
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS393_4-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:    53         8 - 60          4.75     6.92
  LCS_AVERAGE:     75.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28        20 - 47          1.94     6.93
  LCS_AVERAGE:     30.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        34 - 46          0.92     7.73
  LONGEST_CONTINUOUS_SEGMENT:    13        50 - 62          0.97    13.84
  LCS_AVERAGE:     17.07

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   53     0    3   10   13   14   17   26   31   39   41   42   46   48   48   49   53   56   60   61   62 
LCS_GDT     P       9     P       9     12   13   53    11   11   11   13   14   16   23   32   39   41   42   46   48   48   50   53   56   60   61   62 
LCS_GDT     G      10     G      10     12   13   53    11   11   13   21   25   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     D      11     D      11     12   13   53    11   11   11   13   15   21   30   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     I      12     I      12     12   13   53    11   11   11   15   20   27   32   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     I      13     I      13     12   13   53    11   11   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     Q      14     Q      14     12   13   53    11   11   13   20   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     E      15     E      15     12   13   53    11   11   11   13   14   26   32   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     S      16     S      16     12   13   53    11   11   16   20   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     L      17     L      17     12   13   53    11   11   13   16   19   24   29   33   38   41   42   46   48   48   50   53   56   60   61   62 
LCS_GDT     D      18     D      18     12   13   53    11   11   11   12   14   16   18   19   32   38   38   46   48   48   50   53   56   60   61   62 
LCS_GDT     E      19     E      19     12   24   53    11   11   11   13   14   24   28   35   38   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     L      20     L      20      3   28   53     3   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     N      21     N      21      3   28   53     3    3   10   18   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     V      22     V      22      4   28   53     3   12   15   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     S      23     S      23     10   28   53     3    3    8   15   22   29   32   35   38   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     L      24     L      24     10   28   53     9   11   15   19   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     R      25     R      25     10   28   53     9   11   15   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     E      26     E      26     10   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     F      27     F      27     10   28   53     9   11   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     A      28     A      28     10   28   53    10   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     R      29     R      29     10   28   53     9   11   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     A      30     A      30     10   28   53     9   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     M      31     M      31     10   28   53     9   11   15   20   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     E      32     E      32     10   28   53     3   10   15   20   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     I      33     I      33     12   28   53     3    4   11   20   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     A      34     A      34     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     P      35     P      35     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     S      36     S      36     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     T      37     T      37     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     A      38     A      38     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     S      39     S      39     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     R      40     R      40     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     L      41     L      41     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     L      42     L      42     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     T      43     T      43     13   28   53    11   12   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     G      44     G      44     13   28   53     4    8   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     K      45     K      45     13   28   53     3    7   14   21   26   31   34   37   39   41   42   44   48   49   50   53   56   60   61   62 
