
#######################################################
#                                                     #
#                        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 (   88),  selected   18 , name T0301TS239_5_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   18 , name T0301_D1.pdb
# PARAMETERS: T0301TS239_5_2-D1.T0301_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:    18       378 - 395         4.39     4.39
  LCS_AVERAGE:      9.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       378 - 384         1.82    15.26
  LONGEST_CONTINUOUS_SEGMENT:     7       380 - 386         1.94    16.46
  LCS_AVERAGE:      3.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       378 - 383         0.89    22.10
  LCS_AVERAGE:      2.28

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:  200
LCS_GDT     R     378     R     378      6    7   18     4    5    6    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     S     379     S     379      6    7   18     4    5    6    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     A     380     A     380      6    7   18     4    5    6    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     R     381     R     381      6    7   18     4    5    6    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     I     382     I     382      6    7   18     4    5    6    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     L     383     L     383      6    7   18     3    3    6    6    7    8    9    9   11   12   14   16   16   17   17   18   18   18   18   18 
LCS_GDT     M     384     M     384      3    7   18     3    3    4    5    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     E     385     E     385      3    7   18     0    3    4    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     G     386     G     386      3    7   18     0    3    4    5    7    8    9   11   12   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     W     387     W     387      3    6   18     0    4    5    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     V     388     V     388      3    6   18     1    3    3    4    5   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     R     389     R     389      3    4   18     0    4    5    7    9   10   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     V     390     V     390      3    4   18     3    3    3    3    4    5    6    9   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     P     391     P     391      5    5   18     4    4    5    5    5    5    6    6    8    8   12   13   14   17   17   18   18   18   18   18 
LCS_GDT     G     392     G     392      5    5   18     4    4    5    5    5    5    6    8   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     D     393     D     393      5    5   18     4    4    5    5    5    5    6    7    8    8   10   12   14   15   17   18   18   18   18   18 
LCS_GDT     A     394     A     394      5    5   18     4    4    5    5    5    5    6    8   10   13   15   16   16   17   17   18   18   18   18   18 
LCS_GDT     F     395     F     395      5    5   18     3    3    5    5    5    5   11   11   13   13   15   16   16   17   17   18   18   18   18   18 
LCS_AVERAGE  LCS_A:   4.76  (   2.28    3.00    9.00 )

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      5      6      7      9     10     11     11     13     13     15     16     16     17     17     18     18     18     18     18 
GDT PERCENT_CA   2.00   2.50   3.00   3.50   4.50   5.00   5.50   5.50   6.50   6.50   7.50   8.00   8.00   8.50   8.50   9.00   9.00   9.00   9.00   9.00
GDT RMS_LOCAL    0.15   0.48   0.89   1.43   1.75   1.96   2.23   2.23   3.03   2.93   3.49   3.72   3.72   4.05   4.05   4.39   4.39   4.39   4.39   4.39
GDT RMS_ALL_CA  26.05  24.80  22.10   5.11   5.00   4.93   4.83   4.83   4.53   4.69   4.49   4.48   4.48   4.43   4.43   4.39   4.39   4.39   4.39   4.39

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378          0.988
LGA    S     379      S     379          1.864
LGA    A     380      A     380          1.732
LGA    R     381      R     381          1.676
LGA    I     382      I     382          1.591
LGA    L     383      L     383          6.194
LGA    M     384      M     384          2.966
LGA    E     385      E     385          1.626
LGA    G     386      G     386          4.235
LGA    W     387      W     387          1.971
LGA    V     388      V     388          3.174
LGA    R     389      R     389          2.002
LGA    V     390      V     390          6.194
LGA    P     391      P     391          8.926
LGA    G     392      G     392          6.302
LGA    D     393      D     393          9.988
LGA    A     394      A     394          7.404
LGA    F     395      F     395          3.999

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  200    4.0     11    2.23     5.125     4.849     0.472

