
#######################################################
#                                                     #
#                        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   18 (  148),  selected   18 , name T0372TS021_1_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   18 , name T0372_D2.pdb
# PARAMETERS: T0372TS021_1_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       121 - 133         4.92     8.76
  LONGEST_CONTINUOUS_SEGMENT:    13       122 - 134         4.96     8.84
  LCS_AVERAGE:      7.04

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       120 - 124         1.96    18.86
  LONGEST_CONTINUOUS_SEGMENT:     5       121 - 125         1.94    17.81
  LONGEST_CONTINUOUS_SEGMENT:     5       123 - 127         1.95    13.84
  LONGEST_CONTINUOUS_SEGMENT:     5       131 - 135         1.14    22.80
  LCS_AVERAGE:      2.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       124 - 127         0.69    17.10
  LONGEST_CONTINUOUS_SEGMENT:     4       131 - 134         0.32    22.69
  LONGEST_CONTINUOUS_SEGMENT:     4       132 - 135         0.94    25.12
  LCS_AVERAGE:      2.03

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    4    9     3    3    3    4    4    4    5    7    7    7    7    8    8    9    9   11   13   13   13   13 
LCS_GDT     A     119     A     119      3    4    9     3    3    3    4    4    4    5    5    6    7    7    8    8    8    8    8   13   13   13   13 
LCS_GDT     Y     120     Y     120      3    5    9     3    3    3    4    4    5    5    7    7    7    7    8    8    8    9   11   13   13   13   14 
LCS_GDT     A     121     A     121      3    5   13     3    3    4    4    5    5    5    7    7    7   10   11   11   13   14   14   15   15   15   15 
LCS_GDT     D     122     D     122      3    5   13     2    3    4    4    5    6    6    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     Y     123     Y     123      3    5   13     3    3    4    5    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     I     124     I     124      4    5   13     3    4    4    4    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     Y     125     Y     125      4    5   13     3    4    4    4    5    6    7    8    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     L     126     L     126      4    5   13     3    4    4    4    4    6    7    8    9    9   10   11   12   13   14   14   15   15   15   15 
LCS_GDT     R     127     R     127      4    5   13     3    4    4    4    4    6    7    8    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     S     128     S     128      3    4   13     3    3    3    3    4    4    6    8    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     D     129     D     129      3    3   13     3    3    4    4    4    6    7    8    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     L     130     L     130      3    3   13     0    3    4    4    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     A     131     A     131      4    5   13     4    4    4    5    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     T     132     T     132      4    5   13     4    4    4    5    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     L     133     L     133      4    5   13     4    4    4    5    5    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     K     134     K     134      4    5   13     4    4    4    5    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_GDT     G     135     G     135      4    5    9     3    3    4    5    6    8    8    9    9    9   10   11   13   13   14   14   15   15   15   15 