LCS_GDT     A      46     A      46     13   28   53     4    8   16   21   26   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     A      47     A      47      9   28   53     4    7   16   21   25   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     L      48     L      48      9   27   53     4    7   14   19   25   29   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     T      49     T      49      9   23   53     3    6   14   19   23   27   32   36   39   41   42   44   48   49   50   53   56   60   61   62 
LCS_GDT     P      50     P      50     13   17   53     9   11   11   12   17   21   24   28   33   37   41   44   45   47   48   52   54   60   61   62 
LCS_GDT     E      51     E      51     13   14   53     9   11   11   12   15   16   17   18   19   21   22   24   31   38   42   45   47   50   55   59 
LCS_GDT     M      52     M      52     13   14   53     9   11   11   12   17   21   24   28   33   37   41   44   45   47   48   52   55   60   61   62 
LCS_GDT     A      53     A      53     13   14   53     9   11   14   21   25   29   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     I      54     I      54     13   14   53     9   11   11   12   15   16   17   20   29   37   41   46   48   48   49   52   56   60   61   62 
LCS_GDT     K      55     K      55     13   14   53     9   11   11   12   15   16   17   18   19   36   40   46   48   48   50   53   56   60   61   62 
LCS_GDT     L      56     L      56     13   14   53     9   11   11   12   22   31   34   37   39   41   42   46   48   49   50   53   56   60   61   62 
LCS_GDT     S      57     S      57     13   14   53     9   11   11   12   15   16   17   18   23   38   41   46   48   48   50   53   56   60   61   62 
LCS_GDT     V      58     V      58     13   14   53     9   11   11   12   15   16   17   18   19   21   22   24   32   34   38   49   53   53   59   62 
LCS_GDT     V      59     V      59     13   14   53     9   11   11   12   15   16   17   18   24   38   38   46   48   49   50   53   56   60   61   62 
LCS_GDT     I      60     I      60     13   14   53     3    4   11   12   15   16   17   18   19   21   22   28   33   43   48   53   56   60   61   62 
LCS_GDT     G      61     G      61     13   14   25     0    3    4    8   15   16   17   18   19   21   22   26   30   32   37   47   53   56   61   62 
LCS_GDT     S      62     S      62     13   14   25     9   11   11   12   15   16   17   18   19   21   22   24   30   30   45   47   53   53   56   61 
LCS_GDT     S      63     S      63      4   14   25     3    4    4    8   12   16   17   30   34   38   40   43   46   49   50   53   56   60   61   62 
LCS_GDT     P      64     P      64      8    8   25     8    8    8    9   13   13   15   16   31   35   39   42   46   49   50   53   56   60   61   62 
LCS_GDT     Q      65     Q      65      8    8   25     8    8    8    9   13   13   15   16   19   33   37   38   45   49   50   52   56   60   61   62 
LCS_GDT     M      66     M      66      8    8   25     8    8    8    9   13   13   15   18   19   19   22   38   45   49   50   53   56   60   61   62 
LCS_GDT     W      67     W      67      8    8   25     8    8    8    9   13   16   17   28   31   35   39   42   46   49   50   53   56   60   61   62 
LCS_GDT     L      68     L      68      8    8   25     8    8    8    9   13   16   23   28   31   35   39   42   45   49   50   53   56   60   61   62 
LCS_GDT     N      69     N      69      8    8   25     8    8    8    9   13   16   17   18   19   20   27   37   43   46   50   53   56   60   61   62 
LCS_GDT     L      70     L      70      8    8   25     8    8    8    9   13   13   15   18   19   23   27   35   44   49   50   53   56   60   61   62 
LCS_GDT     Q      71     Q      71      8    8   25     8    8    8    9   13   13   15   18   19   29   37   40   45   49   50   53   56   60   61   62 
LCS_AVERAGE  LCS_A:  41.07  (  17.07   30.86   75.29 )

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     16     21     26     31     34     37     39     41     42     46     48     49     50     53     56     60     61     62 
GDT PERCENT_CA  17.19  18.75  25.00  32.81  40.62  48.44  53.12  57.81  60.94  64.06  65.62  71.88  75.00  76.56  78.12  82.81  87.50  93.75  95.31  96.88
GDT RMS_LOCAL    0.21   0.41   0.92   1.31   1.58   1.92   2.11   2.40   2.72   2.83   2.97   3.78   3.84   4.43   4.54   4.75   5.14   5.56   5.72   5.85
