
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS168_3-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:    58         8 - 65          4.98     6.06
  LCS_AVERAGE:     89.36

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        18 - 43          1.95     7.07
  LCS_AVERAGE:     32.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        34 - 46          0.95     8.79
  LCS_AVERAGE:     16.36

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     12   13   58     0    4    8   13   15   16   19   23   27   32   44   50   52   53   53   53   54   55   58   61 
LCS_GDT     P       9     P       9     12   13   58    11   12   13   14   15   17   19   23   29   40   47   51   52   53   53   53   55   56   60   62 
LCS_GDT     G      10     G      10     12   13   58    11   12   13   14   23   34   38   43   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     D      11     D      11     12   13   58    11   12   13   14   18   25   33   39   43   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     I      12     I      12     12   13   58    11   12   13   14   15   26   33   37   43   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     I      13     I      13     12   13   58    11   12   16   22   27   34   39   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     Q      14     Q      14     12   13   58    11   12   15   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     E      15     E      15     12   13   58    11   12   13   21   29   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     S      16     S      16     12   13   58    11   12   17   22   30   34   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      17     L      17     12   15   58    11   12   13   18   23   28   37   41   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     D      18     D      18     12   26   58    11   12   13   14   17   25   28   39   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     E      19     E      19     12   26   58    11   12   15   20   28   34   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      20     L      20      4   26   58     4    4    9   22   30   34   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     N      21     N      21      4   26   58     5   11   15   21   30   34   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     V      22     V      22      4   26   58     3   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     S      23     S      23      4   26   58     3    4    9   16   24   31   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      24     L      24     10   26   58     8    9    9   18   23   32   37   43   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     R      25     R      25     10   26   58     8    9    9   17   24   34   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     E      26     E      26     10   26   58     8    9   16   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     F      27     F      27     10   26   58     8    9   10   21   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      28     A      28     10   26   58     8   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     R      29     R      29     10   26   58     8    9    9   17   29   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      30     A      30     10   26   58     8    9   11   18   23   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     M      31     M      31     10   26   58     8    9    9   18   24   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     E      32     E      32     12   26   58     3    3   13   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     I      33     I      33     12   26   58     3   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      34     A      34     13   26   58    10   11   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     P      35     P      35     13   26   58    10   11   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     S      36     S      36     13   26   58    10   11   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     T      37     T      37     13   26   58    10   11   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      38     A      38     13   26   58    10   11   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     S      39     S      39     13   26   58    10   11   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     R      40     R      40     13   26   58    10   12   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      41     L      41     13   26   58    10   11   15   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      42     L      42     13   26   58    10   11   15   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     T      43     T      43     13   26   58    10   11   15   21   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     G      44     G      44     13   24   58     3   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     K      45     K      45     13   24   58     3   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      46     A      46     13   24   58     3   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      47     A      47      5   24   58     3    8   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      48     L      48     12   24   58     3   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     T      49     T      49     12   24   58     3    9   13   13   16   27   33   39   44   47   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     P      50     P      50     12   24   58     9   10   17   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     E      51     E      51     12   24   58     9   10   15   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     M      52     M      52     12   24   58     9   10   14   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     A      53     A      53     12   24   58     9   10   13   22   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     I      54     I      54     12   24   58     9   10   13   16   30   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     K      55     K      55     12   24   58     9   10   13   16   21   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     L      56     L      56     12   19   58     9   10   13   16   27   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     S      57     S      57     12   19   58     9   10   13   16   20   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     V      58     V      58     12   19   58     9   10   13   16   18   25   36   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     V      59     V      59     12   19   58     9   10   13   16   18   28   36   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     I      60     I      60     12   19   58     4    8   13   16   24   35   40   44   46   48   50   51   52   53   54   57   60   61   62   62 
LCS_GDT     G      61     G      61      4   18   58     1    3    4    7   13   18   24   31   38   40   43   48   51   53   54   57   60   61   62   62 
LCS_GDT     S      62     S      62      4   14   58     0    3    7    9    9   12   15   21   26   32   37   43   44   49   54   57   60   60   62   62 
LCS_GDT     S      63     S      63      4   10   58     1    3    4    7    9   14   16   24   29   36   41   48   51   53   54   57   60   61   62   62 
LCS_GDT     P      64     P      64      8   10   58     8    8    8    9   11   16   20   22   26   27   30   38   40   48   54   57   60   61   62   62 
LCS_GDT     Q      65     Q      65      8   10   58     8    8    8    9    9   10   15   19   21   23   29   31   38   39   42   50   54   61   62   62 
LCS_GDT     M      66     M      66      8   10   57     8    8    8    9    9   10   14   17   21   26   35   41   44   46   52   56   60   61   62   62 
LCS_GDT     W      67     W      67      8   10   57     8    8    8    9    9   16   20   22   26   28   40   43   47   52   54   57   60   61   62   62 
LCS_GDT     L      68     L      68      8   10   47     8    8    8    9   10   13   15   22   25   26   29   38   40   42   47   56   60   61   62   62 
LCS_GDT     N      69     N      69      8   10   45     8    8    8    9    9   13   15   19   21   26   29   35   41   46   49   53   58   61   62   62 
LCS_GDT     L      70     L      70      8   10   45     8    8    8    9    9    9   10   21   25   29   40   43   47   49   54   57   60   61   62   62 
LCS_GDT     Q      71     Q      71      8   10   45     8    8    8    9    9   10   17   22   25   27   30   38   40   48   54   57   60   61   62   62 
LCS_AVERAGE  LCS_A:  45.92  (  16.36   32.06   89.36 )

