
#######################################################
#                                                     #
#                        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   15 (  106),  selected   15 , name T0347TS401_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   15 , name T0347_D2.pdb
# PARAMETERS: T0347TS401_1-D2.T0347_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:    15       134 - 148         1.46     1.46
  LCS_AVERAGE:     21.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       134 - 148         1.46     1.46
  LCS_AVERAGE:     21.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       134 - 147         0.53     1.65
  LCS_AVERAGE:     18.69

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:   71
LCS_GDT     D     134     D     134     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P     135     P     135     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     F     136     F     136     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     137     R     137     14   15   15    11   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     S     138     S     138     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     139     L     139     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     A     140     A     140     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G     141     G     141     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     A     142     A     142     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     143     L     143     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     144     R     144     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     M     145     M     145     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     A     146     A     146     14   15   15    12   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G     147     G     147     14   15   15     3    8   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G     148     G     148      3   15   15     3    3    4    5    6    8   12   15   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  20.31  (  18.69   21.13   21.13 )

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     12     13     14     14     14     14     14     15     15     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA  16.90  18.31  19.72  19.72  19.72  19.72  19.72  21.13  21.13  21.13  21.13  21.13  21.13  21.13  21.13  21.13  21.13  21.13  21.13  21.13
GDT RMS_LOCAL    0.35   0.37   0.53   0.53   0.53   0.53   0.53   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46
GDT RMS_ALL_CA   1.70   1.70   1.65   1.65   1.65   1.65   1.65   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46   1.46

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      D     134          3.196
LGA    P     135      P     135          3.608
LGA    F     136      F     136          2.634
LGA    R     137      R     137          0.908
LGA    S     138      S     138          2.097
LGA    L     139      L     139          2.435
LGA    A     140      A     140          1.464
LGA    G     141      G     141          0.339
LGA    A     142      A     142          0.492
LGA    L     143      L     143          0.961
LGA    R     144      R     144          1.300
LGA    M     145      M     145          1.314
LGA    A     146      A     146          0.621
LGA    G     147      G     147          1.782
LGA    G     148      G     148          3.530

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   71    4.0     15    1.46    20.070    20.441     0.963

LGA_LOCAL      RMSD =  1.457  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.068  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  1.457  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.321695 * X  +   0.744023 * Y  +   0.585612 * Z  + -20.304888
  Y_new =  -0.701258 * X  +   0.602793 * Y  +  -0.380629 * Z  +  50.873196
  Z_new =  -0.636199 * X  +  -0.288219 * Y  +   0.715668 * Z  +  -2.991949 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.382855    2.758737  [ DEG:   -21.9360    158.0640 ]
  Theta =   0.689562    2.452031  [ DEG:    39.5090    140.4910 ]
  Phi   =  -1.140698    2.000894  [ DEG:   -65.3572    114.6428 ]
 
