
#######################################################
#                                                     #
#                        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   11 (   94),  selected   11 , name T0385TS009_4_2-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected   11 , name T0385_D1.pdb
# PARAMETERS: T0385TS009_4_2-D1.T0385_D1.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:    11       141 - 151         3.03     3.03
  LCS_AVERAGE:      8.15

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       141 - 145         1.96     5.45
  LCS_AVERAGE:      3.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       145 - 148         0.60     6.47
  LCS_AVERAGE:      2.49

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:  135
LCS_GDT     A     141     A     141      3    5   11     3    4    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     T     142     T     142      3    5   11     3    4    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     R     143     R     143      3    5   11     3    3    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     W     144     W     144      3    5   11     3    3    4    4    6    6    7    8   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     N     145     N     145      4    5   11     3    4    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     R     146     R     146      4    4   11     3    4    4    5    6    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     V     147     V     147      4    4   11     3    4    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     148     L     148      4    4   11     3    4    4    4    6    6    7    8   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     G     149     G     149      3    4   11     3    4    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A     150     A     150      3    4   11     3    3    6    6    6    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     W     151     W     151      3    4   11     3    4    6    6    7    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   4.65  (   2.49    3.30    8.15 )

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      3      4      6      6      7      7      9      9     10     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   2.22   2.96   4.44   4.44   5.19   5.19   6.67   6.67   7.41   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15
GDT RMS_LOCAL    0.02   0.60   1.00   1.00   1.40   1.40   2.14   2.14   2.58   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03
GDT RMS_ALL_CA  10.12   3.27   3.15   3.15   3.08   3.08   3.19   3.19   3.10   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03

#      Molecule1      Molecule2       DISTANCE
LGA    A     141      A     141          0.911
LGA    T     142      T     142          0.815
LGA    R     143      R     143          1.788
LGA    W     144      W     144          6.292
LGA    N     145      N     145          1.154
LGA    R     146      R     146          3.753
LGA    V     147      V     147          2.132
LGA    L     148      L     148          4.667
LGA    G     149      G     149          1.544
LGA    A     150      A     150          3.846
LGA    W     151      W     151          1.655

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  135    4.0      9    2.14     5.556     5.416     0.402

LGA_LOCAL      RMSD =  2.141  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.103  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  3.034  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.935330 * X  +  -0.148369 * Y  +   0.321160 * Z  +  -0.165211
  Y_new =   0.184399 * X  +   0.979198 * Y  +  -0.084668 * Z  +   6.066897
  Z_new =  -0.301917 * X  +   0.138414 * Y  +   0.943232 * Z  +  44.709332 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.145705   -2.995888  [ DEG:     8.3483   -171.6517 ]
  Theta =   0.306703    2.834890  [ DEG:    17.5728    162.4272 ]
  Phi   =   0.194653   -2.946940  [ DEG:    11.1528   -168.8472 ]
 
