
#######################################################
#                                                     #
#                        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   46 (   46),  selected   46 , name T0363TS168_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS168_5-D1.T0363_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:    31        11 - 41          4.93    11.01
  LCS_AVERAGE:     63.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        24 - 33          1.97     9.41
  LCS_AVERAGE:     18.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        38 - 45          0.39    16.88
  LCS_AVERAGE:     10.96

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:   46
LCS_GDT     N      11     N      11      6    9   31     0    5    7    8   11   13   14   17   19   22   24   27   28   29   32   33   33   34   36   38 
LCS_GDT     Q      12     Q      12      6    9   31     3    5    7    9   11   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     I      13     I      13      6    9   31     3    4    7    9   11   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     N      14     N      14      6    9   31     3    5    7    8    9   11   12   15   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     I      15     I      15      6    9   31     3    5    7    8   11   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     E      16     E      16      6    9   31     3    5    7    9   11   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     I      17     I      17      4    9   31     3    3    6    8   11   13   14   17   19   22   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     A      18     A      18      4    9   31     3    3    7    9   11   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     Y      19     Y      19      3    9   31     3    3    5    9   11   13   14   16   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     A      20     A      20      3    7   31     1    3    4    5    7   10   11   14   16   18   19   21   26   28   31   32   33   34   36   38 
LCS_GDT     F      21     F      21      3    7   31     0    3    4    9   11   13   14   15   18   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     P      22     P      22      3    7   31     3    3    5    9   11   13   14   15   17   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     E      23     E      23      3    7   31     3    3    5    9   11   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     R      24     R      24      3   10   31     3    6    7    8    9   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     Y      25     Y      25      3   10   31     3    6    7    8    9   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     Y      26     Y      26      4   10   31     3    4    4    6    9   10   11   16   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     L      27     L      27      4   10   31     3    6    7    8    9   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     K      28     K      28      4   10   31     3    4    6    8    9   11   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     S      29     S      29      5   10   31     3    6    7    8    9   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     F      30     F      30      5   10   31     3    4    5    7    9   11   12   16   18   21   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     Q      31     Q      31      5   10   31     3    4    5    7    9    9   11   13   16   18   21   25   28   29   32   33   33   34   36   38 
LCS_GDT     V      32     V      32      5   10   31     3    6    7    8    9   13   14   17   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     D      33     D      33      5   10   31     4    6    7    8    9   13   14   16   19   23   25   27   28   29   32   33   33   34   36   38 
LCS_GDT     E      34     E      34      5    8   31     4    5    5    7    7   11   12   16   19   23   25   26   28   29   31   32   33   34   36   38 
LCS_GDT     G      35     G      35      5    8   31     4    5    5    7    7   11   11   15   19   23   25   26   26   29   31   32   33   34   36   37 
LCS_GDT     I      36     I      36      5    7   31     4    5    5    7    7   11   11   16   19   23   25   26   28   29   31   32   33   34   36   37 
LCS_GDT     T      37     T      37      3    9   31     3    3    3    4    8    9   12   14   17   23   25   26   26   28   31   32   32   34   34   37 
LCS_GDT     V      38     V      38      8    9   31     7    8    8    8    8   10   12   15   19   23   25   26   28   29   31   32   33   34   36   38 
LCS_GDT     Q      39     Q      39      8    9   31     7    8    8    8    8   12   13   14   17   21   24   27   28   29   31   32   33   34   36   38 
LCS_GDT     T      40     T      40      8    9   31     7    8    8    8   10   13   14   17   19   22   24   27   28   29   31   32   33   34   36   38 
LCS_GDT     A      41     A      41      8    9   31     7    8    8    8    9   13   14   17   19   22   24   27   28   29   32   33   33   34   36   38 
LCS_GDT     I      42     I      42      8    9   26     7    8    8    8    8   10   13   14   17   21   23   27   27   29   32   33   33   34   36   38 
LCS_GDT     T      43     T      43      8    9   26     7    8    8    8    8    9   10   11   15   18   20   23   26   29   32   33   33   34   36   38 
LCS_GDT     Q      44     Q      44      8    9   26     7    8    8    8    8   10   11   13   16   18   22   23   27   29   32   33   33   34   36   38 
LCS_GDT     S      45     S      45      8    9   26     6    8    8    8    8   10   13   14   17   19   22   25   27   29   32   33   33   34   36   38 
LCS_GDT     G      46     G      46      3    9   26     3    4    6    8    8   10   13   14   17   19   22   25   26   29   32   33   33   34   36   37 
LCS_GDT     I      47     I      47      5    8   26     3    4    6    7    8   10   11   13   16   18   22   25   27   29   32   33   33   34   36   38 
LCS_GDT     L      48     L      48      5    8   26     4    4    6    7    7   10   11   14   17   19   22   25   27   29   32   33   33   34   36   38 
LCS_GDT     S      49     S      49      5    8   26     4    4    6    7    8   10   13   14   17   19   22   25   26   29   32   33   33   34   36   37 
LCS_GDT     Q      50     Q      50      5    8   26     4    4    6    7    8   10   13   14   17   19   22   25   26   27   28   29   31   34   36   37 
LCS_GDT     F      51     F      51      5    8   26     4    4    6    7    7    9   12   14   17   19   22   25   26   27   31   33   33   34   36   38 
LCS_GDT     P      52     P      52      5    8   26     3    4    6    8    8   10   13   14   17   19   22   25   27   29   32   33   33   34   36   38 
LCS_GDT     E      53     E      53      4    8   26     3    4    6    8    8   10   13   14   17   19   22   25   26   27   30   32   33   34   36   38 
LCS_GDT     I      54     I      54      4    7   26     3    4    6    8    8   10   13   14   17   19   22   25   26   27   28   31   33   34   36   38 
LCS_GDT     D      55     D      55      4    7   26     3    4    6    8    8   10   13   14   18   21   24   27   27   28   30   31   33   34   36   38 
LCS_GDT     L      56     L      56      3    7   26     3    3    5    9   11   13   14   17   19   22   24   27   28   29   31   32   33   34   36   38 
LCS_AVERAGE  LCS_A:  31.22  (  10.96   18.86   63.85 )

