
#######################################################
#                                                     #
#                        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   10 (   89),  selected   10 , name T0385TS009_1_4-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected   10 , name T0385_D1.pdb
# PARAMETERS: T0385TS009_1_4-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:    10       142 - 151         3.18     3.18
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       142 - 145         0.67    11.15
  LONGEST_CONTINUOUS_SEGMENT:     4       143 - 146         1.69     8.01
  LONGEST_CONTINUOUS_SEGMENT:     4       146 - 149         1.75     5.46
  LONGEST_CONTINUOUS_SEGMENT:     4       147 - 150         1.92     7.62
  LCS_AVERAGE:      2.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       142 - 145         0.67    11.15
  LCS_AVERAGE:      2.52

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     T     142     T     142      4    4   10     3    4    6    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     143     R     143      4    4   10     3    4    4    4    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     W     144     W     144      4    4   10     3    4    6    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     145     N     145      4    4   10     3    4    4    4    6    6    6    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     146     R     146      3    4   10     3    3    6    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     V     147     V     147      3    4   10     3    3    6    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     148     L     148      3    4   10     3    3    3    4    6    6    6    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     G     149     G     149      3    4   10     3    3    6    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     150     A     150      3    4   10     3    3    6    6    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     W     151     W     151      3    3   10     3    3    3    3    6    6    8    8    9   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   4.27  (   2.52    2.89    7.41 )

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      6      6      8      8      9     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.22   2.96   4.44   4.44   4.44   4.44   5.93   5.93   6.67   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41
GDT RMS_LOCAL    0.01   0.67   1.11   1.11   1.11   1.11   2.32   2.32   3.06   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18
GDT RMS_ALL_CA   9.15  11.15   3.65   3.65   3.65   3.65   3.41   3.41   3.54   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18   3.18

#      Molecule1      Molecule2       DISTANCE
LGA    T     142      T     142          1.896
LGA    R     143      R     143          3.786
LGA    W     144      W     144          3.109
LGA    N     145      N     145          4.644
LGA    R     146      R     146          2.467
LGA    V     147      V     147          1.657
LGA    L     148      L     148          4.555
LGA    G     149      G     149          2.842
LGA    A     150      A     150          2.719
LGA    W     151      W     151          2.652

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  135    4.0      8    2.32     5.185     4.923     0.331

LGA_LOCAL      RMSD =  2.317  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.182  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  3.182  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.507914 * X  +  -0.487343 * Y  +  -0.710295 * Z  +  38.733395
  Y_new =   0.066501 * X  +  -0.799931 * Y  +   0.596396 * Z  +  -2.950172
  Z_new =  -0.858837 * X  +  -0.350153 * Y  +  -0.373888 * Z  + -30.463402 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.388963    0.752629  [ DEG:  -136.8775     43.1225 ]
  Theta =   1.032995    2.108598  [ DEG:    59.1862    120.8138 ]
  Phi   =   0.130188   -3.011405  [ DEG:     7.4592   -172.5408 ]
 
