
#######################################################
#                                                     #
#                        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    9 (   42),  selected    9 , name T0320TS103_1_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected    9 , name T0320_D1.pdb
# PARAMETERS: T0320TS103_1_2-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:     9       218 - 227         3.36     3.36
  LCS_AVERAGE:      4.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       221 - 227         1.88     4.72
  LCS_AVERAGE:      3.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       222 - 227         0.70     6.27
  LCS_AVERAGE:      2.02

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     G     218     G     218      0    5    9     0    2    3    3    5    5    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     219     K     219      0    5    9     0    0    3    4    5    6    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     F     221     F     221      3    7    9     3    3    3    4    5    7    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     T     222     T     222      6    7    9     4    5    6    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S     223     S     223      6    7    9     3    5    6    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     I     224     I     224      6    7    9     4    5    6    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     G     225     G     225      6    7    9     4    5    6    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     G     226     G     226      6    7    9     4    5    6    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     I     227     I     227      6    7    9     3    5    6    6    6    7    7    7    7    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   3.10  (   2.02    3.06    4.21 )

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      6      6      7      7      7      8      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   1.87   2.34   2.80   2.80   2.80   3.27   3.27   3.27   3.74   4.21   4.21   4.21   4.21   4.21   4.21   4.21   4.21   4.21   4.21   4.21
GDT RMS_LOCAL    0.31   0.47   0.70   0.70   0.70   1.88   1.88   1.88   3.17   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36
GDT RMS_ALL_CA   6.38   6.03   6.27   6.27   6.27   4.72   4.72   4.72   3.59   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36

#      Molecule1      Molecule2       DISTANCE
LGA    G     218      G     218         10.251
LGA    K     219      K     219          8.397
LGA    F     221      F     221          3.945
LGA    T     222      T     222          1.319
LGA    S     223      S     223          1.891
LGA    I     224      I     224          0.873
LGA    G     225      G     225          0.552
LGA    G     226      G     226          0.886
LGA    I     227      I     227          1.456

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  214    4.0      7    1.88     3.154     3.295     0.353

LGA_LOCAL      RMSD =  1.884  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.719  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  3.360  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.813457 * X  +  -0.579656 * Y  +   0.047819 * Z  +  48.496445
  Y_new =   0.344479 * X  +   0.546399 * Y  +   0.763401 * Z  + -32.423157
  Z_new =  -0.468639 * X  +  -0.604521 * Y  +   0.644152 * Z  +  26.924171 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.753671    2.387922  [ DEG:   -43.1822    136.8178 ]
  Theta =   0.487749    2.653843  [ DEG:    27.9460    152.0540 ]
  Phi   =   0.400579   -2.741014  [ DEG:    22.9515   -157.0485 ]
 
# 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: T0320TS103_1_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS103_1_2-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  214   4.0    7   1.88   3.295     3.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS103_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1se8_A
ATOM      1  N   GLY   218       7.573  13.811   3.510  1.00  1.00
ATOM      2  CA  GLY   218       9.017  13.830   3.377  1.00  1.00
ATOM      3  C   GLY   218       9.530  15.064   4.093  1.00  1.00
ATOM      4  O   GLY   218       9.334  16.188   3.618  1.00  1.00
ATOM      5  N   LYS   219      10.116  14.859   5.272  1.00  1.00
ATOM      6  CA  LYS   219      10.617  15.960   6.079  1.00  1.00
ATOM      7  C   LYS   219      11.996  15.664   6.652  1.00  1.00
ATOM      8  O   LYS   219      12.249  14.578   7.172  1.00  1.00
ATOM      9  CB  LYS   219       9.659  16.281   7.225  1.00  1.00
ATOM     10  N   PHE   221      12.873  16.661   6.576  1.00  1.00
ATOM     11  CA  PHE   221      14.205  16.573   7.136  1.00  1.00
ATOM     12  C   PHE   221      14.426  17.757   8.060  1.00  1.00
ATOM     13  O   PHE   221      14.010  18.868   7.750  1.00  1.00
ATOM     14  CB  PHE   221      15.291  16.618   6.028  1.00  1.00
ATOM     15  N   THR   222      15.053  17.496   9.200  1.00  1.00
ATOM     16  CA  THR   222      15.522  18.547  10.105  1.00  1.00
ATOM     17  C   THR   222      16.954  18.220  10.457  1.00  1.00
ATOM     18  O   THR   222      17.231  17.167  11.016  1.00  1.00
ATOM     19  CB  THR   222      14.674  18.597  11.396  1.00  1.00
ATOM     20  N   SER   223      17.864  19.116  10.108  1.00  1.00
ATOM     21  CA  SER   223      19.277  18.922  10.441  1.00  1.00
ATOM     22  C   SER   223      19.843  20.205  11.030  1.00  1.00
ATOM     23  O   SER   223      19.408  21.304  10.696  1.00  1.00
ATOM     24  CB  SER   223      20.140  18.478   9.212  1.00  1.00
ATOM     25  N   ILE   224      20.817  20.050  11.900  1.00  1.00
ATOM     26  CA  ILE   224      21.463  21.184  12.531  1.00  1.00
ATOM     27  C   ILE   224      22.923  20.811  12.652  1.00  1.00
ATOM     28  O   ILE   224      23.265  19.748  13.199  1.00  1.00
ATOM     29  CB  ILE   224      20.844  21.459  13.907  1.00  1.00
ATOM     30  N   GLY   225      23.783  21.667  12.108  1.00  1.00
ATOM     31  CA  GLY   225      25.212  21.432  12.126  1.00  1.00
ATOM     32  C   GLY   225      25.962  22.719  11.831  1.00  1.00
ATOM     33  O   GLY   225      25.464  23.809  12.122  1.00  1.00
ATOM     34  N   GLY   226      27.151  22.606  11.250  1.00  1.00
ATOM     35  CA  GLY   226      27.939  23.794  10.925  1.00  1.00
ATOM     36  C   GLY   226      28.373  23.757   9.481  1.00  1.00
ATOM     37  O   GLY   226      28.678  22.690   8.941  1.00  1.00
ATOM     38  N   ILE   227      28.422  24.921   8.855  1.00  1.00
ATOM     39  CA  ILE   227      28.839  25.019   7.464  1.00  1.00
ATOM     40  C   ILE   227      30.300  24.543   7.311  1.00  1.00
ATOM     41  O   ILE   227      31.164  24.938   8.090  1.00  1.00
ATOM     42  CB  ILE   227      28.693  26.461   6.966  1.00  1.00
TER
END
