
#######################################################
#                                                     #
#                        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   17 (  143),  selected   17 , name T0372TS022_5_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   17 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_5_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:    14       121 - 134         4.62     9.25
  LCS_AVERAGE:      7.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       125 - 133         1.96     9.94
  LCS_AVERAGE:      4.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       126 - 132         0.74    10.65
  LONGEST_CONTINUOUS_SEGMENT:     7       127 - 133         0.99    10.63
  LCS_AVERAGE:      3.04

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      3    6    8     0    3    4    6    6    6    7    7    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     119     A     119      4    6    8     3    4    4    6    6    6    7    7    7    7    7    8    8    8    8    8    8    8    8    8 
LCS_GDT     Y     120     Y     120      4    6    8     3    4    4    6    6    6    7    7    7    7    7    8    8    8    8    8    8    8    8    9 
LCS_GDT     A     121     A     121      4    6   14     3    4    4    6    6    6    7    7    7    7    7    8    8   11   13   13   14   14   14   14 
LCS_GDT     D     122     D     122      4    6   14     3    4    4    6    6    6    7    8   10   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     Y     123     Y     123      4    6   14     3    4    4    6    6    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     I     124     I     124      4    5   14     3    4    4    5    7    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     Y     125     Y     125      3    9   14     3    3    4    5    7    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     L     126     L     126      7    9   14     3    4    7    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     R     127     R     127      7    9   14     3    6    7    8    8    8    9   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     S     128     S     128      7    9   14     5    6    7    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     D     129     D     129      7    9   14     5    6    7    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     L     130     L     130      7    9   14     5    6    7    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     A     131     A     131      7    9   14     5    6    7    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     T     132     T     132      7    9   14     5    6    7    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     L     133     L     133      7    9   14     3    4    6    8    8    8   10   10   11   12   12   13   13   13   13   13   14   14   14   14 
LCS_GDT     K     134     K     134      3    3   14     3    3    3    3    3    3    5    5    7    9   12   13   13   13   13   13   14   14   14   14 
LCS_AVERAGE  LCS_A:   4.95  (   3.04    4.27    7.52 )

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      5      6      7      8      8      8     10     10     11     12     12     13     13     13     13     13     14     14     14     14 
GDT PERCENT_CA   2.91   3.49   4.07   4.65   4.65   4.65   5.81   5.81   6.40   6.98   6.98   7.56   7.56   7.56   7.56   7.56   8.14   8.14   8.14   8.14
GDT RMS_LOCAL    0.37   0.64   0.74   1.08   1.08   1.08   2.69   2.53   2.87   3.22   3.22   3.63   3.63   3.63   3.63   3.63   4.62   4.62   4.62   4.62
GDT RMS_ALL_CA  10.62  10.62  10.65  10.55  10.55  10.55   9.91   9.73   9.98   9.60   9.60   9.73   9.73   9.73   9.73   9.73   9.25   9.25   9.25   9.25