# 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: T0347TS401_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS401_1-D2.T0347_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   71   4.0   15   1.46  20.441     1.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS401_1-D2
PFRMAT TS
TARGET T0347
MODEL  1 REFINED
PARENT 5nul
ATOM   1032  N   ASP   134       4.520  52.891  -2.796  1.00103.04       1SG1033
ATOM   1033  CA  ASP   134       5.767  52.223  -3.041  1.00103.04       1SG1034
ATOM   1034  CB  ASP   134       5.605  51.146  -4.131  1.00103.04       1SG1035
ATOM   1035  CG  ASP   134       6.862  50.299  -4.240  1.00103.04       1SG1036
ATOM   1036  OD1 ASP   134       7.807  50.501  -3.431  1.00103.04       1SG1037
ATOM   1037  OD2 ASP   134       6.886  49.423  -5.144  1.00103.04       1SG1038
ATOM   1038  C   ASP   134       6.798  53.198  -3.542  1.00103.04       1SG1039
ATOM   1039  O   ASP   134       7.980  53.025  -3.253  1.00103.04       1SG1040
ATOM   1040  N   PRO   135       6.445  54.218  -4.270  1.00131.03       1SG1041
ATOM   1041  CA  PRO   135       7.486  55.066  -4.774  1.00131.03       1SG1042
ATOM   1042  CD  PRO   135       5.405  54.082  -5.269  1.00131.03       1SG1043
ATOM   1043  CB  PRO   135       6.828  56.015  -5.752  1.00131.03       1SG1044
ATOM   1044  CG  PRO   135       5.766  55.103  -6.358  1.00131.03       1SG1045
ATOM   1045  C   PRO   135       8.409  55.722  -3.819  1.00131.03       1SG1046
ATOM   1046  O   PRO   135       9.501  56.076  -4.257  1.00131.03       1SG1047
ATOM   1047  N   PHE   136       8.032  55.920  -2.549  1.00 85.47       1SG1048
ATOM   1048  CA  PHE   136       8.996  56.524  -1.685  1.00 85.47       1SG1049
ATOM   1049  CB  PHE   136       8.514  56.685  -0.239  1.00 85.47       1SG1050
ATOM   1050  CG  PHE   136       9.704  57.148   0.526  1.00 85.47       1SG1051
ATOM   1051  CD1 PHE   136      10.066  58.475   0.543  1.00 85.47       1SG1052
ATOM   1052  CD2 PHE   136      10.469  56.240   1.221  1.00 85.47       1SG1053
ATOM   1053  CE1 PHE   136      11.171  58.888   1.251  1.00 85.47       1SG1054
ATOM   1054  CE2 PHE   136      11.573  56.647   1.929  1.00 85.47       1SG1055
ATOM   1055  CZ  PHE   136      11.926  57.974   1.944  1.00 85.47       1SG1056
ATOM   1056  C   PHE   136      10.168  55.602  -1.651  1.00 85.47       1SG1057
ATOM   1057  O   PHE   136      11.316  56.032  -1.733  1.00 85.47       1SG1058
ATOM   1058  N   ARG   137       9.890  54.293  -1.556  1.00117.99       1SG1059
ATOM   1059  CA  ARG   137      10.919  53.300  -1.493  1.00117.99       1SG1060
ATOM   1060  CB  ARG   137      10.351  51.906  -1.188  1.00117.99       1SG1061
ATOM   1061  CG  ARG   137       9.647  51.921   0.171  1.00117.99       1SG1062
ATOM   1062  CD  ARG   137       8.884  50.653   0.542  1.00117.99       1SG1063
ATOM   1063  NE  ARG   137       8.275  50.917   1.876  1.00117.99       1SG1064
ATOM   1064  CZ  ARG   137       7.179  50.222   2.300  1.00117.99       1SG1065
ATOM   1065  NH1 ARG   137       6.656  49.227   1.525  1.00117.99       1SG1066
ATOM   1066  NH2 ARG   137       6.603  50.526   3.499  1.00117.99       1SG1067
ATOM   1067  C   ARG   137      11.674  53.297  -2.787  1.00117.99       1SG1068
ATOM   1068  O   ARG   137      12.879  53.056  -2.804  1.00117.99       1SG1069
ATOM   1069  N   SER   138      10.979  53.555  -3.912  1.00 76.81       1SG1070
ATOM   1070  CA  SER   138      11.625  53.581  -5.196  1.00 76.81       1SG1071
ATOM   1071  CB  SER   138      10.638  53.882  -6.339  1.00 76.81       1SG1072
ATOM   1072  OG  SER   138      11.323  53.902  -7.583  1.00 76.81       1SG1073
ATOM   1073  C   SER   138      12.656  54.670  -5.188  1.00 76.81       1SG1074
ATOM   1074  O   SER   138      13.799  54.472  -5.597  1.00 76.81       1SG1075
ATOM   1075  N   LEU   139      12.272  55.864  -4.704  1.00 93.07       1SG1076
ATOM   1076  CA  LEU   139      13.177  56.974  -4.623  1.00 93.07       1SG1077
ATOM   1077  CB  LEU   139      12.492  58.240  -4.071  1.00 93.07       1SG1078
ATOM   1078  CG  LEU   139      11.659  59.040  -5.095  1.00 93.07       1SG1079
ATOM   1079  CD2 LEU   139      11.237  60.404  -4.518  1.00 93.07       1SG1080
ATOM   1080  CD1 LEU   139      10.471  58.235  -5.638  1.00 93.07       1SG1081
ATOM   1081  C   LEU   139      14.286  56.608  -3.684  1.00 93.07       1SG1082
ATOM   1082  O   LEU   139      15.458  56.851  -3.959  1.00 93.07       1SG1083
