
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   22 , name T0320_D1.pdb
# PARAMETERS: T0320TS599_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:    22       206 - 227         4.76     4.76
  LCS_AVERAGE:     10.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       215 - 225         1.99    11.76
  LCS_AVERAGE:      4.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       215 - 223         0.64    12.17
  LCS_AVERAGE:      3.10

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      0   10   22     0    0    3    6   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     L     207     L     207      0   10   22     0    1    3    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     Y     208     Y     208      7   10   22     4    7    7    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     S     209     S     209      7   10   22     4    7    7    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     N     210     N     210      7   10   22     4    7    7    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     E     211     E     211      7   10   22     4    7    7    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     P     212     P     212      7   10   22     4    7    7    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     I     213     I     213      7   10   22     4    7    7    7   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     C     214     C     214      7   10   22     4    7    7    8   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     G     215     G     215      9   11   22     4    7    9    9   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     L     216     L     216      9   11   22     5    8    9    9   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     Y     217     Y     217      9   11   22     6    8    9    9    9   10   13   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     G     218     G     218      9   11   22     6    8    9    9    9   10   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     K     219     K     219      9   11   22     6    8    9    9   11   13   14   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     G     220     G     220      9   11   22     6    8    9    9    9   10   13   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     F     221     F     221      9   11   22     3    8    9    9    9   10   13   13   15   16   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     T     222     T     222      9   11   22     6    8    9    9    9   10   13   13   15   15   15   17   19   20   20   21   21   21   22   22 
LCS_GDT     S     223     S     223      9   11   22     6    8    9    9    9   10   13   13   15   15   16   18   19   20   20   21   21   21   22   22 
LCS_GDT     I     224     I     224      4   11   22     3    4    5    8    9   10   12   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     G     225     G     225      4   11   22     3    4    5    7    9   10   12   14   17   18   19   19   19   20   20   21   21   21   22   22 
LCS_GDT     G     226     G     226      4    6   22     0    4    5    7    8   13   14   14   17   18   19   19   19   19   20   21   21   21   22   22 
LCS_GDT     I     227     I     227      4    6   22     0    4    4    7    7    7    9   11   12   14   15   17   17   17   18   20   20   20   22   22 
LCS_AVERAGE  LCS_A:   6.04  (   3.10    4.74   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      6      8      9      9     11     13     14     14     17     18     19     19     19     20     20     21     21     21     22     22 
GDT PERCENT_CA   2.80   3.74   4.21   4.21   5.14   6.07   6.54   6.54   7.94   8.41   8.88   8.88   8.88   9.35   9.35   9.81   9.81   9.81  10.28  10.28
GDT RMS_LOCAL    0.24   0.47   0.64   0.64   1.91   2.16   2.39   2.39   3.13   3.25   3.51   3.51   3.51   4.10   3.96   4.29   4.29   4.29   4.76   4.76
GDT RMS_ALL_CA  12.91  12.94  12.17  12.17   5.74   5.77   5.75   5.75   4.97   4.98   4.87   4.87   4.87   5.19   4.82   4.88   4.88   4.88   4.76   4.76

#      Molecule1      Molecule2       DISTANCE
LGA    L     206      L     206          2.495
LGA    L     207      L     207          2.562
LGA    Y     208      Y     208          3.330
LGA    S     209      S     209          1.492
LGA    N     210      N     210          3.088
LGA    E     211      E     211          2.144
LGA    P     212      P     212          1.251
LGA    I     213      I     213          1.622
LGA    C     214      C     214          2.445
LGA    G     215      G     215          1.402
LGA    L     216      L     216          1.973
LGA    Y     217      Y     217          5.236
LGA    G     218      G     218          3.738
LGA    K     219      K     219          2.247
LGA    G     220      G     220          6.592
LGA    F     221      F     221          9.227
LGA    T     222      T     222         12.248
LGA    S     223      S     223         12.616
LGA    I     224      I     224          6.398
LGA    G     225      G     225          6.383
LGA    G     226      G     226          2.611
LGA    I     227      I     227          8.100

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  214    4.0     14    2.39     6.075     6.087     0.562

LGA_LOCAL      RMSD =  2.390  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.619  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  4.758  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.553399 * X  +   0.508137 * Y  +   0.659959 * Z  +  16.788130
  Y_new =  -0.829911 * X  +   0.269144 * Y  +   0.488682 * Z  +  22.332684
  Z_new =   0.070693 * X  +  -0.818143 * Y  +   0.570652 * Z  +  14.074868 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.961752    2.179840  [ DEG:   -55.1044    124.8956 ]
  Theta =  -0.070752   -3.070841  [ DEG:    -4.0538   -175.9462 ]
  Phi   =  -0.982689    2.158904  [ DEG:   -56.3039    123.6961 ]
 
# 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_2-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_2-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   2.39   6.087     4.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_2-D1
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206       4.724  23.965  18.569  1.00  0.00              
ATOM    207  CA  LEU   207       2.118  23.854  15.368  1.00  0.00              
ATOM    208  CA  TYR   208      -1.629  25.614  14.515  1.00  0.00              
ATOM    209  CA  SER   209       1.181  25.593  17.067  1.00  0.00              
ATOM    210  CA  ASN   210       2.595  29.151  16.940  1.00  0.00              
ATOM    211  CA  GLU   211       6.101  28.148  16.023  1.00  0.00              
ATOM    212  CA  PRO   212       8.227  30.265  13.678  1.00  0.00              
ATOM    213  CA  ILE   213       9.256  28.238  11.420  1.00  0.00              
ATOM    214  CA  CYS   214      12.730  28.727   8.912  1.00  0.00              
ATOM    215  CA  GLY   215      13.598  26.431   7.070  1.00  0.00              
ATOM    216  CA  LEU   216      17.198  26.379   5.404  1.00  0.00              
ATOM    217  CA  TYR   217      18.135  22.702   5.016  1.00  0.00              
ATOM    218  CA  GLY   218      14.652  21.590   3.863  1.00  0.00              
ATOM    219  CA  LYS   219      14.777  24.022   0.935  1.00  0.00              
ATOM    220  CA  GLY   220      18.125  22.671  -0.203  1.00  0.00              
ATOM    221  CA  PHE   221      20.653  25.297   0.933  1.00  0.00              
ATOM    222  CA  THR   222      23.459  23.470   2.583  1.00  0.00              
ATOM    223  CA  SER   223      25.173  26.156   4.608  1.00  0.00              
ATOM    224  CA  ILE   224      25.027  24.583   8.052  1.00  0.00              
ATOM    225  CA  GLY   225      28.521  25.516   9.346  1.00  0.00              
ATOM    226  CA  GLY   226      29.422  22.274  11.080  1.00  0.00              
ATOM    227  CA  ILE   227      29.218  23.008  14.718  1.00  0.00              
TER                                                                             
END
