
#######################################################
#                                                     #
#                        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 T0379TS168_4-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS168_4-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          3.88     3.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29        55 - 83          1.99     4.56
  LCS_AVERAGE:     36.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        54 - 68          0.89     5.80
  LCS_AVERAGE:     18.63

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     14   15   64     8   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     R      18     R      18     14   15   64    10   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      19     E      19     14   15   64    10   12   19   27   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      20     E      20     14   15   64    10   11   19   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     S      21     S      21     14   19   64    10   15   20   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     I      22     I      22     14   19   64    10   13   19   27   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     R      23     R      23     14   19   64    10   13   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     R      24     R      24     14   19   64    10   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     F      25     F      25     14   19   64    10   11   13   27   27   37   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     K      26     K      26     14   19   64    10   13   19   27   27   33   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     A      27     A      27     14   19   64    10   11   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     I      28     I      28     14   19   64     4    6   18   27   27   37   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     G      29     G      29     14   19   64     4   11   13   16   27   30   34   36   37   52   56   59   61   63   64   64   64   64   64   64 
LCS_GDT     V      30     V      30     14   19   64     4    8   13   14   22   29   34   36   38   47   54   57   60   63   64   64   64   64   64   64 
LCS_GDT     A      31     A      31      4   19   64     3    8   18   27   27   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     D      32     D      32      8   19   64     6    8   12   18   25   37   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     I      33     I      33      8   19   64     6    8   12   18   25   37   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      34     E      34      8   19   64     6    8   12   18   25   37   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      35     E      35      8   19   64     6    8   12   16   25   33   39   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     M      36     M      36      8   19   64     6    8   12   18   25   33   43   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      37     L      37      8   19   64     6    8   12   18   26   35   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     D      38     D      38      8   19   64     3    8   12   17   25   33   39   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     P      39     P      39      8   19   64     0    3    7   16   24   26   32   35   41   50   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     K      43     K      43      0   10   64     0    0    3    7   31   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     G      44     G      44      9   12   64     7    8    9   13   21   31   43   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      45     L      45      9   12   64     7   10   17   24   33   38   43   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     F      46     F      46      9   23   64     7    8   10   18   21   22   25   32   41   48   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      47     L      47      9   23   64     7    8   12   18   21   22   25   33   41   53   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     D      48     D      48      9   23   64     7    8   13   18   22   32   43   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      49     L      49      9   23   64     7    8    9   15   21   22   22   27   38   50   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      50     E      50      9   23   64     7    8    9   17   21   22   22   25   25   28   39   53   60   63   64   64   64   64   64   64 
LCS_GDT     S      51     S      51      9   23   64     5    8    9   17   21   22   22   25   25   33   53   59   61   63   64   64   64   64   64   64 
LCS_GDT     G      52     G      52      9   23   64     3    5    8   10   11   17   20   25   39   52   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     R      53     R      53      7   23   64     3    6   10   14   19   22   37   44   47   52   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     K      54     K      54     15   23   64     3    6   12   18   21   35   41   47   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     S      55     S      55     15   29   64     3   18   21   29   34   38   43   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      56     E      56     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      57     E      57     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      58     E      58     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     F      59     F      59     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     R      60     R      60     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     T      61     T      61     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      62     E      62     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      63     L      63     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     S      64     S      64     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     R      65     R      65     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     Y      66     Y      66     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     I      67     I      67     15   29   64    12   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     G      68     G      68     15   29   64     9   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     K      69     K      69      4   29   64     3    3    4    6   17   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     E      70     E      70     13   29   64     3    7   14   27   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      71     L      71     13   29   64     3   13   19   27   27   36   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     T      72     T      72     13   29   64     5   13   19   27   28   36   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     Y      73     Y      73     13   29   64     5   13   19   27   27   33   43   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     Q      74     Q      74     13   29   64     7   13   19   27   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     Q      75     Q      75     13   29   64     7   13   19   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     V      76     V      76     13   29   64     7   13   19   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     Y      77     Y      77     13   29   64     7   13   19   28   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     D      78     D      78     13   29   64     7   13   20   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     A      79     A      79     13   29   64     7   18   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      80     L      80     13   29   64     7   12   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     L      81     L      81     13   29   64     7   12   19   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     G      82     G      82     13   29   64     7   12   21   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_GDT     F      83     F      83     13   29   64     3   13   19   29   34   38   45   49   54   54   57   59   61   63   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  51.77  (  18.63   36.69  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     18     21     29     34     38     45     49     54     54     57     59     61     63     64     64     64     64     64     64 
GDT PERCENT_CA  18.75  28.12  32.81  45.31  53.12  59.38  70.31  76.56  84.38  84.38  89.06  92.19  95.31  98.44 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.71   0.94   1.36   1.63   1.88   2.42   2.60   2.84   2.84   3.15   3.36   3.54   3.74   3.88   3.88   3.88   3.88   3.88   3.88
GDT RMS_ALL_CA   5.09   4.64   4.64   4.54   4.55   4.39   4.21   4.09   4.04   4.04   3.97   3.92   3.90   3.88   3.88   3.88   3.88   3.88   3.88   3.88

