
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0311TS393_1-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS393_1-D1.T0311_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:    64         8 - 71          4.14     4.14
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40         8 - 47          2.00     4.65
  LONGEST_CONTINUOUS_SEGMENT:    40         9 - 48          1.98     4.61
  LONGEST_CONTINUOUS_SEGMENT:    40        10 - 49          1.97     4.54
  LCS_AVERAGE:     48.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        24 - 36          0.97     5.52
  LCS_AVERAGE:     15.80

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:   64
LCS_GDT     R       8     R       8      3   40   64     0    4    6   17   28   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     P       9     P       9     12   40   64    11   11   14   19   31   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     G      10     G      10     12   40   64    11   11   14   25   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     D      11     D      11     12   40   64    11   11   17   27   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     I      12     I      12     12   40   64    11   11   17   27   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     I      13     I      13     12   40   64    11   11   17   27   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     Q      14     Q      14     12   40   64    11   11   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     E      15     E      15     12   40   64    11   11   18   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      16     S      16     12   40   64    11   11   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      17     L      17     12   40   64    11   11   13   26   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     D      18     D      18     12   40   64    11   11   13   18   34   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     E      19     E      19     12   40   64    11   11   13   24   34   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      20     L      20     12   40   64     4    5   19   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     N      21     N      21      5   40   64     4    9   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     V      22     V      22      5   40   64     3    6   19   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      23     S      23     11   40   64     3    7   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      24     L      24     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     R      25     R      25     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     E      26     E      26     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     F      27     F      27     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      28     A      28     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     R      29     R      29     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      30     A      30     13   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     M      31     M      31     13   40   64     8   14   19   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     E      32     E      32     13   40   64     4   14   19   27   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     I      33     I      33     13   40   64     4   14   19   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      34     A      34     13   40   64     3   10   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     P      35     P      35     13   40   64     9   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      36     S      36     13   40   64     9    9   16   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     T      37     T      37     10   40   64     9    9   12   19   29   41   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      38     A      38     10   40   64     9    9   14   26   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      39     S      39     10   40   64     9   10   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     R      40     R      40     10   40   64     9   14   19   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      41     L      41     10   40   64     9    9   11   23   35   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      42     L      42     10   40   64     9    9   16   27   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     T      43     T      43     10   40   64     9   10   