
#######################################################
#                                                     #
#                        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   67 (   67),  selected   64 , name T0379TS393_2-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS393_2-D2.T0379_D2.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        17 - 83          4.02     4.02
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23        17 - 39          1.92     6.26
  LCS_AVERAGE:     28.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        55 - 69          0.72     6.03
  LCS_AVERAGE:     16.82

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     N      17     N      17     11   23   64     1    4   17   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     R      18     R      18     11   23   64    10   10   17   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      19     E      19     11   23   64    10   10   12   17   23   30   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      20     E      20     11   23   64    10   10   11   17   23   29   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     S      21     S      21     11   23   64    10   10   11   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     I      22     I      22     11   23   64    10   12   17   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     R      23     R      23     11   23   64    10   10   17   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     R      24     R      24     11   23   64    10   10   11   17   23   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     F      25     F      25     11   23   64    10   10   11   17   24   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     K      26     K      26     11   23   64    10   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     A      27     A      27     11   23   64    10   10   12   17   23   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     I      28     I      28     11   23   64     3    7   12   17   23   30   38   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     G      29     G      29      6   23   64     3    5    9   16   23   29   32   35   42   51   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     V      30     V      30      6   23   64     3    4    6    6   18   27   32   35   39   51   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     A      31     A      31      6   23   64     3    5   12   19   24   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     D      32     D      32      7   23   64     6    7   11   15   21   26   31   33   47   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     I      33     I      33      7   23   64     6    7   11   17   23   29   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      34     E      34      7   23   64     6    7   12   17   23   29   37   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      35     E      35      7   23   64     6    7   11   16   23   27   32   35   40   51   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     M      36     M      36      7   23   64     6    7   12   17   23   29   38   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      37     L      37      7   23   64     6    7   10   15   23   29   38   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     D      38     D      38      7   23   64     4    4   12   17   23   29   32   35   44   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     P      39     P      39      4   23   64     4    4   12   17   23   29   32   35   44   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     K      43     K      43      0   13   64     0    0    3   15   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     G      44     G      44     10   13   64     7    8    9   12   18   32   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      45     L      45     10   13   64     7    8   11   18   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     F      46     F      46     10   13   64     7    8    9   12   16   21   23   25   42   48   55   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      47     L      47     10   13   64     7    8    9   12   16   21   23   32   43   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     D      48     D      48     10   13   64     7    8    9   12   19   30   39   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      49     L      49     10   13   64     7    8    9   12   16   21   23   30   43   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      50     E      50     10   13   64     7    8    9   12   15   21   23   25   25   27   41   50   58   60   63   64   64   64   64   64 
LCS_GDT     S      51     S      51     10   13   64     3    7    9   12   16   21   23   25   25   27   41   50   58   60   63   64   64   64   64   64 
LCS_GDT     G      52     G      52     10   13   64     6    8    9   12   16   21   28   40   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     R      53     R      53     10   14   64     3    5    9   12   16   25   35   41   48   52   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     K      54     K      54      9   17   64     3    5    8   12   14   20   38   43   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     S      55     S      55     15   17   64     3    4    7   19   25   33   40   44   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      56     E      56     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      57     E      57     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      58     E      58     15   17   64    12   15   18   20   26   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     F      59     F      59     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     R      60     R      60     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     T      61     T      61     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      62     E      62     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      63     L      63     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     S      64     S      64     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     R      65     R      65     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     Y      66     Y      66     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     I      67     I      67     15   17   64    12   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     G      68     G      68     15   17   64     5   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     K      69     K      69     15   17   64     9   14   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     E      70     E      70      4   17   64     3    4    6   12   19   28   38   46   49   52   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      71     L      71      4   17   64     3    4    4   10   21   29   38   46   49   52   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     T      72     T      72     12   14   64     3   11   11   14   22   29   32   40   46   51   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     Y      73     Y      73     12   14   64     8   11   11   12   15   26   32   40   46   50   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     Q      74     Q      74     12   14   64     9   11   11   18   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     Q      75     Q      75     12   14   64     9   11   11   16   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     V      76     V      76     12   14   64     9   11   12   17   24   32   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     Y      77     Y      77     12   14   64     9   11   11   15   24   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     D      78     D      78     12   14   64    11   15   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     A      79     A      79     12   14   64     9   11   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      80     L      80     12   14   64     9   14   18   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     L      81     L      81     12   14   64     9   11   11   17   22   30   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     G      82     G      82     12   14   64     9   11   11   18   21   29   37   43   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_GDT     F      83     F      83     12   14   64     3    4   10   20   27   33   40   46   49   53   56   59   61   62   63   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  48.27  (  16.82   28.00  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     12     15     18     20     27     33     40     46     49     53     56     59     61     62     63     64     64     64     64     64 
GDT PERCENT_CA  18.75  23.44  28.12  31.25  42.19  51.56  62.50  71.88  76.56  82.81  87.50  92.19  95.31  96.88  98.44 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.44   0.67   0.94   1.78   1.98   2.38   2.77   2.88   3.30   3.41   3.58   3.70   3.78   3.90   4.02   4.02   4.02   4.02   4.02
GDT RMS_ALL_CA   5.71   5.21   5.24   5.00   4.52   4.59   4.39   4.17   4.20   4.10   4.05   4.05   4.04   4.04   4.02   4.02   4.02   4.02   4.02   4.02