# 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: T0385TS009_4_2-D1                             
REMARK     2: T0385_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_4_2-D1.T0385_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  135   4.0    9   2.14   5.416     3.03
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_4_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1021  N   ALA   141      24.276  21.441  17.652  1.00  0.00              
ATOM   1022  CA  ALA   141      23.043  21.979  17.091  1.00  0.00              
ATOM   1023  C   ALA   141      23.094  23.501  17.006  1.00  0.00              
ATOM   1024  O   ALA   141      23.617  24.165  17.901  1.00  0.00              
ATOM   1025  CB  ALA   141      22.784  21.386  15.714  1.00  0.00              
ATOM   1026  N   THR   142      22.547  24.047  15.924  1.00  0.00              
ATOM   1027  CA  THR   142      22.529  25.523  15.716  1.00  0.00              
ATOM   1028  C   THR   142      22.656  25.873  14.237  1.00  0.00              
ATOM   1029  O   THR   142      22.089  26.861  13.773  1.00  0.00              
ATOM   1030  CB  THR   142      21.240  26.156  16.273  1.00  0.00              
ATOM   1031  OG1 THR   142      20.428  25.141  16.876  1.00  0.00              
ATOM   1032  CG2 THR   142      21.574  27.214  17.314  1.00  0.00              
ATOM   1033  N   ARG   143      23.405  25.056  13.504  1.00  0.00              
ATOM   1034  CA  ARG   143      23.610  25.278  12.077  1.00  0.00              
ATOM   1035  C   ARG   143      22.289  25.562  11.369  1.00  0.00              
ATOM   1036  O   ARG   143      21.988  24.967  10.334  1.00  0.00              
ATOM   1037  CB  ARG   143      24.587  26.431  11.849  1.00  0.00              
ATOM   1038  CG  ARG   143      25.906  26.011  11.220  1.00  0.00              
ATOM   1039  CD  ARG   143      26.635  27.202  10.619  1.00  0.00              
ATOM   1040  NE  ARG   143      27.756  26.791   9.778  1.00  0.00              
ATOM   1041  CZ  ARG   143      27.649  26.486   8.488  1.00  0.00              
ATOM   1042  NH1 ARG   143      26.468  26.547   7.889  1.00  0.00              
ATOM   1043  NH2 ARG   143      28.723  26.122   7.802  1.00  0.00              
ATOM   1044  N   TRP   144      21.504  26.474  11.933  1.00  0.00              
ATOM   1045  CA  TRP   144      20.215  26.838  11.358  1.00  0.00              
ATOM   1046  C   TRP   144      19.535  25.631  10.720  1.00  0.00              
ATOM   1047  O   TRP   144      19.400  25.556   9.499  1.00  0.00              
ATOM   1048  CB  TRP   144      19.306  27.452  12.425  1.00  0.00              
ATOM   1049  CG  TRP   144      18.895  28.861  12.123  1.00  0.00              
ATOM   1050  CD1 TRP   144      17.624  29.358  12.107  1.00  0.00              
ATOM   1051  CD2 TRP   144      19.759  29.956  11.793  1.00  0.00              
ATOM   1052  NE1 TRP   144      17.641  30.695  11.789  1.00  0.00              
ATOM   1053  CE2 TRP   144      18.941  31.085  11.592  1.00  0.00              
ATOM   1054  CE3 TRP   144      21.143  30.089  11.651  1.00  0.00              
ATOM   1055  CZ2 TRP   144      19.463  32.333  11.253  1.00  0.00              
ATOM   1056  CZ3 TRP   144      21.657  31.327  11.316  1.00  0.00              
ATOM   1057  CH2 TRP   144      20.820  32.436  11.120  1.00  0.00              
ATOM   1058  N   ASN   145      19.108  24.690  11.555  1.00  0.00              
ATOM   1059  CA  ASN   145      18.442  23.485  11.076  1.00  0.00              
ATOM   1060  C   ASN   145      19.433  22.530  10.421  1.00  0.00              
ATOM   1061  O   ASN   145      19.064  21.730   9.560  1.00  0.00              
ATOM   1062  CB  ASN   145      17.714  22.783  12.224  1.00  0.00              
ATOM   1063  CG  ASN   145      16.806  21.668  11.741  1.00  0.00              
ATOM   1064  OD1 ASN   145      15.661  21.554  12.179  1.00  0.00              
ATOM   1065  ND2 ASN   145      17.316  20.840  10.836  1.00  0.00              
