
#######################################################
#                                                     #
#                        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 T0311TS168_5-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS168_5-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          4.97     4.97
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27        22 - 48          1.92     5.96
  LCS_AVERAGE:     31.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13         8 - 20          0.98    12.81
  LONGEST_CONTINUOUS_SEGMENT:    13        31 - 43          0.99     5.54
  LCS_AVERAGE:     17.24

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     13   14   64     0    8   13   15   20   23   26   38   45   50   52   53   54   54   57   62   64   64   64   64 
LCS_GDT     P       9     P       9     13   14   64    10   12   13   15   20   23   31   41   45   50   52   53   54   54   57   62   64   64   64   64 
LCS_GDT     G      10     G      10     13   14   64    10   12   15   20   26   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     D      11     D      11     13   14   64    10   12   15   19   26   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     I      12     I      12     13   14   64    10   12   15   19   26   32   37   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     I      13     I      13     13   14   64    10   12   13   20   25   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     Q      14     Q      14     13   14   64    10   12   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     E      15     E      15     13   14   64    10   12   13   22   26   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     S      16     S      16     13   17   64    10   14   18   22   27   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      17     L      17     13   26   64    10   12   13   15   28   32   38   41   44   48   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     D      18     D      18     13   26   64    10   12   13   15   16   26   31   38   43   47   51   53   54   58   61   62   64   64   64   64 
LCS_GDT     E      19     E      19     13   26   64     9   12   13   20   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      20     L      20     13   26   64     4    8   13   20   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     N      21     N      21     12   26   64     4    7   13   18   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     V      22     V      22     12   27   64     5   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     S      23     S      23     12   27   64     3   10   13   20   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      24     L      24     12   27   64     8   10   13   18   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     R      25     R      25     12   27   64     8   10   13   18   27   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     E      26     E      26     12   27   64     8   10   17   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     F      27     F      27     12   27   64     8   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      28     A      28     12   27   64     8   13   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     R      29     R      29     12   27   64     8   10   13   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      30     A      30     12   27   64     8   10   13   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     M      31     M      31     13   27   64     8   10   13   21   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     E      32     E      32     13   27   64     3   10   17   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     I      33     I      33     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      34     A      34     13   27   64     7   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     P      35     P      35     13   27   64    10   14   18   21   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     S      36     S      36     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     T      37     T      37     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      38     A      38     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     S      39     S      39     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     R      40     R      40     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      41     L      41     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      42     L      42     13   27   64    10   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     T      43     T      43     13   27   64    10   14   18   22   27   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     G      44     G      44     12   27   64     3    6   10   18   24   31   38   41   46   50   52   53   54   57   61   62   64   64   64   64 
