
#######################################################
#                                                     #
#                        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   72 (   72),  selected   67 , name T0320TS464_5_1
# Molecule2: number of CA atoms  287 ( 2364),  selected   67 , name T0320.pdb
# PARAMETERS: T0320TS464_5_1.T0320.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:    28       103 - 162         4.45    20.08
  LCS_AVERAGE:      7.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       143 - 157         1.97    16.51
  LCS_AVERAGE:      3.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        63 - 73          0.50    20.17
  LCS_AVERAGE:      2.31

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:  287
LCS_GDT     I      34     I      34      5    5   14     5    5    5    5    6    6    6    7    9   11   12   15   15   16   18   20   21   21   22   24 
LCS_GDT     R      35     R      35      5    5   14     5    5    5    5    6    6    6    6    7    8    9   10   12   16   18   20   21   21   22   24 
LCS_GDT     L      36     L      36      5    5   14     5    5    5    5    6    6    6    6    7    8    8   10   11   12   15   16   20   20   22   23 
LCS_GDT     T      37     T      37      5    5   14     5    5    5    5    6    6    6    8   10   11   11   15   15   15   17   20   24   27   30   31 
LCS_GDT     R      38     R      38      5    5   14     5    5    5    5    6    6    6    8   10   11   12   15   15   15   19   21   25   27   30   31 
LCS_GDT     F      58     F      58      4    5   17     3    4    5    9   11   14   15   16   16   16   16   16   16   17   18   22   23   23   27   31 
LCS_GDT     S      59     S      59      4    5   17     3    4    5    6   11   14   15   16   16   16   16   16   17   18   21   22   23   25   25   31 
LCS_GDT     Y      60     Y      60      4    7   17     3    4    5    9   11   14   15   16   16   16   16   16   17   18   21   22   25   27   30   31 
LCS_GDT     N      61     N      61      4    7   20     3    4    5    9   11   13   15   16   16   16   16   16   17   18   21   22   25   27   30   31 
LCS_GDT     G      62     G      62      3   12   20     3    4    5    9   11   11   14   16   16   16   16   16   17   18   20   22   25   27   30   31 
LCS_GDT     G      63     G      63     11   12   20     3   11   11   11   11   14   15   16   16   17   17   18   18   18   20   22   25   27   30   31 
LCS_GDT     K      64     K      64     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   19   21   24   26   29   31 
LCS_GDT     D      65     D      65     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   19   22   24   27   29   31 
LCS_GDT     C      66     C      66     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   20   22   24   27   30   31 
LCS_GDT     Q      67     Q      67     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   19   22   24   27   29   31 
LCS_GDT     V      68     V      68     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   19   22   24   26   29   31 
LCS_GDT     L      69     L      69     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   20   22   24   27   29   31 
LCS_GDT     L      70     L      70     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   20   22   24   27   29   31 
LCS_GDT     L      71     L      71     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   19   22   24   27   29   31 
LCS_GDT     L      72     L      72     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   19   22   24   27   29   31 
LCS_GDT     Y      73     Y      73     11   12   20     9   11   11   11   11   14   15   16   16   17   17   18   18   18   20   22   24   27   29   31 
