    2.72     4.360     4.138     0.283

LGA_LOCAL      RMSD =  2.725  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.445  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  4.841  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.367239 * X  +   0.455737 * Y  +  -0.810826 * Z  +  -5.327829
  Y_new =  -0.925382 * X  +   0.091083 * Y  +  -0.367929 * Z  + 110.292389
  Z_new =  -0.093827 * X  +   0.885442 * Y  +   0.455180 * Z  +  -4.953556 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.095955   -2.045637  [ DEG:    62.7936   -117.2064 ]
  Theta =   0.093965    3.047628  [ DEG:     5.3838    174.6162 ]
  Phi   =  -1.193007    1.948586  [ DEG:   -68.3543    111.6457 ]
 
# 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_2_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_2_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  172   4.0    8   2.72   4.138     4.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1cm0_A
ATOM    953  N   ARG   118      22.924  41.213   9.560  1.00  0.00
ATOM    954  CA  ARG   118      22.874  40.878  10.950  1.00  0.00
ATOM    955  C   ARG   118      24.238  40.469  11.426  1.00  0.00
ATOM    956  O   ARG   118      24.652  40.825  12.528  1.00  0.00
ATOM    957  CB  ARG   118      21.902  39.721  11.188  1.00  0.00
ATOM    958  CG  ARG   118      20.439  40.093  11.013  1.00  0.00
ATOM    959  CD  ARG   118      19.537  38.881  11.186  1.00  0.00
ATOM    960  NE  ARG   118      18.126  39.221  11.015  1.00  0.00
ATOM    961  CZ  ARG   118      17.137  38.334  11.039  1.00  0.00
ATOM    962  NH1 ARG   118      15.883  38.734  10.875  1.00  0.00
ATOM    963  NH2 ARG   118      17.402  37.049  11.224  1.00  0.00
ATOM    964  N   ALA   119      24.992  39.722  10.597  1.00  0.00
ATOM    965  CA  ALA   119      26.254  39.193  11.043  1.00  0.00
ATOM    966  C   ALA   119      27.182  40.305  11.417  1.00  0.00
ATOM    967  O   ALA   119      27.844  40.248  12.452  1.00  0.00
ATOM    968  CB  ALA   119      26.904  38.372   9.940  1.00  0.00
ATOM    969  N   TYR   120      27.242  41.361  10.589  1.00  0.00
ATOM    970  CA  TYR   120      28.102  42.476  10.855  1.00  0.00
ATOM    971  C   TYR   120      27.627  43.123  12.117  1.00  0.00
ATOM    972  O   TYR   120      28.422  43.589  12.932  1.00  0.00
ATOM    973  CB  TYR   120      28.047  43.481   9.704  1.00  0.00
ATOM    974  CG  TYR   120      28.662  42.975   8.418  1.00  0.00
ATOM    975  CD1 TYR   120      29.486  41.856   8.417  1.00  0.00
ATOM    976  CD2 TYR   120      28.419  43.617   7.211  1.00  0.00
ATOM    977  CE1 TYR   120      30.052  41.386   7.248  1.00  0.00
ATOM    978  CE2 TYR   120      28.977  43.161   6.033  1.00  0.00
ATOM    979  CZ  TYR   120      29.799  42.036   6.060  1.00  0.00
ATOM    980  OH  TYR   120      30.362  41.569   4.894  1.00  0.00
ATOM    981  N   ALA   121      26.298  43.123  12.302  1.00  0.00
ATOM    982  CA  ALA   121      25.548  43.807  13.319  1.00  0.00
ATOM    983  C   ALA   121      25.928  43.424  14.722  1.00  0.00
ATOM    984  O   ALA   121      25.829  44.262  15.615  1.00  0.00
ATOM    985  CB  ALA   121      24.063  43.510  13.173  1.00  0.00
ATOM    986  N   ASP   122      26.381  42.180  14.966  1.00  0.00
ATOM    987  CA  ASP   122      26.583  41.682  16.305  1.00  0.00
ATOM    988  C   ASP   122      27.418  42.632  17.112  1.00  0.00
ATOM    989  O   ASP   122      27.181  42.803  18.305  1.00  0.00
ATOM    990  CB  ASP   122      27.298  40.330  16.272  1.00  0.00
ATOM    991  CG  ASP   122      26.400  39.208  15.785  1.00  0.00
ATOM    992  OD1 ASP   122      25.174  39.428  15.690  1.00  0.00
ATOM    993  OD2 ASP   122      26.923  38.111  15.500  1.00  0.00
ATOM    994  N   TYR   123      28.412  43.289  16.497  1.00  0.00
ATOM    995  CA  TYR   123      29.199  44.206  17.267  1.00  0.00
ATOM    996  C   TYR   123      28.328  45.309  17.783  1.00  0.00
ATOM    997  O   TYR   123      28.406  45.663  18.958  1.00  0.00
ATOM    998  CB  TYR   123      30.309  44.813  16.408  1.00  0.00