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     12     17     22     30     35     40     44     46     48     50     51     52     53     54     57     60     61     62     62 
GDT PERCENT_CA  17.19  18.75  26.56  34.38  46.88  54.69  62.50  68.75  71.88  75.00  78.12  79.69  81.25  82.81  84.38  89.06  93.75  95.31  96.88  96.88
GDT RMS_LOCAL    0.21   0.31   1.06   1.29   1.78   2.24   2.41   2.62   2.72   2.86   3.06   3.14   3.31   3.52   3.93   4.60   5.16   5.46   5.51   5.46
GDT RMS_ALL_CA  15.43  15.03   7.69   7.64   7.23   6.55   6.88   6.76   6.79   6.87   6.81   6.82   6.88   6.95   6.33   6.01   5.84   5.81   5.82   5.80

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8         11.280
LGA    P       9      P       9          9.500
LGA    G      10      G      10          4.621
LGA    D      11      D      11          6.562
LGA    I      12      I      12          6.791
LGA    I      13      I      13          3.943
LGA    Q      14      Q      14          1.226
LGA    E      15      E      15          2.462
LGA    S      16      S      16          3.204
LGA    L      17      L      17          5.216
LGA    D      18      D      18          5.486
LGA    E      19      E      19          3.647
LGA    L      20      L      20          3.165
LGA    N      21      N      21          2.977
LGA    V      22      V      22          2.228
LGA    S      23      S      23          3.826
LGA    L      24      L      24          4.556
LGA    R      25      R      25          3.460
LGA    E      26      E      26          1.197
LGA    F      27      F      27          2.318
LGA    A      28      A      28          1.676
LGA    R      29      R      29          1.871
LGA    A      30      A      30          2.934
LGA    M      31      M      31          2.989
LGA    E      32      E      32          1.467
LGA    I      33      I      33          2.651
LGA    A      34      A      34          3.022
LGA    P      35      P      35          2.725
LGA    S      36      S      36          2.636
LGA    T      37      T      37          2.502
LGA    A      38      A      38          2.366
LGA    S      39      S      39          2.276
LGA    R      40      R      40          2.283
LGA    L      41      L      41          2.175
LGA    L      42      L      42          1.909
LGA    T      43      T      43          2.332
LGA    G      44      G      44          2.711
LGA    K      45      K      45          2.397
LGA    A      46      A      46          1.506
LGA    A      47      A      47          1.153
LGA    L      48      L      48          1.966
LGA    T      49      T      49          5.546
LGA    P      50      P      50          3.425
LGA    E      51      E      51          3.064
LGA    M      52      M      52          2.785
LGA    A      53      A      53          2.366
LGA    I      54      I      54          2.186
LGA    K      55      K      55          2.844
LGA    L      56      L      56          2.696
LGA    S      57      S      57          3.089
LGA    V      58      V      58          3.886
LGA    V      59      V      59          3.952
LGA    I      60      I      60          2.995
LGA    G      61      G      61          8.800
LGA    S      62      S      62         11.213
LGA    S      63      S      63          9.842
LGA    P      64      P      64         13.383
LGA    Q      65      Q      65         17.165
LGA    M      66      M      66         14.579
LGA    W      67      W      67         11.368
LGA    L      68      L      68         14.958
LGA    N      69      N      69         16.144
LGA    L      70      L      70         12.330
LGA    Q      71      Q      71         13.563