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          1.218
LGA    R      18      R      18          1.989
LGA    E      19      E      19          3.630
LGA    E      20      E      20          2.201
LGA    S      21      S      21          1.225
LGA    I      22      I      22          3.158
LGA    R      23      R      23          2.545
LGA    R      24      R      24          0.637
LGA    F      25      F      25          3.298
LGA    K      26      K      26          3.974
LGA    A      27      A      27          1.534
LGA    I      28      I      28          3.262
LGA    G      29      G      29          6.302
LGA    V      30      V      30          6.869
LGA    A      31      A      31          3.134
LGA    D      32      D      32          3.700
LGA    I      33      I      33          3.372
LGA    E      34      E      34          3.392
LGA    E      35      E      35          4.746
LGA    M      36      M      36          3.967
LGA    L      37      L      37          3.617
LGA    D      38      D      38          4.768
LGA    P      39      P      39          7.890
LGA    K      43      K      43          2.115
LGA    G      44      G      44          3.715
LGA    L      45      L      45          3.205
LGA    F      46      F      46          6.817
LGA    L      47      L      47          6.867
LGA    D      48      D      48          3.795
LGA    L      49      L      49          6.312
LGA    E      50      E      50          9.528
LGA    S      51      S      51          8.509
LGA    G      52      G      52          6.948
LGA    R      53      R      53          5.749
LGA    K      54      K      54          4.260
LGA    S      55      S      55          3.616
LGA    E      56      E      56          2.921
LGA    E      57      E      57          3.085
LGA    E      58      E      58          2.458
LGA    F      59      F      59          2.547
LGA    R      60      R      60          2.867
LGA    T      61      T      61          2.705
LGA    E      62      E      62          2.660
LGA    L      63      L      63          2.481
LGA    S      64      S      64          2.483
LGA    R      65      R      65          2.494
LGA    Y      66      Y      66          2.279
LGA    I      67      I      67          2.264
LGA    G      68      G      68          2.450
LGA    K      69      K      69          3.061
LGA    E      70      E      70          2.144
LGA    L      71      L      71          4.043
LGA    T      72      T      72          3.916
LGA    Y      73      Y      73          4.224
LGA    Q      74      Q      74          2.854
LGA    Q      75      Q      75          1.583
LGA    V      76      V      76          1.538
LGA    Y      77      Y      77          1.521
LGA    D      78      D      78          0.833
LGA    A      79      A      79          0.380
LGA    L      80      L      80          0.804
LGA    L      81      L      81          1.683
LGA    G      82      G      82          2.070
LGA    F      83      F      83          1.419

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67   64    4.0     49    2.60    62.500    58.817     1.814

LGA_LOCAL      RMSD =  2.601  Number of atoms =   49  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.915  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  3.875  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.165448 * X  +   0.986161 * Y  +  -0.010658 * Z  +  62.597412
  Y_new =   0.536279 * X  +   0.080891 * Y  +  -0.840155 * Z  +   4.496945
  Z_new =  -0.827666 * X  +  -0.144718 * Y  +  -0.542241 * Z  +   8.261829 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.880784    0.260809  [ DEG:  -165.0567     14.9433 ]
  Theta =   0.974936    2.166656  [ DEG:    55.8597    124.1403 ]
  Phi   =   1.870042   -1.271550  [ DEG:   107.1455    -72.8545 ]
 