LCS_GDT     K      45     K      45      4   27   64     3   11   13   18   28   32   37   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      46     A      46      4   27   64     3   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      47     A      47      4   27   64     4   14   18   22   28   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      48     L      48      4   27   64     4    5   13   20   27   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     T      49     T      49     12   17   64    10   11   12   14   18   23   28   41   45   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     P      50     P      50     12   15   64    10   11   12   14   18   23   31   39   44   50   52   53   54   54   57   61   64   64   64   64 
LCS_GDT     E      51     E      51     12   15   64    10   11   12   14   19   30   35   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     M      52     M      52     12   15   64    10   11   12   14   24   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     A      53     A      53     12   15   64    10   11   12   14   18   30   33   39   45   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     I      54     I      54     12   15   64    10   11   12   14   24   31   37   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     K      55     K      55     12   15   64    10   11   12   17   26   32   38   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     L      56     L      56     12   15   64    10   11   12   14   24   31   37   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     S      57     S      57     12   15   64    10   11   12   14   24   31   37   40   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     V      58     V      58     12   15   64    10   11   12   14   26   32   37   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     V      59     V      59     12   15   64    10   11   12   17   25   31   37   41   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     I      60     I      60     12   15   64     4    8   12   17   23   29   37   40   46   50   52   53   54   58   61   62   64   64   64   64 
LCS_GDT     G      61     G      61      4   13   64     3    4    4   10   16   20   28   36   39   43   48   52   54   58   61   62   64   64   64   64 
LCS_GDT     S      62     S      62      4   11   64     2    3    4    7    9   12   15   21   31   41   46   52   54   58   61   62   64   64   64   64 
LCS_GDT     S      63     S      63      4   11   64     2    3    4    7    9   12   14   16   19   22   36   47   50   55   61   62   64   64   64   64 
LCS_GDT     P      64     P      64      8   11   64     8    8    8    8    9   19   28   31   35   42   47   52   54   58   61   62   64   64   64   64 
LCS_GDT     Q      65     Q      65      8   11   64     8    8    8    8    9   12   26   31   35   42   47   52   54   58   61   62   64   64   64   64 
LCS_GDT     M      66     M      66      8   11   64     8    8    8   13   16   19   28   31   35   42   47   52   54   58   61   62   64   64   64   64 
LCS_GDT     W      67     W      67      8   11   64     8    8    8    8   14   19   23   31   35   41   47   52   54   58   61   62   64   64   64   64 
LCS_GDT     L      68     L      68      8   11   64     8    8    8    8    9   12   14   16   35   41   47   52   54   58   61   62   64   64   64   64 
LCS_GDT     N      69     N      69      8   11   64     8    8    8    8    9   19   28   31   35   42   47   52   54   58   61   62   64   64   64   64 
LCS_GDT     L      70     L      70      8   11   64     8    8    8    8   14   17   23   28   35   41   41   52   54   58   61   61   64   64   64   64 
LCS_GDT     Q      71     Q      71      8    9   64     8    8    8    8    8   10   12   16   18   22   36   39   47   56   61   62   64   64   64   64 
LCS_AVERAGE  LCS_A:  49.58  (  17.24   31.52  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     10     14     18     22     28     32     38     41     46     50     52     53     54     58     61     62     64     64     64     64 
GDT PERCENT_CA  15.62  21.88  28.12  34.38  43.75  50.00  59.38  64.06  71.88  78.12  81.25  82.81  84.38  90.62  95.31  96.88 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.19   0.52   0.85   1.42   1.85   1.93   2.34   2.46   2.82   3.11   3.23   3.30   3.45   4.46   4.69   4.81   4.97   4.97   4.97   4.97