ATOM    999  CG  TYR   123      31.451  43.865  16.123  1.00  0.00
ATOM   1000  CD1 TYR   123      31.591  43.276  14.872  1.00  0.00
ATOM   1001  CD2 TYR   123      32.385  43.561  17.104  1.00  0.00
ATOM   1002  CE1 TYR   123      32.633  42.408  14.603  1.00  0.00
ATOM   1003  CE2 TYR   123      33.433  42.695  16.853  1.00  0.00
ATOM   1004  CZ  TYR   123      33.550  42.118  15.589  1.00  0.00
ATOM   1005  OH  TYR   123      34.588  41.254  15.322  1.00  0.00
ATOM   1006  N   ILE   124      27.451  45.873  16.930  1.00  0.00
ATOM   1007  CA  ILE   124      26.641  46.972  17.373  1.00  0.00
ATOM   1008  C   ILE   124      25.681  46.466  18.401  1.00  0.00
ATOM   1009  O   ILE   124      25.206  45.334  18.330  1.00  0.00
ATOM   1010  CB  ILE   124      25.847  47.593  16.209  1.00  0.00
ATOM   1011  CG1 ILE   124      25.249  48.937  16.628  1.00  0.00
ATOM   1012  CG2 ILE   124      24.714  46.672  15.785  1.00  0.00
ATOM   1013  CD1 ILE   124      24.672  49.735  15.479  1.00  0.00
ATOM   1014  N   TYR   125      25.412  47.300  19.422  1.00  0.00
ATOM   1015  CA  TYR   125      24.544  46.920  20.495  1.00  0.00
ATOM   1016  C   TYR   125      23.141  46.990  19.978  1.00  0.00
ATOM   1017  O   TYR   125      22.777  47.937  19.284  1.00  0.00
ATOM   1018  CB  TYR   125      24.714  47.869  21.683  1.00  0.00
ATOM   1019  CG  TYR   125      26.014  47.685  22.433  1.00  0.00
ATOM   1020  CD1 TYR   125      27.110  48.495  22.167  1.00  0.00
ATOM   1021  CD2 TYR   125      26.141  46.701  23.406  1.00  0.00
ATOM   1022  CE1 TYR   125      28.303  48.334  22.847  1.00  0.00
ATOM   1023  CE2 TYR   125      27.325  46.525  24.096  1.00  0.00
ATOM   1024  CZ  TYR   125      28.410  47.353  23.809  1.00  0.00
ATOM   1025  OH  TYR   125      29.596  47.190  24.488  1.00  0.00
ATOM   1026  N   LEU   126      22.322  45.963  20.291  1.00  0.00
ATOM   1027  CA  LEU   126      20.983  45.891  19.780  1.00  0.00
ATOM   1028  C   LEU   126      20.040  46.606  20.690  1.00  0.00
ATOM   1029  O   LEU   126      20.131  46.517  21.913  1.00  0.00
ATOM   1030  CB  LEU   126      20.532  44.433  19.663  1.00  0.00
ATOM   1031  CG  LEU   126      21.343  43.547  18.716  1.00  0.00
ATOM   1032  CD1 LEU   126      20.838  42.112  18.756  1.00  0.00
ATOM   1033  CD2 LEU   126      21.236  44.049  17.285  1.00  0.00
ATOM   1034  N   ARG   127      19.121  47.379  20.077  1.00  0.00
ATOM   1035  CA  ARG   127      18.102  48.082  20.793  1.00  0.00
ATOM   1036  C   ARG   127      17.173  47.065  21.344  1.00  0.00
ATOM   1037  O   ARG   127      16.702  47.188  22.472  1.00  0.00
ATOM   1038  CB  ARG   127      17.349  49.032  19.860  1.00  0.00
ATOM   1039  CG  ARG   127      16.351  49.934  20.567  1.00  0.00
ATOM   1040  CD  ARG   127      15.662  50.870  19.586  1.00  0.00
ATOM   1041  NE  ARG   127      16.595  51.824  18.992  1.00  0.00
ATOM   1042  CZ  ARG   127      16.999  52.942  19.585  1.00  0.00
ATOM   1043  NH1 ARG   127      17.850  53.750  18.968  1.00  0.00
ATOM   1044  NH2 ARG   127      16.552  53.250  20.794  1.00  0.00
ATOM   1045  N   SER   128      16.878  46.035  20.531  1.00  0.00
ATOM   1046  CA  SER   128      15.974  45.004  20.932  1.00  0.00
ATOM   1047  C   SER   128      14.699  45.689  21.287  1.00  0.00
ATOM   1048  O   SER   128      13.923  45.199  22.105  1.00  0.00
ATOM   1049  CB  SER   128      16.532  44.243  22.137  1.00  0.00
ATOM   1050  OG  SER   128      17.776  43.640  21.827  1.00  0.00
ATOM   1051  N   ASP   129      14.441  46.850  20.655  1.00  0.00
ATOM   1052  CA  ASP   129      13.245  47.575  20.963  1.00  0.00
ATOM   1053  C   ASP   129      12.387  47.603  19.704  1.00  0.00
ATOM   1054  O   ASP   129      12.954  47.819  18.599  1.00  0.00
ATOM   1055  CB  ASP   129      13.580  49.004  21.396  1.00  0.00
ATOM   1056  CG  ASP   129      12.370  49.754  21.915  1.00  0.00
ATOM   1057  OD1 ASP   129      11.348  49.101  22.214  1.00  0.00
ATOM   1058  OD2 ASP   129      12.442  50.997  22.022  1.00  0.00
TER
END