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      7      8      8      9     11     13     14     17     19     23     25     27     28     29     32     33     33     34     36     38 
GDT PERCENT_CA  15.22  17.39  17.39  19.57  23.91  28.26  30.43  36.96  41.30  50.00  54.35  58.70  60.87  63.04  69.57  71.74  71.74  73.91  78.26  82.61
GDT RMS_LOCAL    0.32   0.39   0.39   1.54   1.71   1.97   2.21   3.09   3.27   3.89   4.02   4.11   4.36   4.48   5.38   5.51   5.11   5.27   5.99   6.28
GDT RMS_ALL_CA  16.69  16.88  16.88   9.85   9.79   9.60   9.57   8.99   9.07  12.36  12.18   9.10   9.96   9.93   9.26   9.19   9.69   9.88   8.29   8.22

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          3.858
LGA    Q      12      Q      12          3.761
LGA    I      13      I      13          1.472
LGA    N      14      N      14          5.412
LGA    I      15      I      15          3.092
LGA    E      16      E      16          2.775
LGA    I      17      I      17          2.845
LGA    A      18      A      18          2.433
LGA    Y      19      Y      19          4.287
LGA    A      20      A      20          8.733
LGA    F      21      F      21          5.349
LGA    P      22      P      22          6.177
LGA    E      23      E      23          3.287
LGA    R      24      R      24          3.820
LGA    Y      25      Y      25          3.188
LGA    Y      26      Y      26          5.183
LGA    L      27      L      27          1.663
LGA    K      28      K      28          3.757
LGA    S      29      S      29          3.630
LGA    F      30      F      30          5.147
LGA    Q      31      Q      31          6.900
LGA    V      32      V      32          3.890
LGA    D      33      D      33          4.479
LGA    E      34      E      34          8.786
LGA    G      35      G      35         11.799
LGA    I      36      I      36          9.454
LGA    T      37      T      37         11.433
LGA    V      38      V      38          7.384
LGA    Q      39      Q      39          6.116
LGA    T      40      T      40          2.086
LGA    A      41      A      41          3.244
LGA    I      42      I      42          6.647
LGA    T      43      T      43         11.001
LGA    Q      44      Q      44         12.710
LGA    S      45      S      45         12.838
LGA    G      46      G      46         16.203
LGA    I      47      I      47         11.870
LGA    L      48      L      48         14.752
LGA    S      49      S      49         21.664
LGA    Q      50      Q      50         20.611
LGA    F      51      F      51         15.434
LGA    P      52      P      52         14.203
LGA    E      53      E      53         12.779
LGA    I      54      I      54         11.559
LGA    D      55      D      55          6.071
LGA    L      56      L      56          2.528

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     17    3.09    36.413    32.384     0.534

LGA_LOCAL      RMSD =  3.085  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.071  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  7.936  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.124437 * X  +   0.651600 * Y  +  -0.748287 * Z  +  22.793264
  Y_new =   0.727626 * X  +  -0.452802 * Y  +  -0.515297 * Z  +  11.909361
  Z_new =  -0.674593 * X  +  -0.608595 * Y  +  -0.417776 * Z  +   5.842815 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.172377    0.969216  [ DEG:  -124.4680     55.5320 ]
  Theta =   0.740414    2.401179  [ DEG:    42.4226    137.5774 ]
  Phi   =   1.740175   -1.401417  [ DEG:    99.7047    -80.2953 ]
 