LCS_AVERAGE  LCS_A:   3.92  (   2.03    2.68    7.04 )

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      4      5      6      8      8      9      9      9     10     11     13     13     14     14     15     15     15     15 
GDT PERCENT_CA   2.33   2.33   2.33   2.91   3.49   4.65   4.65   5.23   5.23   5.23   5.81   6.40   7.56   7.56   8.14   8.14   8.72   8.72   8.72   8.72
GDT RMS_LOCAL    0.32   0.32   0.32   1.14   1.80   2.35   2.35   2.64   2.64   2.64   3.71   4.10   4.96   4.96   5.27   5.27   5.57   5.57   5.57   5.57
GDT RMS_ALL_CA  22.69  22.69  22.69  22.80   8.93   8.51   8.51   8.20   8.20   8.20  10.93  10.08   8.19   8.19   7.77   7.77   7.88   7.88   7.88   7.88

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118         12.714
LGA    A     119      A     119         13.238
LGA    Y     120      Y     120         12.682
LGA    A     121      A     121          7.048
LGA    D     122      D     122          3.776
LGA    Y     123      Y     123          2.425
LGA    I     124      I     124          2.742
LGA    Y     125      Y     125          8.723
LGA    L     126      L     126         13.095
LGA    R     127      R     127         11.521
LGA    S     128      S     128         11.596
LGA    D     129      D     129          9.250
LGA    L     130      L     130          2.794
LGA    A     131      A     131          1.592
LGA    T     132      T     132          2.827
LGA    L     133      L     133          3.237
LGA    K     134      K     134          2.033
LGA    G     135      G     135          1.424

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  172    4.0      9    2.64     4.651     4.204     0.329

LGA_LOCAL      RMSD =  2.638  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.200  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  7.395  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.043671 * X  +   0.869412 * Y  +   0.492155 * Z  +   6.596829
  Y_new =   0.976806 * X  +  -0.140523 * Y  +   0.161563 * Z  +  21.391184
  Z_new =   0.209623 * X  +   0.473684 * Y  +  -0.855384 * Z  +  14.385439 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.635861   -0.505732  [ DEG:   151.0237    -28.9763 ]
  Theta =  -0.211190   -2.930403  [ DEG:   -12.1003   -167.8997 ]
  Phi   =   1.526118   -1.615475  [ DEG:    87.4401    -92.5599 ]
 
# 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: T0372TS021_1_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS021_1_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  172   4.0    9   2.64   4.204     7.40
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS021_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM    953  N   ARG   118      27.145  37.491  22.330  1.00218.80       1SG 954
ATOM    954  CA  ARG   118      26.394  38.250  21.396  1.00218.80       1SG 955
ATOM    955  CB  ARG   118      24.891  38.310  21.711  1.00218.80       1SG 956
ATOM    956  CG  ARG   118      24.185  36.987  21.404  1.00218.80       1SG 957
ATOM    957  CD  ARG   118      22.663  37.099  21.286  1.00218.80       1SG 958
ATOM    958  NE  ARG   118      22.140  35.739  20.968  1.00218.80       1SG 959
ATOM    959  CZ  ARG   118      22.053  35.318  19.672  1.00218.80       1SG 960
ATOM    960  NH1 ARG   118      22.446  36.139  18.655  1.00218.80       1SG 961
ATOM    961  NH2 ARG   118      21.575  34.071  19.393  1.00218.80       1SG 962
ATOM    962  C   ARG   118      26.936  39.631  21.380  1.00218.80       1SG 963
ATOM    963  O   ARG   118      27.201  40.169  20.307  1.00218.80       1SG 964
ATOM    964  N   ALA   119      27.180  40.228  22.563  1.00292.80       1SG 965