LCS_GDT     P     103     P     103      7    8   28     4    6    7    8   10   11   15   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     T     104     T     104      7    8   28     4    6    7    8   10   11   15   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     V     105     V     105      7    8   28     4    6    7    7   10   11   15   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     F     106     F     106      7    8   28     4    6    7    8   10   11   15   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     I     107     I     107      7    8   28     4    6    7    8   10   11   15   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     D     108     D     108      7    8   28     4    6    7    8   10   10   13   17   19   21   24   25   27   28   28   28   29   29   30   30 
LCS_GDT     Q     109     Q     109      7    8   28     4    6    7    8   10   10   13   15   19   21   24   25   27   28   28   28   29   29   30   30 
LCS_GDT     V     142     V     142      3   14   28     3    3    3    5    7   13   16   17   19   21   24   25   27   28   28   28   29   30   31   31 
LCS_GDT     N     143     N     143     10   15   28     4    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     M     144     M     144     10   15   28     4    9   10   13   14   15   16   17   19   20   21   24   27   28   28   28   29   30   33   34 
LCS_GDT     A     145     A     145     10   15   28     4    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   32   34 
LCS_GDT     D     146     D     146     10   15   28     6    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     A     147     A     147     10   15   28     6    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     F     148     F     148     10   15   28     6    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     R     149     R     149     10   15   28     6    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     D     150     D     150     10   15   28     6    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     F     151     F     151     10   15   28     6    9   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     I     152     I     152     10   15   28     3    7   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     K     153     K     153      9   15   28     3    6   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     I     154     I     154      9   15   28     3    6   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     Y     155     Y     155      9   15   28     3    6   10   13   14   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     P     156     P     156      4   15   28     3    3    4    5    6    9   11   14   17   20   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     E     157     E     157      4   15   28     3    3    6   12   13   14   16   17   19   20   23   25   27   28   28   28   29   30   33   34 
LCS_GDT     T     158     T     158      4    6   28     3    3    4    5   11   15   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     E     159     E     159      4    6   28     3    4    9   13   14   15   16   17   19   20   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     A     160     A     160      4    4   28     3    4    4    4   10   12   16   17   19   20   22   24   27   28   28   28   29   30   33   34 
LCS_GDT     I     161     I     161      4    4   28     3    4    8    8   11   13   16   17   19   21   24   25   27   28   28   28   29   30   33   34 
LCS_GDT     V     162     V     162      4    4   28     3    4    4    8   10   11   12   16   18   19   21   23   27   28   28   28   29   30   33   34 
LCS_GDT     S     223     S     223      3    5    8     0    3    3    3    4    4    5    6    7   12   13   15   15   18   18   20   23   27   29   30 
LCS_GDT     I     224     I     224      4    5    8     3    4    4    4    4    4    7    7    9   12   13   15   15   20   20   22   24   27   29   31 
LCS_GDT     G     225     G     225      4    5    8     3    4    4    4    4    4    9   11   14   15   16   18   19   20   20   22   24   27   29   31 
LCS_GDT     G     226     G     226      4    5   10     3    4    4    6   11   12   12   14   14   16   18   19   20   21   22   23   25   28   30   31 