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   64    4.0     44    2.62    52.734    50.729     1.615

LGA_LOCAL      RMSD =  2.625  Number of atoms =   44  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.488  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  5.784  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.490271 * X  +  -0.869940 * Y  +  -0.053290 * Z  +  32.604679
  Y_new =  -0.635526 * X  +   0.314983 * Y  +   0.704906 * Z  +   3.411098
  Z_new =  -0.596440 * X  +   0.379462 * Y  +  -0.707296 * Z  +  14.312364 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.649176   -0.492416  [ DEG:   151.7866    -28.2134 ]
  Theta =   0.639059    2.502534  [ DEG:    36.6154    143.3846 ]
  Phi   =  -2.227879    0.913714  [ DEG:  -127.6480     52.3520 ]
 
# 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_3-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311TS168_3-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   44   2.62  50.729     5.78
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS168_3-D1
PFRMAT TS
TARGET T0311
MODEL 3
PARENT N/A
ATOM      8  CA  ARG     8      37.544  -2.224  24.098  1.00 25.00           C
ATOM      9  CA  PRO     9      37.398  -1.657  20.304  1.00 25.00           C
ATOM     10  CA  GLY    10      34.793  -2.636  17.673  1.00 25.00           C
ATOM     11  CA  ASP    11      31.984  -1.374  19.950  1.00 25.00           C
ATOM     12  CA  ILE    12      33.846   1.935  20.455  1.00 25.00           C
ATOM     13  CA  ILE    13      34.290   2.291  16.667  1.00 25.00           C
ATOM     14  CA  GLN    14      30.555   1.628  16.142  1.00 25.00           C
ATOM     15  CA  GLU    15      29.690   4.269  18.776  1.00 25.00           C
ATOM     16  CA  SER    16      32.007   6.784  17.051  1.00 25.00           C
ATOM     17  CA  LEU    17      30.349   6.036  13.681  1.00 25.00           C
ATOM     18  CA  ASP    18      26.890   6.550  15.241  1.00 25.00           C
ATOM     19  CA  GLU    19      28.031   9.887  16.735  1.00 25.00           C
ATOM     20  CA  LEU    20      24.377   9.959  17.976  1.00 25.00           C
ATOM     21  CA  ASN    21      23.021   6.398  18.479  1.00 25.00           C
ATOM     22  CA  VAL    22      23.456   2.835  19.823  1.00 25.00           C
ATOM     23  CA  SER    23      26.323   0.370  19.713  1.00 25.00           C
ATOM     24  CA  LEU    24      25.401   0.117  16.026  1.00 25.00           C
ATOM     25  CA  ARG    25      24.093  -3.427  16.648  1.00 25.00           C
ATOM     26  CA  GLU    26      20.510  -2.248  15.987  1.00 25.00           C
ATOM     27  CA  PHE    27      21.634  -0.578  12.730  1.00 25.00           C
ATOM     28  CA  ALA    28      23.398  -3.803  11.656  1.00 25.00           C
ATOM     29  CA  ARG    29      20.232  -5.819  12.422  1.00 25.00           C
ATOM     30  CA  ALA    30      18.139  -3.359  10.365  1.00 25.00           C
ATOM     31  CA  MET    31      20.603  -3.664   7.449  1.00 25.00           C
ATOM     32  CA  GLU    32      21.755  -5.903   4.565  1.00 25.00           C
