
#######################################################
#                                                     #
#                        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   31 (   31),  selected   25 , name T0321TS464_3_2
# Molecule2: number of CA atoms  244 ( 1840),  selected   25 , name T0321.pdb
# PARAMETERS: T0321TS464_3_2.T0321.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:    12       220 - 231         4.02    17.23
  LCS_AVERAGE:      4.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        85 - 90          1.84    17.25
  LCS_AVERAGE:      1.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        86 - 90          0.76    18.69
  LCS_AVERAGE:      1.46

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:  244
LCS_GDT     A      84     A      84      3    4    8     3    3    3    4    4    4    4    6    6    7    7    7    8    8   10   15   16   16   17   18 
LCS_GDT     Y      85     Y      85      3    6    8     3    3    3    5    5    6    7    7    8    8   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     Y      86     Y      86      5    6    8     3    4    5    5    5    6    7    7    9    9   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     N      87     N      87      5    6    8     3    4    5    5    5    6    7    7    9    9   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     N      88     N      88      5    6    8     3    4    5    5    5    6    7    7    9    9   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     P      89     P      89      5    6    8     3    4    5    5    5    6    6    7    7    7    8    9   12   13   13   15   16   16   17   18 
LCS_GDT     Q      90     Q      90      5    6    8     3    4    5    5    5    6    6    7    7    7    7    9    9   10   11   12   14   14   15   15 
LCS_GDT     N     110     N     110      3    4   10     3    3    4    4    4    4    5    5    6    7    7    7    9   10   10   11   11   12   12   18 
LCS_GDT     D     111     D     111      3    4   10     3    3    4    4    4    4    5    5    7    7    9   10   10   10   10   11   11   12   12   13 
LCS_GDT     P     112     P     112      3    4   10     3    3    4    4    4    4    6    6    7    7    9   10   10   10   10   11   11   12   12   13 
LCS_GDT     F     113     F     113      3    4   10     2    3    4    4    4    4    6    6    7    7    9   10   10   10   10   11   11   12   12   13 
LCS_GDT     I     114     I     114      3    3   10     1    3    3    3    4    4    6    6    7    7    9   10   10   10   10   11   11   12   12   14 
LCS_GDT     M     115     M     115      3    3   10     0    3    3    3    3    4    6    6    7    7    9   10   10   10   10   11   11   12   13   14 
LCS_GDT     F     220     F     220      3    3   12     3    3    3    3    3    5    6    8   10   11   11   12   12   12   12   13   14   16   17   18 
LCS_GDT     M     221     M     221      3    3   12     3    3    3    3    3    5    6    6    8    9   10   12   12   12   12   13   14   16   17   18 
LCS_GDT     V     222     V     222      4    5   12     4    4    4    4    4    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     K     223     K     223      4    5   12     4    4    4    4    4    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     D     224     D     224      4    5   12     4    4    4    4    4    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     N     225     N     225      4    5   12     4    4    4    4    4    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     A     226     A     226      3    5   12     3    3    3    4    4    6    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     R     227     R     227      3    5   12     3    3    3    5    5    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     A     228     A     228      3    4   12     3    3    3    5    5    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     F     229     F     229      3    4   12     3    3    3    5    5    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     R     230     R     230      3    3   12     3    3    3    3    3    5    7    8   10   11   11   12   12   13   14   15   16   16   17   18 
LCS_GDT     I     231     I     231      3    3   12     0    3    3    3    3    3    4    6    9   11   11   12   12   13   14   15   16   16   17   18 
LCS_AVERAGE  LCS_A:   2.52  (   1.46    1.84    4.26 )

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      4      5      5      5      6      7      8     10     11     11     12     12     13     14     15     16     16     17     18 
GDT PERCENT_CA   1.64   1.64   2.05   2.05   2.05   2.46   2.87   3.28   4.10   4.51   4.51   4.92   4.92   5.33   5.74   6.15   6.56   6.56   6.97   7.38
GDT RMS_LOCAL    0.22   0.22   0.76   0.76   0.76   1.84   2.61   2.86   3.61   3.79   3.79   4.02   4.02   4.83   5.10   5.35   5.65   5.65   6.10   6.45
GDT RMS_ALL_CA  12.75  12.75  18.69  18.69  18.69  17.25  16.42  15.99  17.28  17.17  17.17  17.23  17.23  13.08  13.04  13.07  12.97  12.97  12.87  13.00