LCS_GDT     I     227     I     227      4    5   11     3    4    4    4    5    7   10   14   14   17   18   19   20   22   23   25   27   30   33   34 
LCS_GDT     Y     292     Y     292      3    4   13     2    3    3    3    4    4    6    8    9   11   11   12   12   15   18   26   28   30   33   34 
LCS_GDT     L     293     L     293      3    4   13     3    3    3    4    4    5    5    8    9   11   11   16   19   21   24   26   28   30   33   34 
LCS_GDT     V     294     V     294      3    4   13     3    3    3    4    4    5    8    9    9   11   11   15   15   18   21   24   27   30   33   34 
LCS_GDT     D     295     D     295      5    8   13     5    5    6    8    8    8    8    9    9   10   11   15   15   16   21   24   27   30   33   34 
LCS_GDT     D     296     D     296      5    8   13     5    5    6    8    8    8    8    9    9   11   14   17   19   22   24   26   28   30   33   34 
LCS_GDT     T     297     T     297      5    8   13     5    5    6    8    8    8    8    9    9   11   11   12   15   18   21   24   27   30   33   34 
LCS_GDT     L     298     L     298      5    8   13     5    5    6    8    8    8    8    9    9   11   11   15   15   16   18   20   24   26   29   32 
LCS_GDT     E     299     E     299      5    8   13     5    5    6    8    8    8    8    9    9   11   11   15   15   16   18   24   27   30   33   34 
LCS_GDT     R     300     R     300      4    8   13     4    4    4    8    8    8    8    9    9   11   14   15   17   18   23   26   29   30   33   34 
LCS_GDT     A     301     A     301      4    8   13     4    4    6    8    8    8    8    9    9   11   12   15   15   16   18   20   21   23   29   31 
LCS_GDT     G     302     G     302      4    8   13     3    4    4    8    8    8    8    9    9   11   12   14   15   16   17   20   21   22   23   25 
LCS_GDT     R     303     R     303      4    5   13     3    4    4    4    4    7    8    8    9   11   11   14   15   16   17   19   20   22   23   25 
LCS_GDT     I     304     I     304      4    5   13     0    4    4    4    4    7    8    8    9   11   12   14   15   16   17   19   20   22   23   29 
LCS_AVERAGE  LCS_A:   4.24  (   2.31    3.24    7.17 )

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      9     11     11     13     14     15     16     17     19     21     24     25     27     28     28     28     29     30     33     34 
GDT PERCENT_CA   3.14   3.83   3.83   4.53   4.88   5.23   5.57   5.92   6.62   7.32   8.36   8.71   9.41   9.76   9.76   9.76  10.10  10.45  11.50  11.85
GDT RMS_LOCAL    0.26   0.50   0.50   1.36   1.52   1.67   1.87   2.15   2.64   3.41   3.91   4.06   4.33   4.45   4.45   4.45   4.94   5.75   6.68   6.73
GDT RMS_ALL_CA  19.75  20.17  20.17  16.63  16.76  16.83  16.84  16.69  17.08  21.07  20.79  20.81  20.35  20.08  20.08  20.08  19.71  17.25  16.22  16.33

#      Molecule1      Molecule2       DISTANCE
LGA    I      34      I      34         21.830
LGA    R      35      R      35         25.665
LGA    L      36      L      36         25.738
LGA    T      37      T      37         18.645
LGA    R      38      R      38         18.970
LGA    F      58      F      58         14.698
LGA    S      59      S      59         12.961
LGA    Y      60      Y      60         14.619
LGA    N      61      N      61         14.838
LGA    G      62      G      62         18.787
LGA    G      63      G      63         19.541
LGA    K      64      K      64         26.734
LGA    D      65      D      65         25.858
LGA    C      66      C      66         19.721
LGA    Q      67      Q      67         23.363
LGA    V      68      V      68         28.873
LGA    L      69      L      69         24.739
LGA    L      70      L      70         20.593
LGA    L      71      L      71         27.178
LGA    L      72      L      72         29.008
LGA    Y      73      Y      73         22.454
LGA    P     103      P     103          9.891