# 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_1_4-D1                             
REMARK     2: T0385_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_1_4-D1.T0385_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  135   4.0    8   2.32   4.923     3.18
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_1_4-D1
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM   1026  N   THR   142      21.072  24.986  16.197  1.00  0.00              
ATOM   1027  CA  THR   142      20.511  24.410  14.941  1.00  0.00              
ATOM   1028  C   THR   142      21.438  23.350  14.357  1.00  0.00              
ATOM   1029  O   THR   142      21.534  23.199  13.139  1.00  0.00              
ATOM   1030  CB  THR   142      19.121  23.790  15.176  1.00  0.00              
ATOM   1031  OG1 THR   142      18.737  23.976  16.544  1.00  0.00              
ATOM   1032  CG2 THR   142      18.086  24.441  14.271  1.00  0.00              
ATOM   1033  N   ARG   143      22.119  22.619  15.234  1.00  0.00              
ATOM   1034  CA  ARG   143      23.040  21.572  14.808  1.00  0.00              
ATOM   1035  C   ARG   143      23.519  21.807  13.379  1.00  0.00              
ATOM   1036  O   ARG   143      22.839  21.445  12.419  1.00  0.00              
ATOM   1037  CB  ARG   143      24.236  21.492  15.757  1.00  0.00              
ATOM   1038  CG  ARG   143      24.401  20.142  16.435  1.00  0.00              
ATOM   1039  CD  ARG   143      25.656  20.104  17.293  1.00  0.00              
ATOM   1040  NE  ARG   143      26.117  18.738  17.527  1.00  0.00              
ATOM   1041  CZ  ARG   143      27.098  18.154  16.848  1.00  0.00              
ATOM   1042  NH1 ARG   143      27.726  18.818  15.888  1.00  0.00              
ATOM   1043  NH2 ARG   143      27.450  16.907  17.131  1.00  0.00              
ATOM   1044  N   TRP   144      24.693  22.415  13.246  1.00  0.00              
ATOM   1045  CA  TRP   144      25.264  22.700  11.935  1.00  0.00              
ATOM   1046  C   TRP   144      24.417  23.712  11.172  1.00  0.00              
ATOM   1047  O   TRP   144      24.157  23.545   9.980  1.00  0.00              
ATOM   1048  CB  TRP   144      26.699  23.214  12.077  1.00  0.00              
ATOM   1049  CG  TRP   144      27.505  23.096  10.820  1.00  0.00              
ATOM   1050  CD1 TRP   144      28.840  23.337  10.676  1.00  0.00              
ATOM   1051  CD2 TRP   144      27.026  22.706   9.526  1.00  0.00              
ATOM   1052  NE1 TRP   144      29.225  23.122   9.376  1.00  0.00              
ATOM   1053  CE2 TRP   144      28.128  22.733   8.649  1.00  0.00              
ATOM   1054  CE3 TRP   144      25.773  22.337   9.027  1.00  0.00              
ATOM   1055  CZ2 TRP   144      28.015  22.406   7.298  1.00  0.00              
ATOM   1056  CZ3 TRP   144      25.664  22.012   7.688  1.00  0.00              
ATOM   1057  CH2 TRP   144      26.778  22.048   6.836  1.00  0.00              
ATOM   1058  N   ASN   145      23.989  24.761  11.866  1.00  0.00              
ATOM   1059  CA  ASN   145      23.170  25.802  11.255  1.00  0.00              
ATOM   1060  C   ASN   145      22.000  25.201  10.485  1.00  0.00              
ATOM   1061  O   ASN   145      21.492  25.804   9.539  1.00  0.00              
ATOM   1062  CB  ASN   145      22.656  26.773  12.320  1.00  0.00              
ATOM   1063  CG  ASN   145      22.941  28.221  11.974  1.00  0.00              
ATOM   1064  OD1 ASN   145      22.666  29.124  12.764  1.00  0.00              
ATOM   1065  ND2 ASN   145      23.495  28.446  10.788  1.00  0.00              
ATOM   1066  N   ARG   146      21.577  24.010  10.895  1.00  0.00              
ATOM   1067  CA  ARG   146      20.465  23.326  10.244  1.00  0.00              