ATOM    965  CA  ALA   119      27.545  41.611  22.540  1.00292.80       1SG 966
ATOM    966  CB  ALA   119      28.815  41.895  21.718  1.00292.80       1SG 967
ATOM    967  C   ALA   119      26.385  42.247  21.866  1.00292.80       1SG 968
ATOM    968  O   ALA   119      26.518  43.185  21.081  1.00292.80       1SG 969
ATOM    969  N   TYR   120      25.197  41.697  22.180  1.00206.78       1SG 970
ATOM    970  CA  TYR   120      23.976  42.123  21.585  1.00206.78       1SG 971
ATOM    971  CB  TYR   120      23.597  43.552  22.000  1.00206.78       1SG 972
ATOM    972  CG  TYR   120      23.452  43.490  23.483  1.00206.78       1SG 973
ATOM    973  CD1 TYR   120      24.565  43.566  24.289  1.00206.78       1SG 974
ATOM    974  CD2 TYR   120      22.215  43.345  24.067  1.00206.78       1SG 975
ATOM    975  CE1 TYR   120      24.449  43.504  25.658  1.00206.78       1SG 976
ATOM    976  CE2 TYR   120      22.092  43.283  25.436  1.00206.78       1SG 977
ATOM    977  CZ  TYR   120      23.209  43.364  26.232  1.00206.78       1SG 978
ATOM    978  OH  TYR   120      23.085  43.300  27.637  1.00206.78       1SG 979
ATOM    979  C   TYR   120      24.141  42.033  20.110  1.00206.78       1SG 980
ATOM    980  O   TYR   120      23.849  42.976  19.378  1.00206.78       1SG 981
ATOM    981  N   ALA   121      24.620  40.861  19.646  1.00100.12       1SG 982
ATOM    982  CA  ALA   121      24.826  40.643  18.247  1.00100.12       1SG 983
ATOM    983  CB  ALA   121      23.525  40.677  17.426  1.00100.12       1SG 984
ATOM    984  C   ALA   121      25.706  41.741  17.781  1.00100.12       1SG 985
ATOM    985  O   ALA   121      25.555  42.257  16.675  1.00100.12       1SG 986
ATOM    986  N   ASP   122      26.685  42.104  18.623  1.00186.82       1SG 987
ATOM    987  CA  ASP   122      27.520  43.192  18.257  1.00186.82       1SG 988
ATOM    988  CB  ASP   122      28.210  43.004  16.896  1.00186.82       1SG 989
ATOM    989  CG  ASP   122      29.254  41.909  17.046  1.00186.82       1SG 990
ATOM    990  OD1 ASP   122      29.493  41.474  18.205  1.00186.82       1SG 991
ATOM    991  OD2 ASP   122      29.833  41.495  16.005  1.00186.82       1SG 992
ATOM    992  C   ASP   122      26.629  44.376  18.171  1.00186.82       1SG 993
ATOM    993  O   ASP   122      26.117  44.855  19.182  1.00186.82       1SG 994
ATOM    994  N   TYR   123      26.436  44.889  16.943  1.00250.31       1SG 995
ATOM    995  CA  TYR   123      25.683  46.090  16.722  1.00250.31       1SG 996
ATOM    996  CB  TYR   123      24.257  46.067  17.310  1.00250.31       1SG 997
ATOM    997  CG  TYR   123      23.408  45.183  16.460  1.00250.31       1SG 998
ATOM    998  CD1 TYR   123      23.312  43.832  16.705  1.00250.31       1SG 999
ATOM    999  CD2 TYR   123      22.702  45.715  15.405  1.00250.31       1SG1000
ATOM   1000  CE1 TYR   123      22.525  43.028  15.912  1.00250.31       1SG1001
ATOM   1001  CE2 TYR   123      21.914  44.918  14.609  1.00250.31       1SG1002
ATOM   1002  CZ  TYR   123      21.826  43.571  14.862  1.00250.31       1SG1003
ATOM   1003  OH  TYR   123      21.018  42.749  14.046  1.00250.31       1SG1004
ATOM   1004  C   TYR   123      26.445  47.203  17.360  1.00250.31       1SG1005
ATOM   1005  O   TYR   123      25.939  48.313  17.523  1.00250.31       1SG1006
ATOM   1006  N   ILE   124      27.710  46.913  17.712  1.00154.32       1SG1007
ATOM   1007  CA  ILE   124      28.629  47.825  18.305  1.00154.32       1SG1008
ATOM   1008  CB  ILE   124      28.606  47.827  19.809  1.00154.32       1SG1009
ATOM   1009  CG2 ILE   124      29.077  46.449  20.303  1.00154.32       1SG1010
ATOM   1010  CG1 ILE   124      29.430  49.005  20.356  1.00154.32       1SG1011