GDT RMS_ALL_CA  14.55   7.54   6.92   7.17   6.90   6.81   6.89   6.83   7.14   6.81   6.87   6.88   6.85   6.44   6.50   6.29   6.22   6.22   6.18   6.17

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8          5.950
LGA    P       9      P       9          5.737
LGA    G      10      G      10          1.462
LGA    D      11      D      11          3.897
LGA    I      12      I      12          3.763
LGA    I      13      I      13          1.698
LGA    Q      14      Q      14          3.196
LGA    E      15      E      15          3.904
LGA    S      16      S      16          1.260
LGA    L      17      L      17          5.504
LGA    D      18      D      18          7.381
LGA    E      19      E      19          5.292
LGA    L      20      L      20          1.023
LGA    N      21      N      21          1.944
LGA    V      22      V      22          3.949
LGA    S      23      S      23          5.465
LGA    L      24      L      24          3.315
LGA    R      25      R      25          3.320
LGA    E      26      E      26          2.716
LGA    F      27      F      27          0.890
LGA    A      28      A      28          1.411
LGA    R      29      R      29          3.191
LGA    A      30      A      30          2.576
LGA    M      31      M      31          3.518
LGA    E      32      E      32          3.866
LGA    I      33      I      33          2.592
LGA    A      34      A      34          2.025
LGA    P      35      P      35          0.788
LGA    S      36      S      36          1.043
LGA    T      37      T      37          1.278
LGA    A      38      A      38          0.483
LGA    S      39      S      39          0.886
LGA    R      40      R      40          1.586
LGA    L      41      L      41          1.336
LGA    L      42      L      42          1.489
LGA    T      43      T      43          2.624
LGA    G      44      G      44          2.532
LGA    K      45      K      45          3.545
LGA    A      46      A      46          2.169
LGA    A      47      A      47          2.080
LGA    L      48      L      48          2.630
LGA    T      49      T      49          4.464
LGA    P      50      P      50          8.100
LGA    E      51      E      51         11.175
LGA    M      52      M      52          7.547
LGA    A      53      A      53          2.354
LGA    I      54      I      54          7.519
LGA    K      55      K      55          7.236
LGA    L      56      L      56          3.129
LGA    S      57      S      57          8.891
LGA    V      58      V      58         12.257
LGA    V      59      V      59          8.518
LGA    I      60      I      60         11.671
LGA    G      61      G      61         14.568
LGA    S      62      S      62         14.880
LGA    S      63      S      63         10.440
LGA    P      64      P      64         11.379
LGA    Q      65      Q      65         14.218
LGA    M      66      M      66         13.958
LGA    W      67      W      67         10.283
LGA    L      68      L      68         11.272
LGA    N      69      N      69         14.549
LGA    L      70      L      70         12.728
LGA    Q      71      Q      71         11.355

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   64    4.0     37    2.40    48.047    45.818     1.481

LGA_LOCAL      RMSD =  2.398  Number of atoms =   37  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.922  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  6.156  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.242283 * X  +   0.955770 * Y  +  -0.166738 * Z  +  32.371376
  Y_new =   0.484426 * X  +   0.029730 * Y  +   0.874327 * Z  +   2.827542
  Z_new =   0.840613 * X  +  -0.292607 * Y  +  -0.455797 * Z  +  12.996387 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.570884    0.570709  [ DEG:  -147.3008     32.6992 ]
  Theta =  -0.998414   -2.143178  [ DEG:   -57.2049   -122.7951 ]
  Phi   =   1.107032   -2.034560  [ DEG:    63.4283   -116.5717 ]
 
# 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_4-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_4-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   37   2.40  45.818     6.16
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_4-D1
PFRMAT TS
TARGET T0311
MODEL 4
PARENT N/A
ATOM      8  CA  ARG     8      40.109   0.805  19.821  1.00 25.00           C
ATOM      9  CA  PRO     9      38.055   2.592  17.164  1.00 25.00           C
ATOM     10  CA  GLY    10      35.858   0.201  15.131  1.00 25.00           C
ATOM     11  CA  ASP    11      33.136   0.379  17.819  1.00 25.00           C
ATOM     12  CA  ILE    12      33.304   4.205  17.771  1.00 25.00           C