LGA    T     104      T     104         11.963
LGA    V     105      V     105          9.643
LGA    F     106      F     106         13.110
LGA    I     107      I     107         11.355
LGA    D     108      D     108         15.213
LGA    Q     109      Q     109         14.061
LGA    V     142      V     142          4.499
LGA    N     143      N     143          3.077
LGA    M     144      M     144          3.021
LGA    A     145      A     145          2.784
LGA    D     146      D     146          0.516
LGA    A     147      A     147          1.602
LGA    F     148      F     148          0.369
LGA    R     149      R     149          1.636
LGA    D     150      D     150          2.468
LGA    F     151      F     151          1.885
LGA    I     152      I     152          1.615
LGA    K     153      K     153          1.546
LGA    I     154      I     154          0.797
LGA    Y     155      Y     155          0.750
LGA    P     156      P     156          5.876
LGA    E     157      E     157          3.564
LGA    T     158      T     158          3.441
LGA    E     159      E     159          1.807
LGA    A     160      A     160          3.996
LGA    I     161      I     161          6.127
LGA    V     162      V     162          8.912
LGA    S     223      S     223         29.963
LGA    I     224      I     224         24.620
LGA    G     225      G     225         20.894
LGA    G     226      G     226         15.374
LGA    I     227      I     227         13.292
LGA    Y     292      Y     292         22.080
LGA    L     293      L     293         19.168
LGA    V     294      V     294         18.638
LGA    D     295      D     295         18.232
LGA    D     296      D     296         17.672
LGA    T     297      T     297         17.437
LGA    L     298      L     298         18.784
LGA    E     299      E     299         19.549
LGA    R     300      R     300         18.047
LGA    A     301      A     301         21.338
LGA    G     302      G     302         23.610
LGA    R     303      R     303         18.343
LGA    I     304      I     304         17.796

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   72  287    4.0     17    2.15     6.010     5.469     0.756

LGA_LOCAL      RMSD =  2.148  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.790  Number of atoms =   67 
Std_ALL_ATOMS  RMSD = 12.613  (standard rmsd on all 67 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.834384 * X  +  -0.039589 * Y  +  -0.549760 * Z  +  31.050318
  Y_new =  -0.547152 * X  +   0.179915 * Y  +   0.817469 * Z  +  -5.100306
  Z_new =   0.066548 * X  +   0.982885 * Y  +  -0.171779 * Z  + -30.846203 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.743819   -1.397774  [ DEG:    99.9135    -80.0865 ]
  Theta =  -0.066597   -3.074996  [ DEG:    -3.8157   -176.1843 ]
  Phi   =  -2.561182    0.580410  [ DEG:  -146.7449     33.2551 ]
 
# 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: T0320TS464_5_1                                
REMARK     2: T0320.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_1.T0320.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   72  287   4.0   17   2.15   5.469    12.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  ILE    34      22.147  31.287  25.775  1.00  0.00
ATOM      2  CA  ARG    35      22.511  32.086  22.100  1.00  0.00
ATOM      3  CA  LEU    36      25.437  29.764  21.556  1.00  0.00
ATOM      4  CA  THR    37      23.721  27.010  23.534  1.00  0.00
ATOM      5  CA  ARG    38      20.541  27.465  21.399  1.00  0.00
ATOM      6  CA  PHE    58      25.161  35.316  16.207  1.00  0.00
ATOM      7  CA  SER    59      27.549  32.554  15.275  1.00  0.00
ATOM      8  CA  TYR    60      31.101  33.858  15.084  1.00  0.00
ATOM      9  CA  ASN    61      33.689  32.044  12.975  1.00  0.00
ATOM     10  CA  GLY    62      35.825  32.078  16.123  1.00  0.00
ATOM     11  CA  GLY    63      35.063  31.172  19.717  1.00  0.00
ATOM     12  CA  LYS    64      37.663  33.761  20.665  1.00  0.00
