
#######################################################
#                                                     #
#                        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   22 (   22),  selected   22 , name T0320TS599_4-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   22 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_4-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:    22       206 - 227         4.28     4.28
  LCS_AVERAGE:     10.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       215 - 227         1.93    12.42
  LCS_AVERAGE:      5.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       206 - 214         0.92     8.71
  LCS_AVERAGE:      3.59

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     L     206     L     206      9   11   22     3    5    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     L     207     L     207      9   11   22     3    7    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     Y     208     Y     208      9   11   22     3    7    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     S     209     S     209      9   11   22     3    7    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     N     210     N     210      9   11   22     3    7    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     E     211     E     211      9   11   22     4    7    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     P     212     P     212      9   11   22     4    7    8   10   11   11   12   13   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     I     213     I     213      9   11   22     4    7    8   10   11   11   12   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     C     214     C     214      9   11   22     4    7    8    9   11   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     G     215     G     215      7   13   22     4    6   10   11   12   12   14   14   15   15   17   21   21   22   22   22   22   22   22   22 
LCS_GDT     L     216     L     216      8   13   22     4    6   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     Y     217     Y     217      8   13   22     4    7   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     G     218     G     218      8   13   22     5    7   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     K     219     K     219      8   13   22     5    7   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     G     220     G     220      8   13   22     5    7   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     F     221     F     221      8   13   22     3    7   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     T     222     T     222      8   13   22     5    7   10   11   12   12   14   14   15   16   17   19   21   22   22   22   22   22   22   22 
LCS_GDT     S     223     S     223      8   13   22     5    7    7   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     I     224     I     224      5   13   22     3    4    5    6   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     G     225     G     225      4   13   22     3    4   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     G     226     G     226      4   13   22     3    3   10   11   12   12   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_GDT     I     227     I     227      4   13   22     0    3    5    7    7   11   14   14   15   17   19   21   21   22   22   22   22   22   22   22 
LCS_AVERAGE  LCS_A:   6.52  (   3.59    5.69   10.28 )

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      7     10     11     12     12     14     14     15     17     19     21     21     22     22     22     22     22     22     22 
GDT PERCENT_CA   2.34   3.27   4.67   5.14   5.61   5.61   6.54   6.54   7.01   7.94   8.88   9.81   9.81  10.28  10.28  10.28  10.28  10.28  10.28  10.28
GDT RMS_LOCAL    0.28   0.55   1.14   1.23   1.42   1.42   2.35   2.35   2.78   3.44   3.78   4.11   4.11   4.28   4.28   4.28   4.28   4.28   4.28   4.28
GDT RMS_ALL_CA  14.00  14.62  13.55  13.36  13.48  13.48  10.58  10.58   8.55   4.57   4.34   4.31   4.31   4.28   4.28   4.28   4.28   4.28   4.28   4.28

#      Molecule1      Molecule2       DISTANCE
LGA    L     206      L     206         17.080
LGA    L     207      L     207         17.763
LGA    Y     208      Y     208         22.079
LGA    S     209      S     209         20.111
LGA    N     210      N     210         18.577
LGA    E     211      E     211         14.264
LGA    P     212      P     212         10.679
LGA    I     213      I     213          7.091
LGA    C     214      C     214          3.836
LGA    G     215      G     215          2.243
LGA    L     216      L     216          2.888
LGA    Y     217      Y     217          2.568
LGA    G     218      G     218          2.950
LGA    K     219      K     219          2.881
LGA    G     220      G     220          1.516
LGA    F     221      F     221          1.435
LGA    T     222      T     222          1.757
LGA    S     223      S     223          1.732
LGA    I     224      I     224          2.897
LGA    G     225      G     225          0.800
LGA    G     226      G     226          1.068
LGA    I     227      I     227          3.140

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  214    4.0     14    2.35     6.308     6.451     0.572

LGA_LOCAL      RMSD =  2.347  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.212  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  4.283  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.791310 * X  +   0.554385 * Y  +  -0.257848 * Z  +  16.828279
  Y_new =  -0.395668 * X  +   0.785831 * Y  +   0.475306 * Z  +  27.621368
  Z_new =   0.466128 * X  +  -0.274092 * Y  +   0.841189 * Z  +   7.437723 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.314991    2.826602  [ DEG:   -18.0476    161.9524 ]
  Theta =  -0.484909   -2.656684  [ DEG:   -27.7832   -152.2168 ]
  Phi   =  -0.463661    2.677932  [ DEG:   -26.5658    153.4342 ]
 
# 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: T0320TS599_4-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_4-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  214   4.0   14   2.35   6.451     4.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_4-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      10.556  38.978  11.818  1.00  0.00              
ATOM    207  CA  LEU   207       8.427  39.408   8.545  1.00  0.00              
ATOM    208  CA  TYR   208       7.204  43.384   8.777  1.00  0.00              
ATOM    209  CA  SER   209      10.508  43.511  10.193  1.00  0.00              
ATOM    210  CA  ASN   210      12.886  42.289   7.571  1.00  0.00              
ATOM    211  CA  GLU   211      14.578  39.464   9.448  1.00  0.00              
ATOM    212  CA  PRO   212      15.525  36.435   7.170  1.00  0.00              
ATOM    213  CA  ILE   213      14.012  33.288   8.960  1.00  0.00              
ATOM    214  CA  CYS   214      14.772  29.819   7.468  1.00  0.00              
ATOM    215  CA  GLY   215      12.774  26.818   8.670  1.00  0.00              
ATOM    216  CA  LEU   216      14.803  23.566   8.514  1.00  0.00              
ATOM    217  CA  TYR   217      11.954  21.087   8.922  1.00  0.00              
ATOM    218  CA  GLY   218       9.498  22.861   6.573  1.00  0.00              
ATOM    219  CA  LYS   219      12.060  23.173   3.734  1.00  0.00              
ATOM    220  CA  GLY   220      13.423  19.710   4.088  1.00  0.00              
ATOM    221  CA  PHE   221      16.636  20.298   5.929  1.00  0.00              
ATOM    222  CA  THR   222      17.087  18.107   8.970  1.00  0.00              
ATOM    223  CA  SER   223      19.507  19.580  11.257  1.00  0.00              
ATOM    224  CA  ILE   224      22.995  20.130  10.232  1.00  0.00              
ATOM    225  CA  GLY   225      24.939  21.932  12.901  1.00  0.00              
ATOM    226  CA  GLY   226      27.046  24.429  11.066  1.00  0.00              
ATOM    227  CA  ILE   227      29.263  22.286   8.796  1.00  0.00              
TER                                                                             
END