ATOM   1068  C   ARG   146      20.667  23.260   8.734  1.00  0.00              
ATOM   1069  O   ARG   146      19.792  22.799   8.000  1.00  0.00              
ATOM   1070  CB  ARG   146      20.297  21.917  10.814  1.00  0.00              
ATOM   1071  CG  ARG   146      19.617  21.874  12.173  1.00  0.00              
ATOM   1072  CD  ARG   146      19.588  20.460  12.732  1.00  0.00              
ATOM   1073  NE  ARG   146      19.637  20.448  14.191  1.00  0.00              
ATOM   1074  CZ  ARG   146      18.673  20.919  14.975  1.00  0.00              
ATOM   1075  NH1 ARG   146      17.580  21.442  14.440  1.00  0.00              
ATOM   1076  NH2 ARG   146      18.806  20.866  16.294  1.00  0.00              
ATOM   1077  N   VAL   147      21.825  23.723   8.275  1.00  0.00              
ATOM   1078  CA  VAL   147      22.151  23.718   6.821  1.00  0.00              
ATOM   1079  C   VAL   147      20.906  23.965   5.975  1.00  0.00              
ATOM   1080  O   VAL   147      20.680  23.286   4.974  1.00  0.00              
ATOM   1081  CB  VAL   147      23.213  24.779   6.476  1.00  0.00              
ATOM   1082  CG1 VAL   147      24.480  24.116   5.960  1.00  0.00              
ATOM   1083  CG2 VAL   147      23.511  25.647   7.688  1.00  0.00              
ATOM   1084  N   LEU   148      20.102  24.941   6.386  1.00  0.00              
ATOM   1085  CA  LEU   148      18.879  25.279   5.668  1.00  0.00              
ATOM   1086  C   LEU   148      18.193  24.028   5.128  1.00  0.00              
ATOM   1087  O   LEU   148      17.740  24.003   3.984  1.00  0.00              
ATOM   1088  CB  LEU   148      17.921  26.052   6.576  1.00  0.00              
ATOM   1089  CG  LEU   148      17.545  25.377   7.897  1.00  0.00              
ATOM   1090  CD1 LEU   148      17.840  23.887   7.842  1.00  0.00              
ATOM   1091  CD2 LEU   148      16.082  25.628   8.230  1.00  0.00              
ATOM   1092  N   GLY   149      18.121  22.994   5.958  1.00  0.00              
ATOM   1093  CA  GLY   149      17.488  21.755   5.542  1.00  0.00              
ATOM   1094  C   GLY   149      17.650  21.490   4.059  1.00  0.00              
ATOM   1095  O   GLY   149      16.802  20.854   3.435  1.00  0.00              
ATOM   1096  N   ALA   150      18.745  21.981   3.487  1.00  0.00              
ATOM   1097  CA  ALA   150      19.018  21.795   2.067  1.00  0.00              
ATOM   1098  C   ALA   150      17.725  21.643   1.272  1.00  0.00              
ATOM   1099  O   ALA   150      17.732  21.679   0.042  1.00  0.00              
ATOM   1100  CB  ALA   150      19.831  22.961   1.526  1.00  0.00              
ATOM   1101  N   TRP   151      16.615  21.472   1.985  1.00  0.00              
ATOM   1102  CA  TRP   151      15.313  21.314   1.348  1.00  0.00              
ATOM   1103  C   TRP   151      15.416  21.474  -0.164  1.00  0.00              
ATOM   1104  O   TRP   151      14.410  21.624  -0.858  1.00  0.00              
ATOM   1105  CB  TRP   151      14.710  19.952   1.695  1.00  0.00              
ATOM   1106  CG  TRP   151      13.412  20.042   2.439  1.00  0.00              
ATOM   1107  CD1 TRP   151      12.699  19.007   2.972  1.00  0.00              
ATOM   1108  CD2 TRP   151      12.673  21.234   2.733  1.00  0.00              
ATOM   1109  NE1 TRP   151      11.562  19.479   3.580  1.00  0.00              
ATOM   1110  CE2 TRP   151      11.523  20.845   3.447  1.00  0.00              
ATOM   1111  CE3 TRP   151      12.873  22.590   2.463  1.00  0.00              
ATOM   1112  CZ2 TRP   151      10.574  21.763   3.895  1.00  0.00              
ATOM   1113  CZ3 TRP   151      11.931  23.500   2.907  1.00  0.00              
ATOM   1114  CH2 TRP   151      10.794  23.084   3.616  1.00  0.00              
TER
END
