
#######################################################
#                                                     #
#                        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   15 (   15),  selected   15 , name T0301TS464_2_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   15 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_2_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:    14       146 - 159         4.39     5.27
  LONGEST_CONTINUOUS_SEGMENT:    14       147 - 160         4.67     5.22
  LCS_AVERAGE:      7.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       146 - 152         0.72     8.75
  LONGEST_CONTINUOUS_SEGMENT:     7       152 - 158         1.99     5.35
  LCS_AVERAGE:      3.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       146 - 152         0.72     8.75
  LCS_AVERAGE:      3.03

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     I     146     I     146      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     A     147     A     147      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     H     148     H     148      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     V     149     V     149      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     P     150     P     150      7    7   14     5    6    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     V     151     V     151      7    7   14     3    6    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     S     152     S     152      7    7   14     3    4    7    7    7    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     G     153     G     153      6    7   14     4    5    6    6    6    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     G     154     G     154      6    7   14     4    5    6    6    6    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     Q     155     Q     155      6    7   14     4    5    6    6    6    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     V     156     V     156      6    7   14     4    5    6    6    6    8   10   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     Q     157     Q     157      6    7   14     3    5    6    6    6    6    9   12   12   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     E     158     E     158      6    7   14     3    4    6    6    6    6    8   10   10   13   13   13   13   13   13   14   14   14   15   15 
LCS_GDT     T     159     T     159      3    5   14     3    3    4    4    5    6    8    8   10   10   11   12   12   12   13   14   14   14   15   15 
LCS_GDT     G     160     G     160      3    5   14     3    3    3    4    5    6    8    8    9    9   11   12   12   12   12   14   14   14   15   15 
LCS_AVERAGE  LCS_A:   4.47  (   3.03    3.37    7.00 )

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      5      6      7      7      7      8     10     12     12     13     13     13     13     13     13     14     14     14     15     15 
GDT PERCENT_CA   2.50   3.00   3.50   3.50   3.50   4.00   5.00   6.00   6.00   6.50   6.50   6.50   6.50   6.50   6.50   7.00   7.00   7.00   7.50   7.50
GDT RMS_LOCAL    0.30   0.43   0.72   0.72   0.72   1.91   2.52   2.99   2.99   3.37   3.37   3.37   3.37   3.37   3.37   4.39   4.39   4.39   5.07   5.07
GDT RMS_ALL_CA   9.46   9.17   8.75   8.75   8.75   7.68   7.14   6.31   6.31   5.86   5.86   5.86   5.86   5.86   5.86   5.27   5.27   5.27   5.07   5.07

#      Molecule1      Molecule2       DISTANCE
LGA    I     146      I     146          3.621
LGA    A     147      A     147          3.322
LGA    H     148      H     148          3.884
LGA    V     149      V     149          3.066
LGA    P     150      P     150          3.281
LGA    V     151      V     151          3.782
LGA    S     152      S     152          3.128
LGA    G     153      G     153          1.925
LGA    G     154      G     154          1.638
LGA    Q     155      Q     155          2.121
LGA    V     156      V     156          2.604
LGA    Q     157      Q     157          3.626
LGA    E     158      E     158          5.810
LGA    T     159      T     159         12.306
LGA    G     160      G     160         14.664

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  200    4.0     12    2.99     4.875     4.543     0.388

LGA_LOCAL      RMSD =  2.989  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.857  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  5.070  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.354842 * X  +   0.585940 * Y  +   0.728533 * Z  +  40.416599
  Y_new =   0.794885 * X  +   0.599301 * Y  +  -0.094843 * Z  + -16.492369
  Z_new =  -0.492183 * X  +   0.545446 * Y  +  -0.678413 * Z  +  42.108398 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.464415   -0.677178  [ DEG:   141.2006    -38.7994 ]
  Theta =   0.514596    2.626997  [ DEG:    29.4842    150.5158 ]
  Phi   =   1.990658   -1.150935  [ DEG:   114.0563    -65.9437 ]
 
# 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: T0301TS464_2_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_2_2-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  200   4.0   12   2.99   4.543     5.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  ILE   146      72.792  13.957  11.759  1.00  0.00
ATOM      2  CA  ALA   147      70.511  15.379  14.373  1.00  0.00
ATOM      3  CA  HIS   148      70.306  14.295  18.014  1.00  0.00
ATOM      4  CA  VAL   149      66.606  14.392  18.792  1.00  0.00
ATOM      5  CA  PRO   150      64.936  14.272  22.217  1.00  0.00
ATOM      6  CA  VAL   151      61.809  12.273  21.557  1.00  0.00
ATOM      7  CA  SER   152      60.202  13.482  24.795  1.00  0.00
ATOM      8  CA  GLY   153      60.640  17.212  24.271  1.00  0.00
ATOM      9  CA  GLY   154      60.336  17.014  20.458  1.00  0.00
ATOM     10  CA  GLN   155      63.428  19.155  19.813  1.00  0.00
ATOM     11  CA  VAL   156      66.863  18.690  18.222  1.00  0.00
ATOM     12  CA  GLN   157      69.550  18.901  20.949  1.00  0.00
ATOM     13  CA  GLU   158      72.664  18.918  18.779  1.00  0.00
ATOM     14  CA  THR   159      73.760  18.660  15.144  1.00  0.00
ATOM     15  CA  GLY   160      76.751  16.440  14.428  1.00  0.00
TER
END