GDT RMS_ALL_CA   8.67   6.53   6.36   5.68   5.90   5.94   6.12   5.88   5.76   5.97   6.03   6.03   5.88   5.01   5.02   4.97   4.97   4.97   4.97   4.97

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8          7.575
LGA    P       9      P       9          6.453
LGA    G      10      G      10          2.620
LGA    D      11      D      11          3.571
LGA    I      12      I      12          4.381
LGA    I      13      I      13          2.747
LGA    Q      14      Q      14          1.375
LGA    E      15      E      15          2.412
LGA    S      16      S      16          1.095
LGA    L      17      L      17          3.973
LGA    D      18      D      18          5.024
LGA    E      19      E      19          3.049
LGA    L      20      L      20          3.381
LGA    N      21      N      21          3.506
LGA    V      22      V      22          0.682
LGA    S      23      S      23          3.085
LGA    L      24      L      24          3.364
LGA    R      25      R      25          3.202
LGA    E      26      E      26          1.756
LGA    F      27      F      27          1.049
LGA    A      28      A      28          0.992
LGA    R      29      R      29          2.416
LGA    A      30      A      30          2.833
LGA    M      31      M      31          2.599
LGA    E      32      E      32          1.223
LGA    I      33      I      33          1.779
LGA    A      34      A      34          2.209
LGA    P      35      P      35          2.170
LGA    S      36      S      36          2.296
LGA    T      37      T      37          1.963
LGA    A      38      A      38          1.202
LGA    S      39      S      39          1.183
LGA    R      40      R      40          1.149
LGA    L      41      L      41          0.776
LGA    L      42      L      42          0.389
LGA    T      43      T      43          0.909
LGA    G      44      G      44          3.309
LGA    K      45      K      45          3.415
LGA    A      46      A      46          0.948
LGA    A      47      A      47          1.480
LGA    L      48      L      48          1.831
LGA    T      49      T      49          6.384
LGA    P      50      P      50          7.369
LGA    E      51      E      51          5.426
LGA    M      52      M      52          3.961
LGA    A      53      A      53          6.097
LGA    I      54      I      54          5.344
LGA    K      55      K      55          3.023
LGA    L      56      L      56          4.555
LGA    S      57      S      57          5.628
LGA    V      58      V      58          3.444
LGA    V      59      V      59          3.667
LGA    I      60      I      60          5.009
LGA    G      61      G      61          8.761
LGA    S      62      S      62         11.957
LGA    S      63      S      63         14.007
LGA    P      64      P      64         11.286
LGA    Q      65      Q      65         12.085
LGA    M      66      M      66         12.279
LGA    W      67      W      67         11.567
LGA    L      68      L      68         10.942
LGA    N      69      N      69         11.724
LGA    L      70      L      70         13.215
LGA    Q      71      Q      71         12.953

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   64    4.0     41    2.46    54.297    51.225     1.599

LGA_LOCAL      RMSD =  2.464  Number of atoms =   41  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.910  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  4.969  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.045934 * X  +   0.961599 * Y  +   0.270586 * Z  +  31.858078
  Y_new =   0.984176 * X  +   0.089969 * Y  +  -0.152656 * Z  +   4.101754
  Z_new =  -0.171138 * X  +   0.259292 * Y  +  -0.950515 * Z  +  13.328802 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.875281   -0.266311  [ DEG:   164.7415    -15.2585 ]
  Theta =   0.171984    2.969608  [ DEG:     9.8540    170.1460 ]
  Phi   =   1.617435   -1.524157  [ DEG:    92.6722    -87.3278 ]
 
# 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: T0311TS168_5-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311TS168_5-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   41   2.46  51.225     4.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS168_5-D1
PFRMAT TS
TARGET T0311
MODEL 5
PARENT N/A
ATOM      8  CA  ARG     8      39.682   1.828  21.437  1.00 25.00           C
ATOM      9  CA  PRO     9      39.441   2.408  17.714  1.00 25.00           C
ATOM     10  CA  GLY    10      36.991  -0.062  16.112  1.00 25.00           C
ATOM     11  CA  ASP    11      34.619   0.317  19.094  1.00 25.00           C
ATOM     12  CA  ILE    12      34.813   4.131  18.796  1.00 25.00           C