ATOM   1083  N   ALA   140      13.948  55.966  -2.555  1.00 36.31       1SG1084
ATOM   1084  CA  ALA   140      14.929  55.647  -1.557  1.00 36.31       1SG1085
ATOM   1085  CB  ALA   140      14.327  54.908  -0.349  1.00 36.31       1SG1086
ATOM   1086  C   ALA   140      15.977  54.758  -2.151  1.00 36.31       1SG1087
ATOM   1087  O   ALA   140      17.165  54.917  -1.872  1.00 36.31       1SG1088
ATOM   1088  N   GLY   141      15.567  53.798  -2.998  1.00 29.89       1SG1089
ATOM   1089  CA  GLY   141      16.514  52.887  -3.571  1.00 29.89       1SG1090
ATOM   1090  C   GLY   141      17.491  53.700  -4.349  1.00 29.89       1SG1091
ATOM   1091  O   GLY   141      18.691  53.428  -4.371  1.00 29.89       1SG1092
ATOM   1092  N   ALA   142      16.971  54.735  -5.014  1.00 52.17       1SG1093
ATOM   1093  CA  ALA   142      17.773  55.606  -5.806  1.00 52.17       1SG1094
ATOM   1094  CB  ALA   142      16.948  56.762  -6.325  1.00 52.17       1SG1095
ATOM   1095  C   ALA   142      18.790  56.240  -4.914  1.00 52.17       1SG1096
ATOM   1096  O   ALA   142      19.962  56.334  -5.273  1.00 52.17       1SG1097
ATOM   1097  N   LEU   143      18.363  56.677  -3.712  1.00108.49       1SG1098
ATOM   1098  CA  LEU   143      19.283  57.342  -2.831  1.00108.49       1SG1099
ATOM   1099  CB  LEU   143      18.746  57.603  -1.398  1.00108.49       1SG1100
ATOM   1100  CG  LEU   143      17.652  58.668  -1.140  1.00108.49       1SG1101
ATOM   1101  CD2 LEU   143      16.275  58.268  -1.692  1.00108.49       1SG1102
ATOM   1102  CD1 LEU   143      18.132  60.081  -1.517  1.00108.49       1SG1103
ATOM   1103  C   LEU   143      20.413  56.400  -2.564  1.00108.49       1SG1104
ATOM   1104  O   LEU   143      21.582  56.764  -2.679  1.00108.49       1SG1105
ATOM   1105  N   ARG   144      20.069  55.143  -2.221  1.00130.55       1SG1106
ATOM   1106  CA  ARG   144      21.051  54.185  -1.809  1.00130.55       1SG1107
ATOM   1107  CB  ARG   144      20.424  52.840  -1.403  1.00130.55       1SG1108
ATOM   1108  CG  ARG   144      21.435  51.839  -0.841  1.00130.55       1SG1109
ATOM   1109  CD  ARG   144      20.803  50.536  -0.348  1.00130.55       1SG1110
ATOM   1110  NE  ARG   144      19.969  50.863   0.844  1.00130.55       1SG1111
ATOM   1111  CZ  ARG   144      19.154  49.912   1.387  1.00130.55       1SG1112
ATOM   1112  NH1 ARG   144      19.116  48.660   0.844  1.00130.55       1SG1113
ATOM   1113  NH2 ARG   144      18.380  50.216   2.470  1.00130.55       1SG1114
ATOM   1114  C   ARG   144      22.012  53.926  -2.921  1.00130.55       1SG1115
ATOM   1115  O   ARG   144      23.223  53.922  -2.711  1.00130.55       1SG1116
ATOM   1116  N   MET   145      21.505  53.724  -4.148  1.00142.29       1SG1117
ATOM   1117  CA  MET   145      22.417  53.440  -5.214  1.00142.29       1SG1118
ATOM   1118  CB  MET   145      21.733  53.146  -6.558  1.00142.29       1SG1119
ATOM   1119  CG  MET   145      22.741  53.015  -7.702  1.00142.29       1SG1120
ATOM   1120  SD  MET   145      23.951  51.672  -7.501  1.00142.29       1SG1121
ATOM   1121  CE  MET   145      22.739  50.328  -7.575  1.00142.29       1SG1122
ATOM   1122  C   MET   145      23.310  54.612  -5.394  1.00142.29       1SG1123
ATOM   1123  O   MET   145      24.517  54.455  -5.578  1.00142.29       1SG1124
ATOM   1124  N   ALA   146      22.741  55.830  -5.330  1.00235.02       1SG1125
ATOM   1125  CA  ALA   146      23.568  56.985  -5.479  1.00235.02       1SG1126
ATOM   1126  CB  ALA   146      22.802  58.312  -5.346  1.00235.02       1SG1127
ATOM   1127  C   ALA   146      24.554  56.914  -4.369  1.00235.02       1SG1128
ATOM   1128  O   ALA   146      24.210  56.600  -3.232  1.00235.02       1SG1129
ATOM   1129  N   GLY   147      25.827  57.193  -4.670  1.00198.39       1SG1130
ATOM   1130  CA  GLY   147      26.790  57.068  -3.625  1.00198.39       1SG1131
ATOM   1131  C   GLY   147      26.813  55.617  -3.289  1.00198.39       1SG1132
ATOM   1132  O   GLY   147      26.744  54.765  -4.173  1.00198.39       1SG1133
ATOM   1133  N   GLY   148      26.904  55.300  -1.985  1.00 38.09       1SG1134
ATOM   1134  CA  GLY   148      26.912  53.927  -1.582  1.00 38.09       1SG1135
ATOM   1135  C   GLY   148      28.343  53.422  -1.678  1.00 38.09       1SG1136
ATOM   1136  O   GLY   148      29.226  54.195  -2.138  1.00 38.09       1SG1137
ATOM   1137  OXT GLY   148      28.570  52.246  -1.288  1.00 38.09       1SG1138
TER
END