ATOM   1011  CD1 ILE   124      29.317  49.184  21.866  1.00154.32       1SG1012
ATOM   1012  C   ILE   124      29.974  47.333  17.882  1.00154.32       1SG1013
ATOM   1013  O   ILE   124      30.070  46.302  17.218  1.00154.32       1SG1014
ATOM   1014  N   TYR   125      31.041  48.076  18.234  1.00104.12       1SG1015
ATOM   1015  CA  TYR   125      32.380  47.661  17.941  1.00104.12       1SG1016
ATOM   1016  CB  TYR   125      33.442  48.539  18.623  1.00104.12       1SG1017
ATOM   1017  CG  TYR   125      33.328  49.898  18.023  1.00104.12       1SG1018
ATOM   1018  CD1 TYR   125      32.250  50.700  18.318  1.00104.12       1SG1019
ATOM   1019  CD2 TYR   125      34.305  50.380  17.181  1.00104.12       1SG1020
ATOM   1020  CE1 TYR   125      32.139  51.957  17.771  1.00104.12       1SG1021
ATOM   1021  CE2 TYR   125      34.200  51.635  16.631  1.00104.12       1SG1022
ATOM   1022  CZ  TYR   125      33.115  52.425  16.926  1.00104.12       1SG1023
ATOM   1023  OH  TYR   125      33.003  53.715  16.362  1.00104.12       1SG1024
ATOM   1024  C   TYR   125      32.503  46.269  18.469  1.00104.12       1SG1025
ATOM   1025  O   TYR   125      31.937  45.931  19.507  1.00104.12       1SG1026
ATOM   1026  N   LEU   126      33.229  45.405  17.740  1.00117.10       1SG1027
ATOM   1027  CA  LEU   126      33.312  44.031  18.132  1.00117.10       1SG1028
ATOM   1028  CB  LEU   126      34.205  43.207  17.172  1.00117.10       1SG1029
ATOM   1029  CG  LEU   126      34.278  41.673  17.379  1.00117.10       1SG1030
ATOM   1030  CD1 LEU   126      35.204  41.043  16.326  1.00117.10       1SG1031
ATOM   1031  CD2 LEU   126      34.709  41.261  18.795  1.00117.10       1SG1032
ATOM   1032  C   LEU   126      33.882  43.989  19.512  1.00117.10       1SG1033
ATOM   1033  O   LEU   126      34.816  44.717  19.842  1.00117.10       1SG1034
ATOM   1034  N   ARG   127      33.289  43.127  20.361  1.00120.69       1SG1035
ATOM   1035  CA  ARG   127      33.756  42.923  21.699  1.00120.69       1SG1036
ATOM   1036  CB  ARG   127      35.159  42.293  21.751  1.00120.69       1SG1037
ATOM   1037  CG  ARG   127      35.635  41.946  23.163  1.00120.69       1SG1038
ATOM   1038  CD  ARG   127      37.059  41.387  23.203  1.00120.69       1SG1039
ATOM   1039  NE  ARG   127      37.975  42.492  22.802  1.00120.69       1SG1040
ATOM   1040  CZ  ARG   127      39.326  42.306  22.823  1.00120.69       1SG1041
ATOM   1041  NH1 ARG   127      39.847  41.106  23.210  1.00120.69       1SG1042
ATOM   1042  NH2 ARG   127      40.158  43.324  22.452  1.00120.69       1SG1043
ATOM   1043  C   ARG   127      33.797  44.228  22.424  1.00120.69       1SG1044
ATOM   1044  O   ARG   127      34.793  44.555  23.066  1.00120.69       1SG1045
ATOM   1045  N   SER   128      32.711  45.018  22.344  1.00140.05       1SG1046
ATOM   1046  CA  SER   128      32.717  46.251  23.073  1.00140.05       1SG1047
ATOM   1047  CB  SER   128      31.609  47.235  22.659  1.00140.05       1SG1048
ATOM   1048  OG  SER   128      31.857  47.731  21.352  1.00140.05       1SG1049
ATOM   1049  C   SER   128      32.516  45.925  24.520  1.00140.05       1SG1050
ATOM   1050  O   SER   128      31.835  44.957  24.859  1.00140.05       1SG1051
ATOM   1051  N   ASP   129      33.138  46.732  25.408  1.00242.92       1SG1052
ATOM   1052  CA  ASP   129      33.037  46.563  26.832  1.00242.92       1SG1053
ATOM   1053  CB  ASP   129      34.230  47.153  27.605  1.00242.92       1SG1054
ATOM   1054  CG  ASP   129      35.452  46.295  27.309  1.00242.92       1SG1055
ATOM   1055  OD1 ASP   129      35.267  45.117  26.902  1.00242.92       1SG1056