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     G      44     G      44      4   40   64     3    3    7   25   35   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     K      45     K      45      4   40   64     3    7   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      46     A      46      4   40   64     4    4   17   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      47     A      47      4   40   64     8   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      48     L      48      4   40   64     4   14   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     T      49     T      49     12   40   64     9   11   12   22   35   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     P      50     P      50     12   14   64     9   11   12   12   12   13   14   16   17   25   38   53   60   61   63   64   64   64   64   64 
LCS_GDT     E      51     E      51     12   14   64     9   11   12   12   12   13   16   19   23   28   29   31   39   60   63   64   64   64   64   64 
LCS_GDT     M      52     M      52     12   14   64     9   11   14   19   32   41   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     A      53     A      53     12   14   64     9   11   12   12   14   27   41   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     I      54     I      54     12   14   64     9   11   12   12   12   13   15   18   24   31   38   46   60   61   63   64   64   64   64   64 
LCS_GDT     K      55     K      55     12   14   64     9   11   12   12   12   19   28   37   41   50   54   55   60   61   63   64   64   64   64   64 
LCS_GDT     L      56     L      56     12   14   64     9   11   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      57     S      57     12   14   64     9   11   12   12   12   18   31   42   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     V      58     V      58     12   14   64     9   11   12   12   12   18   25   36   43   50   54   55   60   61   63   64   64   64   64   64 
LCS_GDT     V      59     V      59     12   14   64     9   11   12   19   31   38   44   47   49   52   54   55   60   61   63   64   64   64   64   64 
LCS_GDT     I      60     I      60     12   14   64     4    8   12   21   29   38   44   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     G      61     G      61      4   14   64     4    8   10   12   17   23   35   40   49   50   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      62     S      62      4   12   64     4    7    8    9   13   21   30   44   46   48   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     S      63     S      63      4   12   64     4    5    6   10   14   21   32   44   46   49   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     P      64     P      64      8   12   64     8    8   20   28   36   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     Q      65     Q      65      8   12   64     8    8   15   27   35   42   46   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     M      66     M      66      8   12   64     8    8    9   15   29   36   44   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     W      67     W      67      8   12   64     8    8    9   15   27   34   44   48   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     L      68     L      68      8   12   64     8    8    9   15   18   29   37   46   52   52   55   56   60   61   63   64   64   64   64   64 
LCS_GDT     N      69     N      69      8   12   64     8    8    9   11   15   22   26   37   40   49   53   56   59   61   63   64   64   64   64   64 
LCS_GDT     L      70     L      70      8   12   64     8    8    9   11   15   17   19   20   30   38   41   50   54   60   63   64   64   64   64   64 
LCS_GDT     Q      71     Q      71      8   12   64     8    8    9   11   15   17   19   20   23   28   29   50   53   58   59   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  54.61  (  15.80   48.05  100.00 )

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     11     14     20     28     36     42     46     48     52     52     55     56     60     61     63     64     64     64     64     64 
GDT PERCENT_CA  17.19  21.88  31.25  43.75  56.25  65.62  71.88  75.00  81.25  81.25  85.94  87.50  93.75  95.31  98.44 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.21   0.67   1.17   1.42   1.72   1.93   2.09   2.26   2.66   2.60   2.98   3.13   3.57   3.68   3.98   4.14   4.14   4.14   4.14   4.14
GDT RMS_ALL_CA   7.41   5.39   4.66   4.50   4.51   4.45   4.48   4.41   4.24   4.30   4.25   4.21   4.21   4.17   4.15   4.14   4.14   4.14   4.14   4.14