LGA_LOCAL      RMSD =  2.228  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.870  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  4.394  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.042460 * X  +   0.845717 * Y  +  -0.531940 * Z  +  76.364853
  Y_new =  -0.508507 * X  +  -0.440007 * Y  +  -0.740145 * Z  +  54.682270
  Z_new =  -0.860010 * X  +   0.301921 * Y  +   0.411370 * Z  +  12.690273 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.633144   -2.508449  [ DEG:    36.2765   -143.7235 ]
  Theta =   1.035290    2.106303  [ DEG:    59.3177    120.6823 ]
  Phi   =  -1.487490    1.654102  [ DEG:   -85.2269     94.7731 ]
 
# 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: T0301TS239_5_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS239_5_2-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  200   4.0   11   2.23   4.849     4.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS239_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT 1xub_A
ATOM    554  N   ARG   378      80.483  16.644  19.781  1.00  9.99
ATOM    555  CA  ARG   378      79.076  16.755  19.422  1.00  9.99
ATOM    556  C   ARG   378      78.580  18.135  19.781  1.00  9.99
ATOM    557  O   ARG   378      78.644  18.537  20.927  1.00  9.99
ATOM    558  CB  ARG   378      78.255  15.692  20.125  1.00  9.99
ATOM    559  N   SER   379      78.076  18.875  18.781  1.00  9.99
ATOM    560  CA  SER   379      77.625  20.233  19.025  1.00  9.99
ATOM    561  C   SER   379      76.327  20.341  19.795  1.00  9.99
ATOM    562  O   SER   379      75.593  19.378  19.922  1.00  9.99
ATOM    563  CB  SER   379      77.464  20.801  17.660  1.00  9.99
ATOM    564  N   ALA   380      76.077  21.587  20.253  1.00  9.99
ATOM    565  CA  ALA   380      74.777  22.035  20.710  1.00  9.99
ATOM    566  C   ALA   380      74.334  23.156  19.870  1.00  9.99
ATOM    567  O   ALA   380      75.093  23.675  19.046  1.00  9.99
ATOM    568  CB  ALA   380      74.905  22.428  22.163  1.00  9.99
ATOM    569  N   ARG   381      73.031  23.503  19.948  1.00  9.99
ATOM    570  CA  ARG   381      72.492  24.490  19.037  1.00  9.99
ATOM    571  C   ARG   381      71.213  25.106  19.620  1.00  9.99
ATOM    572  O   ARG   381      70.542  24.486  20.445  1.00  9.99
ATOM    573  CB  ARG   381      72.188  23.848  17.655  1.00  9.99
ATOM    574  N   ILE   382      70.929  26.260  19.116  1.00  9.99
ATOM    575  CA  ILE   382      69.690  26.974  19.428  1.00  9.99
ATOM    576  C   ILE   382      69.365  27.978  18.346  1.00  9.99
ATOM    577  O   ILE   382      70.219  28.268  17.486  1.00  9.99
ATOM    578  CB  ILE   382      69.784  27.569  20.859  1.00  9.99
ATOM    579  N   LEU   383      68.184  28.573  18.387  1.00  9.99
ATOM    580  CA  LEU   383      67.829  29.619  17.426  1.00  9.99
ATOM    581  C   LEU   383      68.705  30.844  17.709  1.00  9.99
ATOM    582  O   LEU   383      68.974  31.197  18.903  1.00  9.99
ATOM    583  CB  LEU   383      66.422  30.082  17.630  1.00  9.99
ATOM    584  N   MET   384      69.230  31.510  16.693  1.00  9.99
ATOM    585  CA  MET   384      70.007  32.687  16.849  1.00  9.99
ATOM    586  C   MET   384      69.182  33.780  17.525  1.00  9.99
ATOM    587  O   MET   384      69.731  34.529  18.368  1.00  9.99
ATOM    588  CB  MET   384      70.499  33.171  15.489  1.00  9.99
ATOM    589  N   GLU   385      67.973  34.030  17.057  1.00  9.99
ATOM    590  CA  GLU   385      67.083  35.053  17.563  1.00  9.99