ATOM   1056  OD2 ASP   129      36.589  46.807  27.484  1.00242.92       1SG1057
ATOM   1057  C   ASP   129      31.801  47.271  27.292  1.00242.92       1SG1058
ATOM   1058  O   ASP   129      31.172  47.986  26.515  1.00242.92       1SG1059
ATOM   1059  N   LEU   130      31.400  47.071  28.568  1.00212.10       1SG1060
ATOM   1060  CA  LEU   130      30.181  47.687  29.027  1.00212.10       1SG1061
ATOM   1061  CB  LEU   130      28.910  46.855  28.773  1.00212.10       1SG1062
ATOM   1062  CG  LEU   130      28.590  46.520  27.303  1.00212.10       1SG1063
ATOM   1063  CD1 LEU   130      29.547  45.461  26.733  1.00212.10       1SG1064
ATOM   1064  CD2 LEU   130      27.112  46.133  27.136  1.00212.10       1SG1065
ATOM   1065  C   LEU   130      30.203  47.865  30.523  1.00212.10       1SG1066
ATOM   1066  O   LEU   130      31.257  47.828  31.159  1.00212.10       1SG1067
ATOM   1067  N   ALA   131      28.988  48.114  31.089  1.00 66.69       1SG1068
ATOM   1068  CA  ALA   131      28.719  48.261  32.500  1.00 66.69       1SG1069
ATOM   1069  CB  ALA   131      28.395  49.702  32.927  1.00 66.69       1SG1070
ATOM   1070  C   ALA   131      27.513  47.414  32.831  1.00 66.69       1SG1071
ATOM   1071  O   ALA   131      26.614  47.243  32.007  1.00 66.69       1SG1072
ATOM   1072  N   THR   132      27.480  46.872  34.072  1.00207.67       1SG1073
ATOM   1073  CA  THR   132      26.504  45.927  34.560  1.00207.67       1SG1074
ATOM   1074  CB  THR   132      26.890  45.276  35.857  1.00207.67       1SG1075
ATOM   1075  OG1 THR   132      26.042  44.164  36.108  1.00207.67       1SG1076
ATOM   1076  CG2 THR   132      26.760  46.305  36.991  1.00207.67       1SG1077
ATOM   1077  C   THR   132      25.120  46.471  34.736  1.00207.67       1SG1078
ATOM   1078  O   THR   132      24.172  45.730  34.491  1.00207.67       1SG1079
ATOM   1079  N   LEU   133      24.958  47.733  35.197  1.00187.13       1SG1080
ATOM   1080  CA  LEU   133      23.659  48.327  35.388  1.00187.13       1SG1081
ATOM   1081  CB  LEU   133      22.966  48.690  34.063  1.00187.13       1SG1082
ATOM   1082  CG  LEU   133      23.688  49.779  33.252  1.00187.13       1SG1083
ATOM   1083  CD1 LEU   133      25.126  49.369  32.900  1.00187.13       1SG1084
ATOM   1084  CD2 LEU   133      22.871  50.172  32.009  1.00187.13       1SG1085
ATOM   1085  C   LEU   133      22.762  47.385  36.129  1.00187.13       1SG1086
ATOM   1086  O   LEU   133      21.811  46.863  35.547  1.00187.13       1SG1087
ATOM   1087  N   LYS   134      23.050  47.122  37.424  1.00205.93       1SG1088
ATOM   1088  CA  LYS   134      22.245  46.188  38.162  1.00205.93       1SG1089
ATOM   1089  CB  LYS   134      22.578  46.088  39.662  1.00205.93       1SG1090
ATOM   1090  CG  LYS   134      23.896  45.388  39.994  1.00205.93       1SG1091
ATOM   1091  CD  LYS   134      24.251  45.476  41.481  1.00205.93       1SG1092
ATOM   1092  CE  LYS   134      25.451  44.619  41.889  1.00205.93       1SG1093
ATOM   1093  NZ  LYS   134      25.680  44.736  43.347  1.00205.93       1SG1094
ATOM   1094  C   LYS   134      20.824  46.623  38.081  1.00205.93       1SG1095
ATOM   1095  O   LYS   134      20.486  47.764  38.388  1.00205.93       1SG1096
ATOM   1096  N   GLY   135      19.955  45.690  37.651  1.00 36.72       1SG1097
ATOM   1097  CA  GLY   135      18.564  45.985  37.514  1.00 36.72       1SG1098
ATOM   1098  C   GLY   135      17.908  44.712  37.000  1.00 36.72       1SG1099
ATOM   1099  O   GLY   135      18.634  43.693  36.848  1.00 36.72       1SG1100
ATOM   1100  OXT GLY   135      16.672  44.739  36.752  1.00 36.72       1SG1101
TER
END