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8          3.738
LGA    P       9      P       9          3.912
LGA    G      10      G      10          2.902
LGA    D      11      D      11          2.421
LGA    I      12      I      12          2.686
LGA    I      13      I      13          2.692
LGA    Q      14      Q      14          2.081
LGA    E      15      E      15          1.745
LGA    S      16      S      16          2.301
LGA    L      17      L      17          3.313
LGA    D      18      D      18          3.251
LGA    E      19      E      19          3.096
LGA    L      20      L      20          1.807
LGA    N      21      N      21          1.102
LGA    V      22      V      22          0.515
LGA    S      23      S      23          1.259
LGA    L      24      L      24          2.337
LGA    R      25      R      25          2.157
LGA    E      26      E      26          2.575
LGA    F      27      F      27          2.254
LGA    A      28      A      28          1.289
LGA    R      29      R      29          1.629
LGA    A      30      A      30          1.902
LGA    M      31      M      31          1.871
LGA    E      32      E      32          1.503
LGA    I      33      I      33          1.195
LGA    A      34      A      34          1.668
LGA    P      35      P      35          1.493
LGA    S      36      S      36          3.268
LGA    T      37      T      37          3.488
LGA    A      38      A      38          1.703
LGA    S      39      S      39          1.086
LGA    R      40      R      40          2.161
LGA    L      41      L      41          2.232
LGA    L      42      L      42          2.018
LGA    T      43      T      43          1.762
LGA    G      44      G      44          3.553
LGA    K      45      K      45          3.246
LGA    A      46      A      46          2.347
LGA    A      47      A      47          2.261
LGA    L      48      L      48          2.449
LGA    T      49      T      49          2.117
LGA    P      50      P      50          7.720
LGA    E      51      E      51          8.775
LGA    M      52      M      52          3.770
LGA    A      53      A      53          3.999
LGA    I      54      I      54          8.348
LGA    K      55      K      55          6.898
LGA    L      56      L      56          1.420
LGA    S      57      S      57          5.619
LGA    V      58      V      58          7.352
LGA    V      59      V      59          5.161
LGA    I      60      I      60          3.749
LGA    G      61      G      61          5.840
LGA    S      62      S      62          6.744
LGA    S      63      S      63          6.081
LGA    P      64      P      64          0.806
LGA    Q      65      Q      65          1.777
LGA    M      66      M      66          4.761
LGA    W      67      W      67          4.561
LGA    L      68      L      68          5.836
LGA    N      69      N      69          8.355
LGA    L      70      L      70         10.287
LGA    Q      71      Q      71         10.769

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   64    4.0     48    2.26    60.156    60.792     2.031

LGA_LOCAL      RMSD =  2.264  Number of atoms =   48  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.221  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  4.138  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.100022 * X  +   0.907508 * Y  +  -0.407952 * Z  +  33.707664
  Y_new =   0.763701 * X  +   0.192788 * Y  +   0.616111 * Z  +   1.799132
  Z_new =   0.637774 * X  +  -0.373178 * Y  +  -0.673782 * Z  +  14.612849 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.635794    0.505798  [ DEG:  -151.0199     28.9801 ]
  Theta =  -0.691605   -2.449988  [ DEG:   -39.6261   -140.3739 ]
  Phi   =   1.440568   -1.701025  [ DEG:    82.5385    -97.4615 ]
 
# 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: T0311TS393_1-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_1-D1.T0311_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   64   64   4.0   48   2.26  60.792     4.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_1-D1
PFRMAT TS
TARGET T0311
MODEL 1
PARENT N/A
ATOM      8  CA  ARG     8      44.424   0.740  14.291  1.00 25.00           C
ATOM      9  CA  PRO     9      40.706   1.772  14.183  1.00 25.00           C
ATOM     10  CA  GLY    10      38.333  -1.106  15.050  1.00 25.00           C
ATOM     11  CA  ASP    11      37.306   0.680  18.279  1.00 25.00           C
ATOM     12  CA  ILE    12      36.651   3.904  16.316  1.00 25.00           C
ATOM     13  CA  ILE    13      34.518   1.964  13.796  1.00 25.00           C