ATOM    591  C   GLU   385      67.523  36.452  17.225  1.00  9.99
ATOM    592  O   GLU   385      67.031  37.416  17.857  1.00  9.99
ATOM    593  CB  GLU   385      66.952  34.883  19.086  1.00  9.99
ATOM    594  N   GLY   386      68.257  36.616  16.147  1.00  9.99
ATOM    595  CA  GLY   386      68.685  37.918  15.583  1.00  9.99
ATOM    596  C   GLY   386      68.524  37.963  14.054  1.00  9.99
ATOM    597  O   GLY   386      69.302  38.488  13.316  1.00  9.99
ATOM    598  N   TRP   387      67.373  37.385  13.596  1.00  9.99
ATOM    599  CA  TRP   387      67.252  37.058  12.174  1.00  9.99
ATOM    600  C   TRP   387      67.224  38.295  11.322  1.00  9.99
ATOM    601  O   TRP   387      67.940  38.394  10.305  1.00  9.99
ATOM    602  CB  TRP   387      66.037  36.202  11.890  1.00  9.99
ATOM    603  N   VAL   388      66.343  39.283  11.644  1.00  9.99
ATOM    604  CA  VAL   388      66.260  40.458  10.800  1.00  9.99
ATOM    605  C   VAL   388      67.637  41.172  10.689  1.00  9.99
ATOM    606  O   VAL   388      67.991  41.586   9.581  1.00  9.99
ATOM    607  CB  VAL   388      65.133  41.443  11.218  1.00  9.99
ATOM    608  N   ARG   389      68.296  41.322  11.824  1.00  9.99
ATOM    609  CA  ARG   389      69.614  41.981  11.822  1.00  9.99
ATOM    610  C   ARG   389      70.657  41.225  10.926  1.00  9.99
ATOM    611  O   ARG   389      71.334  41.822  10.088  1.00  9.99
ATOM    612  CB  ARG   389      70.115  42.007  13.221  1.00  9.99
ATOM    613  N   VAL   390      70.646  39.876  11.047  1.00  9.99
ATOM    614  CA  VAL   390      71.614  39.110  10.294  1.00  9.99
ATOM    615  C   VAL   390      71.296  39.154   8.787  1.00  9.99
ATOM    616  O   VAL   390      72.189  39.312   7.962  1.00  9.99
ATOM    617  CB  VAL   390      71.632  37.685  10.799  1.00  9.99
ATOM    618  N   PRO   391      70.004  38.958   8.433  1.00  9.99
ATOM    619  CA  PRO   391      69.585  38.976   7.080  1.00  9.99
ATOM    620  C   PRO   391      69.893  40.327   6.422  1.00  9.99
ATOM    621  O   PRO   391      70.356  40.351   5.311  1.00  9.99
ATOM    622  CB  PRO   391      68.094  38.630   7.019  1.00  9.99
ATOM    623  N   GLY   392      69.643  41.401   7.166  1.00  9.99
ATOM    624  CA  GLY   392      70.003  42.771   6.716  1.00  9.99
ATOM    625  C   GLY   392      71.519  42.834   6.335  1.00  9.99
ATOM    626  O   GLY   392      71.857  43.324   5.261  1.00  9.99
ATOM    627  N   ASP   393      72.323  42.336   7.268  1.00  9.99
ATOM    628  CA  ASP   393      73.758  42.364   7.100  1.00  9.99
ATOM    629  C   ASP   393      74.166  41.581   5.894  1.00  9.99
ATOM    630  O   ASP   393      75.079  41.999   5.139  1.00  9.99
ATOM    631  CB  ASP   393      74.378  41.938   8.317  1.00  9.99
ATOM    632  N   ALA   394      73.522  40.436   5.656  1.00  9.99
ATOM    633  CA  ALA   394      73.804  39.673   4.428  1.00  9.99
ATOM    634  C   ALA   394      73.245  40.180   3.136  1.00  9.99
ATOM    635  O   ALA   394      73.672  39.750   2.065  1.00  9.99
ATOM    636  CB  ALA   394      73.314  38.222   4.643  1.00  9.99
ATOM    637  N   PHE   395      72.267  41.093   3.235  1.00  9.99
ATOM    638  CA  PHE   395      71.669  41.652   2.054  1.00  9.99
ATOM    639  C   PHE   395      70.503  40.889   1.462  1.00  9.99
ATOM    640  O   PHE   395      70.208  41.036   0.245  1.00  9.99
ATOM    641  CB  PHE   395      72.782  41.812   1.005  1.00  9.99
TER
END