#      Molecule1      Molecule2       DISTANCE
LGA    A      84      A      84         17.403
LGA    Y      85      Y      85         18.383
LGA    Y      86      Y      86         16.472
LGA    N      87      N      87         12.657
LGA    N      88      N      88         13.063
LGA    P      89      P      89         17.667
LGA    Q      90      Q      90         23.313
LGA    N     110      N     110         16.406
LGA    D     111      D     111         19.662
LGA    P     112      P     112         23.510
LGA    F     113      F     113         25.335
LGA    I     114      I     114         29.381
LGA    M     115      M     115         33.211
LGA    F     220      F     220          9.839
LGA    M     221      M     221          9.372
LGA    V     222      V     222          2.834
LGA    K     223      K     223          0.580
LGA    D     224      D     224          3.349
LGA    N     225      N     225          3.505
LGA    A     226      A     226          2.329
LGA    R     227      R     227          5.407
LGA    A     228      A     228          3.380
LGA    F     229      F     229          3.542
LGA    R     230      R     230          3.228
LGA    I     231      I     231          4.599

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31  244    4.0      8    2.86     3.279     2.952     0.271

LGA_LOCAL      RMSD =  2.857  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.776  Number of atoms =   25 
Std_ALL_ATOMS  RMSD = 10.956  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.189172 * X  +   0.901721 * Y  +   0.388732 * Z  +  -0.306649
  Y_new =   0.010892 * X  +   0.397783 * Y  +  -0.917415 * Z  +  96.483398
  Z_new =  -0.981884 * X  +  -0.169315 * Y  +  -0.085071 * Z  + 122.092918 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.036397    1.105195  [ DEG:  -116.6770     63.3230 ]
  Theta =   1.380159    1.761434  [ DEG:    79.0773    100.9227 ]
  Phi   =   3.084077   -0.057516  [ DEG:   176.7046     -3.2954 ]
 
# 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: T0321TS464_3_2                                
REMARK     2: T0321.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_3_2.T0321.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31  244   4.0    8   2.86   2.952    10.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  ALA    84      -3.868  56.724  54.145  1.00  0.00
ATOM      2  CA  TYR    85      -1.492  55.580  56.863  1.00  0.00
ATOM      3  CA  TYR    86      -2.760  56.365  60.348  1.00  0.00
ATOM      4  CA  ASN    87      -5.065  54.137  62.363  1.00  0.00
ATOM      5  CA  ASN    88      -5.214  56.888  65.024  1.00  0.00
ATOM      6  CA  PRO    89      -7.510  59.870  64.559  1.00  0.00
ATOM      7  CA  GLN    90      -5.810  62.936  63.096  1.00  0.00
ATOM      8  CA  ARG   104       6.226  54.879  63.178  1.00  0.00
ATOM      9  CA  VAL   105       4.619  57.902  64.808  1.00  0.00
ATOM     10  CA  GLU   106       1.153  56.377  64.403  1.00  0.00
ATOM     11  CA  ASP   107       2.345  53.177  66.129  1.00  0.00
ATOM     12  CA  ARG   108       3.612  55.071  69.183  1.00  0.00
ATOM     13  CA  MET   109       0.530  57.291  69.381  1.00  0.00
ATOM     14  CA  ASN   110      -2.235  56.490  71.865  1.00  0.00
ATOM     15  CA  ASP   111      -4.038  59.854  71.746  1.00  0.00
ATOM     16  CA  PRO   112      -4.083  61.266  68.200  1.00  0.00
ATOM     17  CA  PHE   113      -1.665  62.391  65.506  1.00  0.00
ATOM     18  CA  ILE   114      -1.270  66.148  65.227  1.00  0.00
ATOM     19  CA  MET   115      -0.487  67.453  61.733  1.00  0.00
ATOM     20  CA  PHE   220       0.863  58.946  80.646  1.00  0.00
ATOM     21  CA  MET   221      -1.302  61.346  78.658  1.00  0.00
ATOM     22  CA  VAL   222      -2.999  58.568  76.710  1.00  0.00
ATOM     23  CA  LYS   223      -3.618  56.701  79.968  1.00  0.00
ATOM     24  CA  ASP   224      -5.261  59.658  81.623  1.00  0.00
ATOM     25  CA  ASN   225      -7.875  60.499  79.059  1.00  0.00
ATOM     26  CA  ALA   226      -6.110  63.010  76.814  1.00  0.00
ATOM     27  CA  ARG   227      -7.842  62.719  73.436  1.00  0.00
ATOM     28  CA  ALA   228      -4.928  63.498  71.154  1.00  0.00
ATOM     29  CA  PHE   229      -1.316  64.655  71.166  1.00  0.00
ATOM     30  CA  ARG   230      -0.493  67.351  68.660  1.00  0.00
ATOM     31  CA  ILE   231       3.038  67.515  67.254  1.00  0.00
TER
END