ATOM     14  CA  GLN    14      32.529   0.381  16.659  1.00 25.00           C
ATOM     15  CA  GLU    15      31.967   3.835  18.213  1.00 25.00           C
ATOM     16  CA  SER    16      30.765   5.184  14.836  1.00 25.00           C
ATOM     17  CA  LEU    17      28.359   2.227  14.482  1.00 25.00           C
ATOM     18  CA  ASP    18      27.010   2.870  18.007  1.00 25.00           C
ATOM     19  CA  GLU    19      26.499   6.571  17.164  1.00 25.00           C
ATOM     20  CA  LEU    20      22.764   6.497  16.262  1.00 25.00           C
ATOM     21  CA  ASN    21      22.487   5.162  19.844  1.00 25.00           C
ATOM     22  CA  VAL    22      22.119   1.620  18.567  1.00 25.00           C
ATOM     23  CA  SER    23      24.314  -1.419  19.247  1.00 25.00           C
ATOM     24  CA  LEU    24      25.364  -2.583  15.754  1.00 25.00           C
ATOM     25  CA  ARG    25      21.950  -4.241  15.236  1.00 25.00           C
ATOM     26  CA  GLU    26      20.711  -1.151  13.341  1.00 25.00           C
ATOM     27  CA  PHE    27      23.838  -1.220  11.133  1.00 25.00           C
ATOM     28  CA  ALA    28      23.276  -4.938  10.409  1.00 25.00           C
ATOM     29  CA  ARG    29      19.628  -4.232   9.485  1.00 25.00           C
ATOM     30  CA  ALA    30      20.741  -1.412   7.145  1.00 25.00           C
ATOM     31  CA  MET    31      23.286  -3.752   5.498  1.00 25.00           C
ATOM     32  CA  GLU    32      22.206  -7.387   5.277  1.00 25.00           C
ATOM     33  CA  ILE    33      25.567  -8.531   6.741  1.00 25.00           C
ATOM     34  CA  ALA    34      23.551  -9.955   9.654  1.00 25.00           C
ATOM     35  CA  PRO    35      25.669  -9.090  12.689  1.00 25.00           C
ATOM     36  CA  SER    36      28.766 -10.380  10.841  1.00 25.00           C
ATOM     37  CA  THR    37      29.509  -6.844   9.569  1.00 25.00           C
ATOM     38  CA  ALA    38      29.163  -5.465  13.125  1.00 25.00           C
ATOM     39  CA  SER    39      31.550  -8.162  14.429  1.00 25.00           C
ATOM     40  CA  ARG    40      34.077  -7.287  11.687  1.00 25.00           C
ATOM     41  CA  LEU    41      33.822  -3.577  12.602  1.00 25.00           C
ATOM     42  CA  LEU    42      34.394  -4.422  16.293  1.00 25.00           C
ATOM     43  CA  THR    43      37.459  -6.522  15.363  1.00 25.00           C
ATOM     44  CA  GLY    44      39.602  -8.503  12.998  1.00 25.00           C
ATOM     45  CA  LYS    45      38.552 -10.305   9.861  1.00 25.00           C
ATOM     46  CA  ALA    46      38.820  -6.922   8.138  1.00 25.00           C
ATOM     47  CA  ALA    47      38.697  -5.659   4.551  1.00 25.00           C
ATOM     48  CA  LEU    48      37.032  -2.555   3.251  1.00 25.00           C
ATOM     49  CA  THR    49      33.619  -4.032   2.272  1.00 25.00           C
ATOM     50  CA  PRO    50      32.035  -5.316   5.514  1.00 25.00           C
ATOM     51  CA  GLU    51      33.454  -2.682   7.906  1.00 25.00           C
ATOM     52  CA  MET    52      33.051   0.013   5.214  1.00 25.00           C
ATOM     53  CA  ALA    53      29.428  -1.079   4.628  1.00 25.00           C
ATOM     54  CA  ILE    54      28.744  -0.917   8.394  1.00 25.00           C
ATOM     55  CA  LYS    55      30.261   2.597   8.542  1.00 25.00           C
ATOM     56  CA  LEU    56      28.073   3.693   5.596  1.00 25.00           C
ATOM     57  CA  SER    57      24.971   2.277   7.341  1.00 25.00           C
ATOM     58  CA  VAL    58      25.891   4.151  10.552  1.00 25.00           C
ATOM     59  CA  VAL    59      26.328   7.395   8.562  1.00 25.00           C
ATOM     60  CA  ILE    60      22.912   6.872   6.912  1.00 25.00           C
ATOM     61  CA  GLY    61      23.351   5.823   3.237  1.00 25.00           C
ATOM     62  CA  SER    62      26.583   5.897   1.288  1.00 25.00           C
ATOM     63  CA  SER    63      29.364   3.289   0.687  1.00 25.00           C
ATOM     64  CA  PRO    64      32.909   4.737   0.914  1.00 25.00           C
ATOM     65  CA  GLN    65      34.861   8.029   1.045  1.00 25.00           C
ATOM     66  CA  MET    66      31.834   9.791   2.595  1.00 25.00           C
ATOM     67  CA  TRP    67      31.523   7.010   5.209  1.00 25.00           C
ATOM     68  CA  LEU    68      35.248   7.339   6.037  1.00 25.00           C
ATOM     69  CA  ASN    69      34.855  11.128   6.418  1.00 25.00           C
ATOM     70  CA  LEU    70      31.857  10.608   8.744  1.00 25.00           C
ATOM     71  CA  GLN    71      33.881   8.122  10.838  1.00 25.00           C
TER
END