ATOM     13  CA  ILE    13      32.994   4.195  13.954  1.00 25.00           C
ATOM     14  CA  GLN    14      29.961   1.869  14.181  1.00 25.00           C
ATOM     15  CA  GLU    15      28.350   4.184  16.773  1.00 25.00           C
ATOM     16  CA  SER    16      28.970   7.202  14.499  1.00 25.00           C
ATOM     17  CA  LEU    17      27.391   5.336  11.550  1.00 25.00           C
ATOM     18  CA  ASP    18      24.346   4.462  13.701  1.00 25.00           C
ATOM     19  CA  GLU    19      24.009   8.128  14.756  1.00 25.00           C
ATOM     20  CA  LEU    20      23.941   6.704  18.231  1.00 25.00           C
ATOM     21  CA  ASN    21      22.153   3.487  19.346  1.00 25.00           C
ATOM     22  CA  VAL    22      25.418   1.838  20.483  1.00 25.00           C
ATOM     23  CA  SER    23      28.383  -0.328  19.334  1.00 25.00           C
ATOM     24  CA  LEU    24      27.199  -2.002  16.166  1.00 25.00           C
ATOM     25  CA  ARG    25      24.215  -4.010  17.485  1.00 25.00           C
ATOM     26  CA  GLU    26      21.826  -1.224  16.392  1.00 25.00           C
ATOM     27  CA  PHE    27      23.419  -1.190  12.909  1.00 25.00           C
ATOM     28  CA  ALA    28      23.037  -4.992  12.670  1.00 25.00           C
ATOM     29  CA  ARG    29      19.357  -4.711  13.694  1.00 25.00           C
ATOM     30  CA  ALA    30      18.798  -2.011  11.036  1.00 25.00           C
ATOM     31  CA  MET    31      20.452  -4.235   8.394  1.00 25.00           C
ATOM     32  CA  GLU    32      19.185  -7.879   8.272  1.00 25.00           C
ATOM     33  CA  ILE    33      22.360  -9.227   6.594  1.00 25.00           C
ATOM     34  CA  ALA    34      23.678  -9.342  10.100  1.00 25.00           C
ATOM     35  CA  PRO    35      24.960  -9.523  13.723  1.00 25.00           C
ATOM     36  CA  SER    36      27.856 -11.941  13.061  1.00 25.00           C
ATOM     37  CA  THR    37      28.766 -10.018   9.877  1.00 25.00           C
ATOM     38  CA  ALA    38      28.711  -6.720  11.824  1.00 25.00           C
ATOM     39  CA  SER    39      30.977  -8.240  14.511  1.00 25.00           C
ATOM     40  CA  ARG    40      33.402  -9.461  11.811  1.00 25.00           C
ATOM     41  CA  LEU    41      33.451  -5.968  10.240  1.00 25.00           C
ATOM     42  CA  LEU    42      34.166  -4.412  13.666  1.00 25.00           C
ATOM     43  CA  THR    43      37.026  -6.897  14.225  1.00 25.00           C
ATOM     44  CA  GLY    44      40.185  -6.789  12.112  1.00 25.00           C
ATOM     45  CA  LYS    45      40.151  -9.647   9.600  1.00 25.00           C
ATOM     46  CA  ALA    46      37.903  -7.743   7.284  1.00 25.00           C
ATOM     47  CA  ALA    47      40.327  -5.347   5.636  1.00 25.00           C
ATOM     48  CA  LEU    48      38.717  -1.888   5.291  1.00 25.00           C
ATOM     49  CA  THR    49      37.193   0.294   2.549  1.00 25.00           C
ATOM     50  CA  PRO    50      36.997   2.868   5.421  1.00 25.00           C
ATOM     51  CA  GLU    51      36.124   0.882   8.577  1.00 25.00           C
ATOM     52  CA  MET    52      32.667   2.528   8.686  1.00 25.00           C
ATOM     53  CA  ALA    53      32.110   1.655   4.999  1.00 25.00           C
ATOM     54  CA  ILE    54      33.128  -1.974   5.677  1.00 25.00           C
ATOM     55  CA  LYS    55      30.701  -2.127   8.635  1.00 25.00           C
ATOM     56  CA  LEU    56      27.893  -0.732   6.436  1.00 25.00           C
ATOM     57  CA  SER    57      28.664  -3.349   3.749  1.00 25.00           C
ATOM     58  CA  VAL    58      28.573  -6.123   6.387  1.00 25.00           C
ATOM     59  CA  VAL    59      25.202  -4.829   7.666  1.00 25.00           C
ATOM     60  CA  ILE    60      23.833  -4.791   4.089  1.00 25.00           C
ATOM     61  CA  GLY    61      22.475  -3.840   0.656  1.00 25.00           C
ATOM     62  CA  SER    62      25.844  -2.758  -0.745  1.00 25.00           C
ATOM     63  CA  SER    63      24.967   0.785   0.248  1.00 25.00           C
ATOM     64  CA  PRO    64      21.903   1.380   2.447  1.00 25.00           C
ATOM     65  CA  GLN    65      21.882   5.011   1.230  1.00 25.00           C
ATOM     66  CA  MET    66      22.282   6.247   4.832  1.00 25.00           C
ATOM     67  CA  TRP    67      25.218   3.845   5.357  1.00 25.00           C
ATOM     68  CA  LEU    68      26.854   5.101   2.131  1.00 25.00           C
ATOM     69  CA  ASN    69      26.405   8.726   3.285  1.00 25.00           C
ATOM     70  CA  LEU    70      27.980   7.868   6.670  1.00 25.00           C
ATOM     71  CA  GLN    71      30.938   6.200   4.898  1.00 25.00           C
TER
END