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          1.220
LGA    R      18      R      18          1.780
LGA    E      19      E      19          3.077
LGA    E      20      E      20          3.621
LGA    S      21      S      21          2.497
LGA    I      22      I      22          1.110
LGA    R      23      R      23          2.009
LGA    R      24      R      24          3.261
LGA    F      25      F      25          2.966
LGA    K      26      K      26          1.771
LGA    A      27      A      27          2.833
LGA    I      28      I      28          3.449
LGA    G      29      G      29          6.041
LGA    V      30      V      30          6.060
LGA    A      31      A      31          2.465
LGA    D      32      D      32          4.782
LGA    I      33      I      33          2.832
LGA    E      34      E      34          3.614
LGA    E      35      E      35          5.797
LGA    M      36      M      36          3.513
LGA    L      37      L      37          3.651
LGA    D      38      D      38          5.868
LGA    P      39      P      39          5.826
LGA    K      43      K      43          2.131
LGA    G      44      G      44          3.209
LGA    L      45      L      45          3.918
LGA    F      46      F      46          7.272
LGA    L      47      L      47          6.683
LGA    D      48      D      48          3.659
LGA    L      49      L      49          6.466
LGA    E      50      E      50          9.570
LGA    S      51      S      51          9.123
LGA    G      52      G      52          5.552
LGA    R      53      R      53          5.603
LGA    K      54      K      54          4.762
LGA    S      55      S      55          4.234
LGA    E      56      E      56          2.496
LGA    E      57      E      57          2.849
LGA    E      58      E      58          3.265
LGA    F      59      F      59          2.759
LGA    R      60      R      60          2.355
LGA    T      61      T      61          3.304
LGA    E      62      E      62          3.616
LGA    L      63      L      63          2.302
LGA    S      64      S      64          2.503
LGA    R      65      R      65          3.550
LGA    Y      66      Y      66          2.851
LGA    I      67      I      67          1.815
LGA    G      68      G      68          2.240
LGA    K      69      K      69          2.462
LGA    E      70      E      70          3.968
LGA    L      71      L      71          3.975
LGA    T      72      T      72          5.532
LGA    Y      73      Y      73          5.727
LGA    Q      74      Q      74          2.773
LGA    Q      75      Q      75          1.921
LGA    V      76      V      76          2.858
LGA    Y      77      Y      77          2.427
LGA    D      78      D      78          2.178
LGA    A      79      A      79          2.370
LGA    L      80      L      80          1.165
LGA    L      81      L      81          3.234
LGA    G      82      G      82          4.617
LGA    F      83      F      83          2.552

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67   64    4.0     46    2.77    56.641    52.464     1.605

LGA_LOCAL      RMSD =  2.767  Number of atoms =   46  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.093  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  4.016  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.784537 * X  +   0.396385 * Y  +  -0.476844 * Z  +  62.444286
  Y_new =   0.304076 * X  +  -0.916124 * Y  +  -0.261256 * Z  +   5.865720
  Z_new =  -0.540406 * X  +   0.059968 * Y  +  -0.839265 * Z  +   7.912263 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.070261   -0.071332  [ DEG:   175.9130     -4.0870 ]
  Theta =   0.570920    2.570673  [ DEG:    32.7113    147.2887 ]
  Phi   =   0.369759   -2.771833  [ DEG:    21.1857   -158.8143 ]
 