ATOM     13  CA  ASP    65      35.437  36.317  18.951  1.00  0.00
ATOM     14  CA  CYS    66      32.639  34.311  20.606  1.00  0.00
ATOM     15  CA  GLN    67      34.227  34.626  24.049  1.00  0.00
ATOM     16  CA  VAL    68      35.065  38.287  23.459  1.00  0.00
ATOM     17  CA  LEU    69      31.512  38.889  22.222  1.00  0.00
ATOM     18  CA  LEU    70      30.058  37.443  25.470  1.00  0.00
ATOM     19  CA  LEU    71      32.270  39.796  27.487  1.00  0.00
ATOM     20  CA  LEU    72      30.877  42.742  25.542  1.00  0.00
ATOM     21  CA  TYR    73      27.333  41.436  25.955  1.00  0.00
ATOM     22  CA  PRO   103      20.353  32.676  38.750  1.00  0.00
ATOM     23  CA  THR   104      20.913  29.130  37.518  1.00  0.00
ATOM     24  CA  VAL   105      21.932  28.492  33.907  1.00  0.00
ATOM     25  CA  PHE   106      21.596  24.951  32.570  1.00  0.00
ATOM     26  CA  ILE   107      23.869  24.349  29.632  1.00  0.00
ATOM     27  CA  ASP   108      22.824  21.545  27.289  1.00  0.00
ATOM     28  CA  GLN   109      25.606  20.859  24.755  1.00  0.00
ATOM     29  CA  SER   138      32.594  17.980  15.019  1.00  0.00
ATOM     30  CA  GLY   139      34.705  21.136  14.567  1.00  0.00
ATOM     31  CA  ALA   140      31.775  23.435  15.453  1.00  0.00
ATOM     32  CA  SER   141      30.859  21.703  18.742  1.00  0.00
ATOM     33  CA  VAL   142      34.550  21.947  19.644  1.00  0.00
ATOM     34  CA  ASN   143      34.478  25.716  19.061  1.00  0.00
ATOM     35  CA  MET   144      31.187  26.142  20.945  1.00  0.00
ATOM     36  CA  ALA   145      32.570  24.239  23.942  1.00  0.00
ATOM     37  CA  ASP   146      35.486  25.784  25.753  1.00  0.00
ATOM     38  CA  ALA   147      33.753  29.171  25.704  1.00  0.00
ATOM     39  CA  PHE   148      30.936  27.618  27.759  1.00  0.00
ATOM     40  CA  ARG   149      33.577  26.713  30.371  1.00  0.00
ATOM     41  CA  ASP   150      35.030  30.235  30.390  1.00  0.00
ATOM     42  CA  PHE   151      31.590  31.850  30.531  1.00  0.00
ATOM     43  CA  ILE   152      31.176  30.882  34.182  1.00  0.00
ATOM     44  CA  LYS   153      33.705  33.655  34.778  1.00  0.00
ATOM     45  CA  ILE   154      32.124  36.047  32.304  1.00  0.00
ATOM     46  CA  TYR   155      28.466  36.039  33.204  1.00  0.00
ATOM     47  CA  PRO   156      25.393  37.230  35.010  1.00  0.00
ATOM     48  CA  GLU   157      24.586  33.563  35.648  1.00  0.00
ATOM     49  CA  THR   158      25.303  32.813  39.335  1.00  0.00
ATOM     50  CA  GLU   159      25.834  29.105  38.547  1.00  0.00
ATOM     51  CA  ALA   160      26.207  27.160  35.329  1.00  0.00
ATOM     52  CA  ILE   161      25.575  23.402  35.299  1.00  0.00
ATOM     53  CA  VAL   162      26.535  21.718  32.053  1.00  0.00
ATOM     54  CA  SER   223      33.067  44.441  15.357  1.00  0.00
ATOM     55  CA  ILE   224      34.222  41.420  17.367  1.00  0.00
ATOM     56  CA  GLY   225      35.085  39.416  14.259  1.00  0.00
ATOM     57  CA  GLY   226      33.633  37.464  11.349  1.00  0.00
ATOM     58  CA  ILE   227      30.135  36.235  12.069  1.00  0.00
ATOM     59  CA  TYR   292      24.933   7.598  19.101  1.00  0.00
ATOM     60  CA  LEU   293      27.544   9.487  17.048  1.00  0.00
ATOM     61  CA  VAL   294      26.520  12.914  18.354  1.00  0.00
ATOM     62  CA  ASP   295      26.660  11.575  21.957  1.00  0.00
ATOM     63  CA  ASP   296      30.316  10.685  21.335  1.00  0.00
ATOM     64  CA  THR   297      31.141  14.130  19.969  1.00  0.00
ATOM     65  CA  LEU   298      29.508  15.845  22.950  1.00  0.00
ATOM     66  CA  GLU   299      31.578  13.652  25.303  1.00  0.00
ATOM     67  CA  ARG   300      34.754  14.333  23.315  1.00  0.00
ATOM     68  CA  ALA   301      34.298  18.068  23.905  1.00  0.00
ATOM     69  CA  GLY   302      33.256  17.916  27.546  1.00  0.00
ATOM     70  CA  ARG   303      29.625  18.872  26.885  1.00  0.00
ATOM     71  CA  ILE   304      27.788  15.582  27.652  1.00  0.00
ATOM     72  CA  LYS   305      25.232  17.297  29.945  1.00  0.00
TER
END