# 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: T0379TS168_4-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0379TS168_4-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   49   2.60  58.817     3.88
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS168_4-D2
PFRMAT TS
TARGET T0379
MODEL 4
PARENT N/A
ATOM     17  CA  ASN    17      69.141   7.563  12.687  1.00 25.00           C
ATOM     18  CA  ARG    18      68.071   4.863  15.099  1.00 25.00           C
ATOM     19  CA  GLU    19      71.459   5.518  16.760  1.00 25.00           C
ATOM     20  CA  GLU    20      69.896   8.264  18.923  1.00 25.00           C
ATOM     21  CA  SER    21      67.074   5.885  19.946  1.00 25.00           C
ATOM     22  CA  ILE    22      69.642   3.195  20.863  1.00 25.00           C
ATOM     23  CA  ARG    23      71.595   5.739  22.956  1.00 25.00           C
ATOM     24  CA  ARG    24      68.373   6.775  24.748  1.00 25.00           C
ATOM     25  CA  PHE    25      67.562   3.102  25.468  1.00 25.00           C
ATOM     26  CA  LYS    26      71.090   2.571  26.862  1.00 25.00           C
ATOM     27  CA  ALA    27      70.698   5.658  29.093  1.00 25.00           C
ATOM     28  CA  ILE    28      68.997   4.857  32.464  1.00 25.00           C
ATOM     29  CA  GLY    29      70.936   1.577  32.025  1.00 25.00           C
ATOM     30  CA  VAL    30      68.428  -0.647  30.350  1.00 25.00           C
ATOM     31  CA  ALA    31      66.135  -2.860  28.194  1.00 25.00           C
ATOM     32  CA  ASP    32      62.820  -1.895  29.850  1.00 25.00           C
ATOM     33  CA  ILE    33      62.491   1.110  27.498  1.00 25.00           C
ATOM     34  CA  GLU    34      63.167  -1.147  24.480  1.00 25.00           C
ATOM     35  CA  GLU    35      60.508  -3.618  25.700  1.00 25.00           C
ATOM     36  CA  MET    36      58.001  -0.751  26.114  1.00 25.00           C
ATOM     37  CA  LEU    37      58.778   0.474  22.570  1.00 25.00           C
ATOM     38  CA  ASP    38      57.426  -2.805  21.198  1.00 25.00           C
ATOM     39  CA  PRO    39      53.732  -2.092  21.765  1.00 25.00           C
ATOM     40  CA  TYR    40      51.389  -1.203  24.662  1.00 25.00           C
ATOM     41  CA  LEU    41      52.874   2.323  24.815  1.00 25.00           C
ATOM     42  CA  GLN    42      52.377   2.723  21.038  1.00 25.00           C
ATOM     43  CA  LYS    43      48.740   1.570  21.370  1.00 25.00           C
ATOM     44  CA  GLY    44      48.176   4.083  24.204  1.00 25.00           C
ATOM     45  CA  LEU    45      49.685   6.875  22.061  1.00 25.00           C
ATOM     46  CA  PHE    46      47.402   5.905  19.144  1.00 25.00           C
ATOM     47  CA  LEU    47      44.362   5.962  21.472  1.00 25.00           C
ATOM     48  CA  ASP    48      45.378   9.425  22.754  1.00 25.00           C
ATOM     49  CA  LEU    49      45.741  10.678  19.153  1.00 25.00           C
ATOM     50  CA  GLU    50      42.275   9.292  18.296  1.00 25.00           C
ATOM     51  CA  SER    51      40.215  11.002  20.916  1.00 25.00           C
ATOM     52  CA  GLY    52      41.542  13.052  23.808  1.00 25.00           C
ATOM     53  CA  ARG    53      42.659  16.344  22.199  1.00 25.00           C
ATOM     54  CA  LYS    54      45.932  15.640  24.042  1.00 25.00           C
ATOM     55  CA  SER    55      49.208  16.488  22.183  1.00 25.00           C
ATOM     56  CA  GLU    56      52.713  15.474  23.286  1.00 25.00           C
ATOM     57  CA  GLU    57      52.909  15.989  27.076  1.00 25.00           C
ATOM     58  CA  GLU    58      50.004  13.547  27.583  1.00 25.00           C
ATOM     59  CA  PHE    59      51.753  10.966  25.359  1.00 25.00           C
ATOM     60  CA  ARG    60      54.987  11.391  27.365  1.00 25.00           C
ATOM     61  CA  THR    61      53.050  10.911  30.634  1.00 25.00           C
ATOM     62  CA  GLU    62      51.426   7.738  29.234  1.00 25.00           C
ATOM     63  CA  LEU    63      54.862   6.407  28.193  1.00 25.00           C
ATOM     64  CA  SER    64      56.230   7.128  31.696  1.00 25.00           C
ATOM     65  CA  ARG    65      53.255   5.296  33.262  1.00 25.00           C
ATOM     66  CA  TYR    66      53.856   2.298  30.956  1.00 25.00           C
ATOM     67  CA  ILE    67      57.558   2.258  31.933  1.00 25.00           C
ATOM     68  CA  GLY    68      57.758   3.703  35.449  1.00 25.00           C
ATOM     69  CA  LYS    69      57.953   4.659  39.102  1.00 25.00           C
ATOM     70  CA  GLU    70      60.049   7.656  38.005  1.00 25.00           C
ATOM     71  CA  LEU    71      61.943   7.364  34.736  1.00 25.00           C
ATOM     72  CA  THR    72      61.743  11.143  34.209  1.00 25.00           C
ATOM     73  CA  TYR    73      59.636  12.657  31.362  1.00 25.00           C
ATOM     74  CA  GLN    74      62.634  14.976  30.804  1.00 25.00           C
ATOM     75  CA  GLN    75      64.813  11.971  29.859  1.00 25.00           C
ATOM     76  CA  VAL    76      62.137  10.776  27.393  1.00 25.00           C
ATOM     77  CA  TYR    77      61.965  14.274  25.845  1.00 25.00           C
ATOM     78  CA  ASP    78      65.779  14.335  25.497  1.00 25.00           C
ATOM     79  CA  ALA    79      65.705  10.895  23.815  1.00 25.00           C
ATOM     80  CA  LEU    80      62.995  12.108  21.396  1.00 25.00           C
ATOM     81  CA  LEU    81      65.088  15.206  20.568  1.00 25.00           C
ATOM     82  CA  GLY    82      68.149  12.996  19.924  1.00 25.00           C
ATOM     83  CA  PHE    83      66.071  10.745  17.626  1.00 25.00           C
TER
END