ATOM     33  CA  ILE    33      25.116  -5.902   6.335  1.00 25.00           C
ATOM     34  CA  ALA    34      24.045  -9.366   7.603  1.00 25.00           C
ATOM     35  CA  PRO    35      24.674  -8.973  11.347  1.00 25.00           C
ATOM     36  CA  SER    36      27.796 -11.193  11.328  1.00 25.00           C
ATOM     37  CA  THR    37      29.162  -9.289   8.300  1.00 25.00           C
ATOM     38  CA  ALA    38      28.525  -5.957  10.077  1.00 25.00           C
ATOM     39  CA  SER    39      30.338  -7.244  13.194  1.00 25.00           C
ATOM     40  CA  ARG    40      33.304  -8.355  11.040  1.00 25.00           C
ATOM     41  CA  LEU    41      33.418  -4.908   9.376  1.00 25.00           C
ATOM     42  CA  LEU    42      33.372  -3.220  12.813  1.00 25.00           C
ATOM     43  CA  THR    43      36.231  -5.480  13.989  1.00 25.00           C
ATOM     44  CA  GLY    44      39.304  -7.690  13.642  1.00 25.00           C
ATOM     45  CA  LYS    45      37.437 -10.843  12.813  1.00 25.00           C
ATOM     46  CA  ALA    46      37.781  -9.633   9.263  1.00 25.00           C
ATOM     47  CA  ALA    47      38.060  -6.184   7.680  1.00 25.00           C
ATOM     48  CA  LEU    48      38.187  -2.701   6.153  1.00 25.00           C
ATOM     49  CA  THR    49      37.990   0.573   4.322  1.00 25.00           C
ATOM     50  CA  PRO    50      36.128   0.757   0.962  1.00 25.00           C
ATOM     51  CA  GLU    51      33.503  -2.016   0.671  1.00 25.00           C
ATOM     52  CA  MET    52      33.481  -2.429   4.479  1.00 25.00           C
ATOM     53  CA  ALA    53      33.030   1.350   4.909  1.00 25.00           C
ATOM     54  CA  ILE    54      30.123   1.313   2.415  1.00 25.00           C
ATOM     55  CA  LYS    55      28.500  -1.590   4.313  1.00 25.00           C
ATOM     56  CA  LEU    56      28.884   0.317   7.611  1.00 25.00           C
ATOM     57  CA  SER    57      27.291   3.420   6.031  1.00 25.00           C
ATOM     58  CA  VAL    58      24.375   1.297   4.744  1.00 25.00           C
ATOM     59  CA  VAL    59      23.897  -0.206   8.234  1.00 25.00           C
ATOM     60  CA  ILE    60      23.894   3.301   9.772  1.00 25.00           C
ATOM     61  CA  GLY    61      20.200   3.136   8.776  1.00 25.00           C
ATOM     62  CA  SER    62      20.342   4.313   5.116  1.00 25.00           C
ATOM     63  CA  SER    63      21.799   6.319   2.267  1.00 25.00           C
ATOM     64  CA  PRO    64      20.017   8.992   4.406  1.00 25.00           C
ATOM     65  CA  GLN    65      20.860  11.720   6.959  1.00 25.00           C
ATOM     66  CA  MET    66      22.491   9.113   9.241  1.00 25.00           C
ATOM     67  CA  TRP    67      24.545   7.783   6.296  1.00 25.00           C
ATOM     68  CA  LEU    68      25.664  11.343   5.436  1.00 25.00           C
ATOM     69  CA  ASN    69      26.686  11.928   9.081  1.00 25.00           C
ATOM     70  CA  LEU    70      28.674   8.656   9.075  1.00 25.00           C
ATOM     71  CA  GLN    71      30.426   9.698   5.833  1.00 25.00           C
TER
END