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118         21.111
LGA    A     119      A     119         21.131
LGA    Y     120      Y     120         18.329
LGA    A     121      A     121         12.189
LGA    D     122      D     122          5.939
LGA    Y     123      Y     123          6.052
LGA    I     124      I     124          3.266
LGA    Y     125      Y     125          2.372
LGA    L     126      L     126          3.194
LGA    R     127      R     127          3.604
LGA    S     128      S     128          2.467
LGA    D     129      D     129          0.938
LGA    L     130      L     130          2.568
LGA    A     131      A     131          1.026
LGA    T     132      T     132          1.151
LGA    L     133      L     133          3.242
LGA    K     134      K     134          8.471

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  172    4.0     10    2.53     5.378     5.302     0.380

LGA_LOCAL      RMSD =  2.532  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.660  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  8.269  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.669805 * X  +   0.740668 * Y  +   0.052659 * Z  + -63.270718
  Y_new =   0.367847 * X  +   0.392584 * Y  +  -0.842951 * Z  + -15.922037
  Z_new =  -0.645020 * X  +  -0.545242 * Y  +  -0.535407 * Z  +  93.190575 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.347094    0.794499  [ DEG:  -134.4786     45.5214 ]
  Theta =   0.701049    2.440544  [ DEG:    40.1671    139.8329 ]
  Phi   =   2.639375   -0.502217  [ DEG:   151.2251    -28.7749 ]
 
# 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_5_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_5_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  172   4.0   10   2.53   5.302     8.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1th8_B
ATOM    953  N   ARG   118      22.761  49.986  27.650  1.00  0.00
ATOM    954  CA  ARG   118      22.268  48.783  28.276  1.00  0.00
ATOM    955  C   ARG   118      23.413  47.860  28.588  1.00  0.00
ATOM    956  O   ARG   118      24.580  48.229  28.493  1.00  0.00
ATOM    957  CB  ARG   118      21.292  48.057  27.348  1.00  0.00
ATOM    958  CG  ARG   118      20.890  46.673  27.830  1.00  0.00
ATOM    959  CD  ARG   118      21.926  45.631  27.444  1.00  0.00
ATOM    960  NE  ARG   118      21.978  45.420  25.998  1.00  0.00
ATOM    961  CZ  ARG   118      23.008  44.876  25.358  1.00  0.00
ATOM    962  NH1 ARG   118      22.966  44.724  24.042  1.00  0.00
ATOM    963  NH2 ARG   118      24.078  44.486  26.037  1.00  0.00
ATOM    964  N   ALA   119      23.102  46.643  29.066  1.00  0.00
ATOM    965  CA  ALA   119      24.099  45.685  29.437  1.00  0.00
ATOM    966  C   ALA   119      24.979  45.459  28.254  1.00  0.00
ATOM    967  O   ALA   119      24.591  45.718  27.121  1.00  0.00
ATOM    968  CB  ALA   119      23.446  44.376  29.853  1.00  0.00
ATOM    969  N   TYR   120      26.208  44.974  28.510  1.00  0.00
ATOM    970  CA  TYR   120      27.223  44.794  27.518  1.00  0.00
ATOM    971  C   TYR   120      26.638  44.064  26.361  1.00  0.00
ATOM    972  O   TYR   120      25.814  43.163  26.512  1.00  0.00
ATOM    973  CB  TYR   120      28.391  43.986  28.088  1.00  0.00
ATOM    974  CG  TYR   120      29.497  43.724  27.090  1.00  0.00
ATOM    975  CD1 TYR   120      30.414  44.716  26.769  1.00  0.00
ATOM    976  CD2 TYR   120      29.621  42.486  26.475  1.00  0.00
ATOM    977  CE1 TYR   120      31.429  44.485  25.859  1.00  0.00
ATOM    978  CE2 TYR   120      30.628  42.236  25.562  1.00  0.00
ATOM    979  CZ  TYR   120      31.536  43.250  25.258  1.00  0.00
ATOM    980  OH  TYR   120      32.544  43.017  24.351  1.00  0.00
ATOM    981  N   ALA   121      27.039  44.506  25.159  1.00  0.00