ATOM     13  CA  ILE    13      34.041   3.902  15.051  1.00 25.00           C
ATOM     14  CA  GLN    14      31.036   1.643  15.785  1.00 25.00           C
ATOM     15  CA  GLU    15      29.775   4.131  18.409  1.00 25.00           C
ATOM     16  CA  SER    16      30.140   7.001  15.900  1.00 25.00           C
ATOM     17  CA  LEU    17      28.197   4.991  13.282  1.00 25.00           C
ATOM     18  CA  ASP    18      25.429   4.295  15.836  1.00 25.00           C
ATOM     19  CA  GLU    19      25.256   8.022  16.701  1.00 25.00           C
ATOM     20  CA  LEU    20      21.815   8.075  14.951  1.00 25.00           C
ATOM     21  CA  ASN    21      20.862   5.747  17.846  1.00 25.00           C
ATOM     22  CA  VAL    22      21.542   2.094  18.336  1.00 25.00           C
ATOM     23  CA  SER    23      24.992   0.818  19.465  1.00 25.00           C
ATOM     24  CA  LEU    24      26.452  -1.250  16.627  1.00 25.00           C
ATOM     25  CA  ARG    25      24.639  -4.587  17.125  1.00 25.00           C
ATOM     26  CA  GLU    26      21.270  -2.879  16.488  1.00 25.00           C
ATOM     27  CA  PHE    27      22.654  -1.284  13.293  1.00 25.00           C
ATOM     28  CA  ALA    28      23.943  -4.695  12.120  1.00 25.00           C
ATOM     29  CA  ARG    29      20.513  -6.254  12.804  1.00 25.00           C
ATOM     30  CA  ALA    30      18.816  -3.452  10.821  1.00 25.00           C
ATOM     31  CA  MET    31      21.236  -4.015   7.906  1.00 25.00           C
ATOM     32  CA  GLU    32      21.189  -7.182   5.799  1.00 25.00           C
ATOM     33  CA  ILE    33      24.915  -7.043   6.167  1.00 25.00           C
ATOM     34  CA  ALA    34      24.420 -10.351   7.940  1.00 25.00           C
ATOM     35  CA  PRO    35      25.172  -9.565  11.612  1.00 25.00           C
ATOM     36  CA  SER    36      28.421 -11.583  11.416  1.00 25.00           C
ATOM     37  CA  THR    37      29.864  -9.060   8.922  1.00 25.00           C
ATOM     38  CA  ALA    38      28.900  -6.173  11.245  1.00 25.00           C
ATOM     39  CA  SER    39      30.578  -7.953  14.192  1.00 25.00           C
ATOM     40  CA  ARG    40      33.745  -8.476  12.105  1.00 25.00           C
ATOM     41  CA  LEU    41      33.754  -4.769  11.144  1.00 25.00           C
ATOM     42  CA  LEU    42      33.369  -3.788  14.825  1.00 25.00           C
ATOM     43  CA  THR    43      36.280  -6.090  15.769  1.00 25.00           C
ATOM     44  CA  GLY    44      38.636  -8.338  13.770  1.00 25.00           C
ATOM     45  CA  LYS    45      40.696  -6.683  10.954  1.00 25.00           C
ATOM     46  CA  ALA    46      38.040  -8.359   8.793  1.00 25.00           C
ATOM     47  CA  ALA    47      39.146  -6.497   5.663  1.00 25.00           C
ATOM     48  CA  LEU    48      35.817  -4.714   5.448  1.00 25.00           C
ATOM     49  CA  THR    49      36.716  -1.935   7.908  1.00 25.00           C
ATOM     50  CA  PRO    50      35.793   1.131   5.884  1.00 25.00           C
ATOM     51  CA  GLU    51      33.101  -0.756   3.918  1.00 25.00           C
ATOM     52  CA  MET    52      31.772  -2.291   7.164  1.00 25.00           C
ATOM     53  CA  ALA    53      31.656   1.176   8.787  1.00 25.00           C
ATOM     54  CA  ILE    54      29.757   2.555   5.762  1.00 25.00           C
ATOM     55  CA  LYS    55      27.264  -0.344   5.974  1.00 25.00           C
ATOM     56  CA  LEU    56      26.760   0.331   9.710  1.00 25.00           C
ATOM     57  CA  SER    57      26.160   4.043   8.985  1.00 25.00           C
ATOM     58  CA  VAL    58      23.602   3.127   6.285  1.00 25.00           C
ATOM     59  CA  VAL    59      21.822   0.780   8.733  1.00 25.00           C
ATOM     60  CA  ILE    60      21.729   3.558  11.367  1.00 25.00           C
ATOM     61  CA  GLY    61      19.294   6.431  10.718  1.00 25.00           C
ATOM     62  CA  SER    62      18.916   5.719   6.951  1.00 25.00           C
ATOM     63  CA  SER    63      18.751   3.063   4.185  1.00 25.00           C
ATOM     64  CA  PRO    64      21.214   4.838   1.875  1.00 25.00           C
ATOM     65  CA  GLN    65      24.131   4.632  -0.598  1.00 25.00           C
ATOM     66  CA  MET    66      24.623   8.423  -0.372  1.00 25.00           C
ATOM     67  CA  TRP    67      24.621   8.219   3.453  1.00 25.00           C
ATOM     68  CA  LEU    68      27.217   5.406   3.328  1.00 25.00           C
ATOM     69  CA  ASN    69      29.403   7.493   0.978  1.00 25.00           C
ATOM     70  CA  LEU    70      29.136  10.489   3.348  1.00 25.00           C
ATOM     71  CA  GLN    71      30.129   8.267   6.306  1.00 25.00           C
TER
END