# 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: T0363TS168_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS168_5-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   46   46   4.0   17   3.09  32.384     7.94
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS168_5-D1
PFRMAT TS
TARGET T0363
MODEL 5
PARENT N/A
ATOM     11  CA  ASN    11      12.717  -0.536  12.020  1.00 25.00           C
ATOM     12  CA  GLN    12      14.481   2.603  10.851  1.00 25.00           C
ATOM     13  CA  ILE    13      17.192   4.932   9.470  1.00 25.00           C
ATOM     14  CA  ASN    14      20.165   7.160  10.363  1.00 25.00           C
ATOM     15  CA  ILE    15      20.296   8.403   6.709  1.00 25.00           C
ATOM     16  CA  GLU    16      21.294  12.014   6.005  1.00 25.00           C
ATOM     17  CA  ILE    17      23.750  14.861   6.595  1.00 25.00           C
ATOM     18  CA  ALA    18      25.146  17.357   4.119  1.00 25.00           C
ATOM     19  CA  TYR    19      27.595  17.286   1.190  1.00 25.00           C
ATOM     20  CA  ALA    20      29.846  15.938  -1.544  1.00 25.00           C
ATOM     21  CA  PHE    21      29.429  19.373  -3.167  1.00 25.00           C
ATOM     22  CA  PRO    22      30.156  21.911  -5.972  1.00 25.00           C
ATOM     23  CA  GLU    23      29.831  24.218  -9.022  1.00 25.00           C
ATOM     24  CA  ARG    24      29.107  27.192  -6.747  1.00 25.00           C
ATOM     25  CA  TYR    25      26.418  25.480  -4.601  1.00 25.00           C
ATOM     26  CA  TYR    26      24.021  22.611  -3.897  1.00 25.00           C
ATOM     27  CA  LEU    27      23.779  19.304  -2.018  1.00 25.00           C
ATOM     28  CA  LYS    28      24.742  16.052  -3.676  1.00 25.00           C
ATOM     29  CA  SER    29      23.204  13.717  -1.157  1.00 25.00           C
ATOM     30  CA  PHE    30      24.927  12.611   2.033  1.00 25.00           C
ATOM     31  CA  GLN    31      25.630   9.705   4.331  1.00 25.00           C
ATOM     32  CA  VAL    32      25.367   6.295   6.083  1.00 25.00           C
ATOM     33  CA  ASP    33      25.463   2.770   7.601  1.00 25.00           C
ATOM     34  CA  GLU    34      27.686   0.921  10.073  1.00 25.00           C
ATOM     35  CA  GLY    35      31.186   0.714   8.528  1.00 25.00           C
ATOM     36  CA  ILE    36      31.954   4.099   6.956  1.00 25.00           C
ATOM     37  CA  THR    37      30.366   6.144   4.208  1.00 25.00           C
ATOM     38  CA  VAL    38      30.064   8.773   7.009  1.00 25.00           C
ATOM     39  CA  GLN    39      28.543   6.823   9.934  1.00 25.00           C
ATOM     40  CA  THR    40      29.607   9.589  12.362  1.00 25.00           C
ATOM     41  CA  ALA    41      28.029  12.230  10.082  1.00 25.00           C
ATOM     42  CA  ILE    42      24.784  10.201   9.935  1.00 25.00           C
ATOM     43  CA  THR    43      24.759   9.917  13.753  1.00 25.00           C
ATOM     44  CA  GLN    44      25.283  13.698  14.063  1.00 25.00           C
ATOM     45  CA  SER    45      22.397  14.322  11.625  1.00 25.00           C
ATOM     46  CA  GLY    46      23.927  17.795  11.515  1.00 25.00           C
ATOM     47  CA  ILE    47      25.727  19.666   8.729  1.00 25.00           C
ATOM     48  CA  LEU    48      27.162  22.053  11.394  1.00 25.00           C
ATOM     49  CA  SER    49      25.723  22.147  14.942  1.00 25.00           C
ATOM     50  CA  GLN    50      27.194  18.683  15.656  1.00 25.00           C
ATOM     51  CA  PHE    51      30.390  18.352  13.607  1.00 25.00           C
ATOM     52  CA  PRO    52      32.942  21.103  13.103  1.00 25.00           C
ATOM     53  CA  GLU    53      36.205  20.753  14.999  1.00 25.00           C
ATOM     54  CA  ILE    54      35.908  17.254  16.430  1.00 25.00           C
ATOM     55  CA  ASP    55      37.951  15.859  13.570  1.00 25.00           C
ATOM     56  CA  LEU    56      36.028  15.443  10.304  1.00 25.00           C
TER
END