ATOM    982  CA  ALA   121      26.595  43.970  23.913  1.00  0.00
ATOM    983  C   ALA   121      27.685  44.312  22.956  1.00  0.00
ATOM    984  O   ALA   121      28.831  44.507  23.362  1.00  0.00
ATOM    985  CB  ALA   121      25.274  44.602  23.504  1.00  0.00
ATOM    986  N   ASP   122      27.360  44.379  21.651  1.00  0.00
ATOM    987  CA  ASP   122      28.378  44.715  20.704  1.00  0.00
ATOM    988  C   ASP   122      28.897  46.059  21.104  1.00  0.00
ATOM    989  O   ASP   122      28.273  46.770  21.890  1.00  0.00
ATOM    990  CB  ASP   122      27.799  44.760  19.289  1.00  0.00
ATOM    991  CG  ASP   122      27.494  43.381  18.739  1.00  0.00
ATOM    992  OD1 ASP   122      27.885  42.385  19.384  1.00  0.00
ATOM    993  OD2 ASP   122      26.864  43.296  17.665  1.00  0.00
ATOM    994  N   TYR   123      30.069  46.440  20.566  1.00  0.00
ATOM    995  CA  TYR   123      30.771  47.585  21.069  1.00  0.00
ATOM    996  C   TYR   123      29.934  48.820  20.976  1.00  0.00
ATOM    997  O   TYR   123      29.821  49.550  21.959  1.00  0.00
ATOM    998  CB  TYR   123      32.053  47.822  20.270  1.00  0.00
ATOM    999  CG  TYR   123      32.835  49.039  20.711  1.00  0.00
ATOM   1000  CD1 TYR   123      33.652  48.991  21.832  1.00  0.00
ATOM   1001  CD2 TYR   123      32.752  50.231  20.004  1.00  0.00
ATOM   1002  CE1 TYR   123      34.369  50.098  22.243  1.00  0.00
ATOM   1003  CE2 TYR   123      33.462  51.349  20.400  1.00  0.00
ATOM   1004  CZ  TYR   123      34.276  51.273  21.530  1.00  0.00
ATOM   1005  OH  TYR   123      34.989  52.378  21.937  1.00  0.00
ATOM   1006  N   ILE   124      29.297  49.100  19.824  1.00  0.00
ATOM   1007  CA  ILE   124      28.560  50.333  19.782  1.00  0.00
ATOM   1008  C   ILE   124      27.132  49.990  20.066  1.00  0.00
ATOM   1009  O   ILE   124      26.301  50.000  19.158  1.00  0.00
ATOM   1010  CB  ILE   124      28.672  51.012  18.404  1.00  0.00
ATOM   1011  CG1 ILE   124      30.133  51.338  18.088  1.00  0.00
ATOM   1012  CG2 ILE   124      27.872  52.305  18.381  1.00  0.00
ATOM   1013  CD1 ILE   124      30.380  51.684  16.636  1.00  0.00
ATOM   1014  N   TYR   125      26.809  49.690  21.346  1.00  0.00
ATOM   1015  CA  TYR   125      25.487  49.248  21.695  1.00  0.00
ATOM   1016  C   TYR   125      25.192  49.595  23.121  1.00  0.00
ATOM   1017  O   TYR   125      25.624  50.624  23.637  1.00  0.00
ATOM   1018  CB  TYR   125      25.367  47.732  21.524  1.00  0.00
ATOM   1019  CG  TYR   125      23.955  47.210  21.668  1.00  0.00
ATOM   1020  CD1 TYR   125      22.865  48.013  21.356  1.00  0.00
ATOM   1021  CD2 TYR   125      23.717  45.916  22.114  1.00  0.00
ATOM   1022  CE1 TYR   125      21.572  47.543  21.484  1.00  0.00
ATOM   1023  CE2 TYR   125      22.430  45.431  22.248  1.00  0.00
ATOM   1024  CZ  TYR   125      21.354  46.257  21.928  1.00  0.00
ATOM   1025  OH  TYR   125      20.067  45.788  22.056  1.00  0.00
ATOM   1026  N   LEU   126      24.412  48.714  23.779  1.00  0.00
ATOM   1027  CA  LEU   126      23.949  48.838  25.122  1.00  0.00
ATOM   1028  C   LEU   126      25.162  49.053  25.964  1.00  0.00
ATOM   1029  O   LEU   126      25.216  49.988  26.752  1.00  0.00
ATOM   1030  CB  LEU   126      23.212  47.568  25.554  1.00  0.00
ATOM   1031  CG  LEU   126      21.845  47.326  24.912  1.00  0.00
ATOM   1032  CD1 LEU   126      21.313  45.950  25.282  1.00  0.00
ATOM   1033  CD2 LEU   126      20.839  48.366  25.382  1.00  0.00
ATOM   1034  N   ARG   127      26.172  48.178  25.875  1.00  0.00
ATOM   1035  CA  ARG   127      27.392  48.574  26.511  1.00  0.00
ATOM   1036  C   ARG   127      27.336  48.628  28.008  1.00  0.00
ATOM   1037  O   ARG   127      27.167  47.624  28.697  1.00  0.00
ATOM   1038  CB  ARG   127      27.806  49.973  26.052  1.00  0.00