ATOM   1066  N   ARG   146      20.694  22.619  10.833  1.00  0.00              
ATOM   1067  CA  ARG   146      21.740  21.763  10.287  1.00  0.00              
ATOM   1068  C   ARG   146      21.637  21.665   8.769  1.00  0.00              
ATOM   1069  O   ARG   146      22.459  22.224   8.043  1.00  0.00              
ATOM   1070  CB  ARG   146      23.122  22.285  10.687  1.00  0.00              
ATOM   1071  CG  ARG   146      23.581  21.834  12.064  1.00  0.00              
ATOM   1072  CD  ARG   146      24.843  22.565  12.493  1.00  0.00              
ATOM   1073  NE  ARG   146      24.959  22.650  13.946  1.00  0.00              
ATOM   1074  CZ  ARG   146      25.081  21.598  14.748  1.00  0.00              
ATOM   1075  NH1 ARG   146      25.102  20.374  14.238  1.00  0.00              
ATOM   1076  NH2 ARG   146      25.180  21.772  16.059  1.00  0.00              
ATOM   1077  N   VAL   147      20.621  20.951   8.295  1.00  0.00              
ATOM   1078  CA  VAL   147      20.404  20.775   6.830  1.00  0.00              
ATOM   1079  C   VAL   147      20.478  22.110   6.097  1.00  0.00              
ATOM   1080  O   VAL   147      19.825  22.302   5.071  1.00  0.00              
ATOM   1081  CB  VAL   147      21.433  19.807   6.219  1.00  0.00              
ATOM   1082  CG1 VAL   147      20.735  18.594   5.622  1.00  0.00              
ATOM   1083  CG2 VAL   147      22.452  19.382   7.265  1.00  0.00              
ATOM   1084  N   LEU   148      21.276  23.029   6.630  1.00  0.00              
ATOM   1085  CA  LEU   148      21.436  24.347   6.028  1.00  0.00              
ATOM   1086  C   LEU   148      20.229  24.711   5.170  1.00  0.00              
ATOM   1087  O   LEU   148      20.299  24.688   3.941  1.00  0.00              
ATOM   1088  CB  LEU   148      21.653  25.407   7.109  1.00  0.00              
ATOM   1089  CG  LEU   148      20.455  25.712   8.011  1.00  0.00              
ATOM   1090  CD1 LEU   148      19.217  24.973   7.526  1.00  0.00              
ATOM   1091  CD2 LEU   148      20.199  27.208   8.078  1.00  0.00              
ATOM   1092  N   GLY   149      19.124  25.049   5.826  1.00  0.00              
ATOM   1093  CA  GLY   149      17.918  25.413   5.104  1.00  0.00              
ATOM   1094  C   GLY   149      17.362  24.265   4.286  1.00  0.00              
ATOM   1095  O   GLY   149      17.136  24.399   3.084  1.00  0.00              
ATOM   1096  N   ALA   150      17.139  23.128   4.939  1.00  0.00              
ATOM   1097  CA  ALA   150      16.607  21.950   4.265  1.00  0.00              
ATOM   1098  C   ALA   150      17.550  21.466   3.170  1.00  0.00              
ATOM   1099  O   ALA   150      17.728  20.263   2.977  1.00  0.00              
ATOM   1100  CB  ALA   150      16.352  20.836   5.268  1.00  0.00              
ATOM   1101  N   TRP   151      18.155  22.410   2.456  1.00  0.00              
ATOM   1102  CA  TRP   151      19.081  22.082   1.379  1.00  0.00              
ATOM   1103  C   TRP   151      20.073  21.008   1.814  1.00  0.00              
ATOM   1104  O   TRP   151      21.082  20.768   1.151  1.00  0.00              
ATOM   1105  CB  TRP   151      18.317  21.622   0.136  1.00  0.00              
ATOM   1106  CG  TRP   151      17.666  22.743  -0.615  1.00  0.00              
ATOM   1107  CD1 TRP   151      17.428  22.800  -1.958  1.00  0.00              
ATOM   1108  CD2 TRP   151      17.166  23.968  -0.067  1.00  0.00              
ATOM   1109  NE1 TRP   151      16.812  23.985  -2.282  1.00  0.00              
ATOM   1110  CE2 TRP   151      16.639  24.720  -1.136  1.00  0.00              
ATOM   1111  CE3 TRP   151      17.112  24.502   1.225  1.00  0.00              
ATOM   1112  CZ2 TRP   151      16.067  25.978  -0.954  1.00  0.00              
ATOM   1113  CZ3 TRP   151      16.545  25.749   1.403  1.00  0.00              
ATOM   1114  CH2 TRP   151      16.029  26.476   0.320  1.00  0.00              
TER
END