# 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: T0379TS393_2-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0379TS393_2-D2.T0379_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   67   64   4.0   46   2.77  52.464     4.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS393_2-D2
PFRMAT TS
TARGET T0379
MODEL 2
PARENT N/A
ATOM     17  CA  ASN    17      67.517   6.512  13.204  1.00 25.00           C
ATOM     18  CA  ARG    18      65.230   3.822  14.617  1.00 25.00           C
ATOM     19  CA  GLU    19      66.717   0.960  16.681  1.00 25.00           C
ATOM     20  CA  GLU    20      69.929   2.976  17.208  1.00 25.00           C
ATOM     21  CA  SER    21      67.874   6.007  18.327  1.00 25.00           C
ATOM     22  CA  ILE    22      65.921   3.808  20.780  1.00 25.00           C
ATOM     23  CA  ARG    23      69.202   2.410  22.177  1.00 25.00           C
ATOM     24  CA  ARG    24      70.562   5.964  22.607  1.00 25.00           C
ATOM     25  CA  PHE    25      67.355   6.997  24.429  1.00 25.00           C
ATOM     26  CA  LYS    26      67.656   3.953  26.734  1.00 25.00           C
ATOM     27  CA  ALA    27      71.305   4.847  27.480  1.00 25.00           C
ATOM     28  CA  ILE    28      69.731   5.608  30.819  1.00 25.00           C
ATOM     29  CA  GLY    29      70.747   2.049  31.620  1.00 25.00           C
ATOM     30  CA  VAL    30      67.351   0.520  32.232  1.00 25.00           C
ATOM     31  CA  ALA    31      66.220  -0.889  28.845  1.00 25.00           C
ATOM     32  CA  ASP    32      62.876   0.769  29.703  1.00 25.00           C
ATOM     33  CA  ILE    33      62.717   2.316  26.204  1.00 25.00           C
ATOM     34  CA  GLU    34      63.435  -1.102  24.633  1.00 25.00           C
ATOM     35  CA  GLU    35      60.665  -2.685  26.750  1.00 25.00           C
ATOM     36  CA  MET    36      58.228   0.061  25.658  1.00 25.00           C
ATOM     37  CA  LEU    37      59.164  -0.534  21.992  1.00 25.00           C
ATOM     38  CA  ASP    38      56.310  -3.131  22.048  1.00 25.00           C
ATOM     39  CA  PRO    39      53.612  -1.809  19.652  1.00 25.00           C
ATOM     40  CA  TYR    40      51.484  -1.226  22.782  1.00 25.00           C
ATOM     41  CA  LEU    41      53.032   2.250  23.218  1.00 25.00           C
ATOM     42  CA  GLN    42      52.289   3.068  19.552  1.00 25.00           C
ATOM     43  CA  LYS    43      48.664   1.916  20.003  1.00 25.00           C
ATOM     44  CA  GLY    44      48.332   4.106  23.128  1.00 25.00           C
ATOM     45  CA  LEU    45      49.739   7.105  21.206  1.00 25.00           C
ATOM     46  CA  PHE    46      47.249   6.482  18.364  1.00 25.00           C
ATOM     47  CA  LEU    47      44.374   6.308  20.888  1.00 25.00           C
ATOM     48  CA  ASP    48      45.529   9.600  22.468  1.00 25.00           C
ATOM     49  CA  LEU    49      45.670  11.239  19.010  1.00 25.00           C
ATOM     50  CA  GLU    50      42.132   9.986  18.245  1.00 25.00           C
ATOM     51  CA  SER    51      39.295  11.671  20.195  1.00 25.00           C
ATOM     52  CA  GLY    52      41.869  14.420  20.547  1.00 25.00           C
ATOM     53  CA  ARG    53      42.426  15.562  24.140  1.00 25.00           C
ATOM     54  CA  LYS    54      46.187  16.274  24.119  1.00 25.00           C
ATOM     55  CA  SER    55      49.043  16.997  21.720  1.00 25.00           C
ATOM     56  CA  GLU    56      51.576  15.174  23.958  1.00 25.00           C
ATOM     57  CA  GLU    57      50.472  14.922  27.618  1.00 25.00           C
ATOM     58  CA  GLU    58      48.548  11.703  26.841  1.00 25.00           C
ATOM     59  CA  PHE    59      51.632  10.250  25.098  1.00 25.00           C
ATOM     60  CA  ARG    60      53.798  11.152  28.125  1.00 25.00           C
ATOM     61  CA  THR    61      51.274   9.470  30.463  1.00 25.00           C
ATOM     62  CA  GLU    62      51.297   6.330  28.269  1.00 25.00           C
ATOM     63  CA  LEU    63      55.126   6.281  28.339  1.00 25.00           C
ATOM     64  CA  SER    64      55.086   6.614  32.154  1.00 25.00           C
ATOM     65  CA  ARG    65      52.584   3.727  32.406  1.00 25.00           C
ATOM     66  CA  TYR    66      54.807   1.573  30.149  1.00 25.00           C
ATOM     67  CA  ILE    67      57.849   2.388  32.328  1.00 25.00           C
ATOM     68  CA  GLY    68      56.838   1.861  35.971  1.00 25.00           C
ATOM     69  CA  LYS    69      57.847   5.351  37.090  1.00 25.00           C
ATOM     70  CA  GLU    70      60.921   6.350  39.005  1.00 25.00           C
ATOM     71  CA  LEU    71      62.017   9.393  37.074  1.00 25.00           C
ATOM     72  CA  THR    72      64.630  11.582  35.380  1.00 25.00           C
ATOM     73  CA  TYR    73      61.968  12.072  32.706  1.00 25.00           C
ATOM     74  CA  GLN    74      62.975  15.548  31.450  1.00 25.00           C
ATOM     75  CA  GLN    75      66.290  14.143  30.146  1.00 25.00           C
ATOM     76  CA  VAL    76      64.419  11.326  28.349  1.00 25.00           C
ATOM     77  CA  TYR    77      62.039  13.879  26.772  1.00 25.00           C
ATOM     78  CA  ASP    78      65.024  15.980  25.612  1.00 25.00           C
ATOM     79  CA  ALA    79      66.653  12.867  24.086  1.00 25.00           C
ATOM     80  CA  LEU    80      63.389  12.018  22.272  1.00 25.00           C
ATOM     81  CA  LEU    81      63.179  15.596  20.922  1.00 25.00           C
ATOM     82  CA  GLY    82      66.802  15.374  19.700  1.00 25.00           C
ATOM     83  CA  PHE    83      66.039  12.043  17.969  1.00 25.00           C
TER
END