ATOM   1039  CG  ARG   127      28.205  50.053  24.588  1.00  0.00
ATOM   1040  CD  ARG   127      28.612  51.465  24.202  1.00  0.00
ATOM   1041  NE  ARG   127      27.477  52.386  24.225  1.00  0.00
ATOM   1042  CZ  ARG   127      27.577  53.699  24.037  1.00  0.00
ATOM   1043  NH1 ARG   127      26.490  54.457  24.076  1.00  0.00
ATOM   1044  NH2 ARG   127      28.762  54.249  23.811  1.00  0.00
ATOM   1045  N   SER   128      27.491  49.877  28.507  1.00  0.00
ATOM   1046  CA  SER   128      27.801  50.271  29.854  1.00  0.00
ATOM   1047  C   SER   128      26.832  49.845  30.909  1.00  0.00
ATOM   1048  O   SER   128      27.234  49.798  32.069  1.00  0.00
ATOM   1049  CB  SER   128      27.874  51.796  29.964  1.00  0.00
ATOM   1050  OG  SER   128      28.937  52.312  29.182  1.00  0.00
ATOM   1051  N   ASP   129      25.557  49.539  30.598  1.00  0.00
ATOM   1052  CA  ASP   129      24.713  49.156  31.701  1.00  0.00
ATOM   1053  C   ASP   129      25.277  47.927  32.344  1.00  0.00
ATOM   1054  O   ASP   129      25.312  47.832  33.566  1.00  0.00
ATOM   1055  CB  ASP   129      23.294  48.860  31.212  1.00  0.00
ATOM   1056  CG  ASP   129      22.334  48.571  32.349  1.00  0.00
ATOM   1057  OD1 ASP   129      22.124  49.470  33.191  1.00  0.00
ATOM   1058  OD2 ASP   129      21.792  47.447  32.398  1.00  0.00
ATOM   1059  N   LEU   130      25.772  46.961  31.557  1.00  0.00
ATOM   1060  CA  LEU   130      26.310  45.799  32.199  1.00  0.00
ATOM   1061  C   LEU   130      27.513  46.215  32.979  1.00  0.00
ATOM   1062  O   LEU   130      27.763  45.698  34.066  1.00  0.00
ATOM   1063  CB  LEU   130      26.709  44.750  31.160  1.00  0.00
ATOM   1064  CG  LEU   130      27.277  43.437  31.705  1.00  0.00
ATOM   1065  CD1 LEU   130      26.258  42.738  32.590  1.00  0.00
ATOM   1066  CD2 LEU   130      27.644  42.496  30.567  1.00  0.00
ATOM   1067  N   ALA   131      28.286  47.177  32.447  1.00  0.00
ATOM   1068  CA  ALA   131      29.491  47.577  33.108  1.00  0.00
ATOM   1069  C   ALA   131      29.138  48.077  34.469  1.00  0.00
ATOM   1070  O   ALA   131      29.846  47.808  35.438  1.00  0.00
ATOM   1071  CB  ALA   131      30.185  48.681  32.324  1.00  0.00
ATOM   1072  N   THR   132      28.011  48.802  34.587  1.00  0.00
ATOM   1073  CA  THR   132      27.682  49.364  35.863  1.00  0.00
ATOM   1074  C   THR   132      27.520  48.263  36.861  1.00  0.00
ATOM   1075  O   THR   132      27.992  48.381  37.989  1.00  0.00
ATOM   1076  CB  THR   132      26.372  50.169  35.804  1.00  0.00
ATOM   1077  OG1 THR   132      26.518  51.261  34.887  1.00  0.00
ATOM   1078  CG2 THR   132      26.024  50.723  37.177  1.00  0.00
ATOM   1079  N   LEU   133      26.864  47.149  36.488  1.00  0.00
ATOM   1080  CA  LEU   133      26.662  46.141  37.484  1.00  0.00
ATOM   1081  C   LEU   133      27.973  45.599  37.930  1.00  0.00
ATOM   1082  O   LEU   133      28.179  45.388  39.123  1.00  0.00
ATOM   1083  CB  LEU   133      25.822  44.993  36.922  1.00  0.00
ATOM   1084  CG  LEU   133      24.353  45.307  36.633  1.00  0.00
ATOM   1085  CD1 LEU   133      23.687  44.143  35.913  1.00  0.00
ATOM   1086  CD2 LEU   133      23.594  45.564  37.926  1.00  0.00
ATOM   1087  N   LYS   134      28.906  45.365  36.991  1.00  0.00
ATOM   1088  CA  LYS   134      30.160  44.827  37.421  1.00  0.00
ATOM   1089  C   LYS   134      30.839  45.879  38.292  1.00  0.00
ATOM   1090  O   LYS   134      30.980  45.624  39.518  1.00  0.00
ATOM   1091  CB  LYS   134      31.044  44.499  36.216  1.00  0.00
ATOM   1092  CG  LYS   134      30.517  43.367  35.349  1.00  0.00
ATOM   1093  CD  LYS   134      31.477  43.045  34.216  1.00  0.00
ATOM   1094  CE  LYS   134      30.940  41.929  33.337  1.00  0.00
ATOM   1095  NZ  LYS   134      31.858  41.623  32.205  1.00  0.00
TER
END
