
#######################################################
#                                                     #
#                        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    6 (   42),  selected    6 , name T0320TS074_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected    6 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_1-D1.T0320_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:     6       222 - 227         3.20     3.20
  LCS_AVERAGE:      2.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       224 - 227         1.68     4.69
  LCS_AVERAGE:      1.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       222 - 224         0.51     7.83
  LONGEST_CONTINUOUS_SEGMENT:     3       224 - 226         0.58     4.92
  LONGEST_CONTINUOUS_SEGMENT:     3       225 - 227         0.74     7.42
  LCS_AVERAGE:      1.40

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:  214
LCS_GDT     T     222     T     222      3    3    6     0    3    3    3    3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     223     S     223      3    3    6     1    3    3    3    3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     224     I     224      3    4    6     0    3    3    3    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     225     G     225      3    4    6     0    3    3    3    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     226     G     226      3    4    6     0    3    3    3    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     227     I     227      3    4    6     0    3    3    3    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   1.97  (   1.40    1.71    2.80 )

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      1      3      3      3      4      4      4      5      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   0.47   1.40   1.40   1.40   1.87   1.87   1.87   2.34   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_LOCAL   31.63   0.51   0.51   0.51   1.68   1.68   1.68   2.56   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20
GDT RMS_ALL_CA   7.83   7.83   7.83   7.83   4.69   4.69   4.69   3.81   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20   3.20

#      Molecule1      Molecule2       DISTANCE
LGA    T     222      T     222          7.357
LGA    S     223      S     223          3.593
LGA    I     224      I     224          1.337
LGA    G     225      G     225          1.637
LGA    G     226      G     226          2.354
LGA    I     227      I     227          3.147

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  214    4.0      5    2.56     1.986     2.021     0.188

LGA_LOCAL      RMSD =  2.562  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.807  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.198  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.692313 * X  +  -0.677682 * Y  +   0.247893 * Z  +  14.941325
  Y_new =   0.149689 * X  +  -0.470934 * Y  +  -0.869376 * Z  +  27.288742
  Z_new =   0.705901 * X  +  -0.564773 * Y  +   0.427475 * Z  +   7.733218 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.922895    2.218697  [ DEG:   -52.8780    127.1220 ]
  Theta =  -0.783694   -2.357898  [ DEG:   -44.9024   -135.0976 ]
  Phi   =   2.928654   -0.212938  [ DEG:   167.7995    -12.2005 ]
 
# 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: T0320TS074_1-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_1-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  214   4.0    5   2.56   2.021     3.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_1-D1
PFRMAT TS
TARGET T0320
MODEL  1
PARENT N/A
ATOM      1  N   THR   222      21.154  16.424  13.352  1.00  1.00
ATOM      2  CA  THR   222      22.322  17.303  13.634  1.00  1.00
ATOM      3  C   THR   222      22.564  18.201  12.407  1.00  1.00
ATOM      4  O   THR   222      23.570  18.892  12.328  1.00  1.00
ATOM      5  CB  THR   222      23.622  16.523  13.930  1.00  1.00
ATOM      6  OG1 THR   222      24.095  15.667  12.772  1.00  1.00
ATOM      7  CG2 THR   222      23.507  15.568  15.102  1.00  1.00
ATOM      8  N   SER   223      21.608  18.276  11.501  1.00  1.00
ATOM      9  CA  SER   223      21.858  19.076  10.306  1.00  1.00
ATOM     10  C   SER   223      22.044  20.560  10.488  1.00  1.00
ATOM     11  O   SER   223      22.924  21.136   9.846  1.00  1.00
ATOM     12  HN  SER   223      20.705  17.845  11.520  1.00  1.00
ATOM     13  CB  SER   223      20.798  18.835   9.244  1.00  1.00
ATOM     14  OG  SER   223      20.793  17.534   8.731  1.00  1.00
ATOM     15  N   ILE   224      21.220  21.193  11.333  1.00  1.00
ATOM     16  CA  ILE   224      21.352  22.652  11.506  1.00  1.00
ATOM     17  C   ILE   224      22.772  23.036  11.933  1.00  1.00
ATOM     18  O   ILE   224      23.348  23.947  11.384  1.00  1.00
ATOM     19  HN  ILE   224      20.495  20.781  11.885  1.00  1.00
ATOM     20  CB  ILE   224      20.375  23.171  12.579  1.00  1.00
ATOM     21  CG1 ILE   224      18.889  22.885  12.370  1.00  1.00
ATOM     22  CG2 ILE   224      20.661  24.664  12.758  1.00  1.00
ATOM     23  CD1 ILE   224      18.264  23.400  11.187  1.00  1.00
ATOM     24  N   GLY   225      23.306  22.336  12.924  1.00  1.00
ATOM     25  CA  GLY   225      24.638  22.602  13.449  1.00  1.00
ATOM     26  C   GLY   225      25.759  22.516  12.392  1.00  1.00
ATOM     27  O   GLY   225      26.656  23.364  12.288  1.00  1.00
ATOM     28  HN  GLY   225      22.834  21.580  13.378  1.00  1.00
ATOM     29  N   GLY   226      25.708  21.450  11.608  1.00  1.00
ATOM     30  CA  GLY   226      26.735  21.220  10.592  1.00  1.00
ATOM     31  C   GLY   226      26.518  22.209   9.449  1.00  1.00
ATOM     32  O   GLY   226      27.449  22.879   9.027  1.00  1.00
ATOM     33  HN  GLY   226      25.000  20.745  11.638  1.00  1.00
ATOM     34  N   ILE   227      25.283  22.320   8.967  1.00  1.00
ATOM     35  CA  ILE   227      24.979  23.246   7.891  1.00  1.00
ATOM     36  C   ILE   227      25.448  24.657   8.239  1.00  1.00
ATOM     37  O   ILE   227      26.115  25.310   7.448  1.00  1.00
ATOM     38  HN  ILE   227      24.492  21.799   9.290  1.00  1.00
ATOM     39  CB  ILE   227      23.476  23.271   7.580  1.00  1.00
ATOM     40  CG1 ILE   227      23.205  24.185   6.414  1.00  1.00
ATOM     41  CG2 ILE   227      22.750  23.609   8.886  1.00  1.00
ATOM     42  CD1 ILE   227      21.714  23.898   5.856  1.00  1.00
TER
END
