
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0349TS599_4-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS599_4-D1.T0349_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:    32        26 - 72          4.95    13.94
  LCS_AVERAGE:     50.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22         8 - 29          1.41    13.85
  LCS_AVERAGE:     30.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21         9 - 29          0.99    13.78
  LCS_AVERAGE:     22.53

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:   57
LCS_GDT     M       1     M       1      0    3    9     0    0    0    3    3    3    3    4    5    6    7    8   10   12   14   17   18   19   19   21 
LCS_GDT     R       2     R       2      3    3    9     0    3    3    3    3    4    4    5    8   10   13   17   17   17   20   21   21   22   22   23 
LCS_GDT     E       3     E       3      3    4   13     3    3    3    4    4    4    4    5    8   10   13   17   17   17   20   21   21   22   22   23 
LCS_GDT     L       4     L       4      3    4   26     3    3    3    4    4    4    4    5    8   10   13   17   17   17   20   21   21   24   26   26 
LCS_GDT     L       5     L       5      3    4   26     3    3    3    4    4    6    9   11   15   17   18   21   23   25   25   25   25   25   28   34 
LCS_GDT     R       6     R       6      4    6   26     0    3    5    5    6    7    9   11   15   17   18   21   23   25   25   25   25   28   38   40 
LCS_GDT     T       7     T       7      4    6   26     3    4    5    5    6    7   11   14   20   22   23   24   26   30   33   37   41   42   43   43 
LCS_GDT     N       8     N       8      4   22   26     3    5    5    8   15   20   22   22   23   24   24   28   30   33   37   40   41   42   43   43 
LCS_GDT     D       9     D       9     21   22   26     4   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     A      10     A      10     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     V      11     V      11     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   36   40   41   42   43   43 
LCS_GDT     L      12     L      12     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     L      13     L      13     21   22   26    11   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     S      14     S      14     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     A      15     A      15     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     V      16     V      16     21   22   26    11   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     G      17     G      17     21   22   26    11   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     A      18     A      18     21   22   26    11   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     L      19     L      19     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     L      20     L      20     21   22   26    11   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     D      21     D      21     21   22   26     8   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     G      22     G      22     21   22   26     7   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     A      23     A      23     21   22   26     7   17   18   20   21   21   22   22   23   25   25   27   28   33   36   40   41   42   43   43 
LCS_GDT     D      24     D      24     21   22   26     7   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     I      25     I      25     21   22   26    11   17   18   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     G      26     G      26     21   22   32     3    5    9   20   21   21   22   22   23   25   25   27   30   33   37   40   41   42   43   43 
LCS_GDT     H      27     H      27     21   22   32     3   17   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     L      28     L      28     21   22   32     3    7   18   20   21   21   22   22   23   25   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     V      29     V      29     21   22   32     3    5   16   19   21   21   22   22   23   25   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     P      45     P      45      3    3   32     0    3    3    3    3    5    7    9   10   13   14   17   19   23   24   28   30   30   31   32 
LCS_GDT     R      46     R      46      4   12   32     3    4    6    8   10   11   14   14   16   18   21   22   24   26   28   29   30   30   31   32 
LCS_GDT     R      47     R      47      5   14   32     3    4    8   10   11   12   14   14   16   19   21   22   27   27   28   29   30   30   31   32 
LCS_GDT     V      48     V      48      5   14   32     4    5    8   10   11   14   16   19   21   25   25   26   27   27   28   31   33   37   41   43 
LCS_GDT     L      49     L      49      5   16   32     4    4    8   10   11   14   15   21   22   25   25   26   27   27   30   39   40   42   43   43 
LCS_GDT     V      50     V      50     10   20   32     4    6   12   14   17   20   21   22   23   24   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     H      51     H      51     13   20   32     4    6   13   15   18   20   21   22   22   24   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     E      52     E      52     14   20   32     4    6   13   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     D      53     D      53     14   20   32     4   13   14   15   18   20   21   22   22   23   25   26   29   33   37   40   41   42   43   43 
LCS_GDT     D      54     D      54     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     L      55     L      55     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     A      56     A      56     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     G      57     G      57     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     A      58     A      58     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     R      59     R      59     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     R      60     R      60     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   30   33   37   40   41   42   43   43 
LCS_GDT     L      61     L      61     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     L      62     L      62     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     T      63     T      63     14   20   32    10   13   14   15   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     D      64     D      64     14   20   32     7   13   14   15   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     A      65     A      65     14   20   32     4   11   14   15   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     G      66     G      66      4   20   32     3    4    4   11   13   20   21   22   22   23   25   26   28   31   33   37   40   41   43   43 
LCS_GDT     L      67     L      67      3   20   32     3   13   14   15   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     A      68     A      68      4   20   32     3    4    6   11   18   20   21   22   22   23   25   28   29   33   37   40   41   42   43   43 
LCS_GDT     H      69     H      69      4   20   32     3    4    4   11   15   19   21   22   22   23   25   26   28   29   32   36   38   41   43   43 
LCS_GDT     E      70     E      70      4    5   32     3    4    4    5    5    9   11   17   21   23   25   26   28   29   30   34   35   38   41   42 
LCS_GDT     L      71     L      71      4    5   32     3    4    4    5    6   10   14   18   21   25   25   26   27   29   30   34   35   40   41   43 
LCS_GDT     R      72     R      72      3    5   32     3    3    3    3    4    6    8   18   21   25   25   25   26   27   28   29   31   34   34   39 
LCS_AVERAGE  LCS_A:  34.34  (  22.53   30.41   50.08 )

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     17     18     20     21     21     22     22     23     25     25     28     30     33     37     40     41     42     43     43 
GDT PERCENT_CA  19.30  29.82  31.58  35.09  36.84  36.84  38.60  38.60  40.35  43.86  43.86  49.12  52.63  57.89  64.91  70.18  71.93  73.68  75.44  75.44
GDT RMS_LOCAL    0.26   0.58   0.63   0.86   0.99   0.99   1.41   1.41   1.83   3.13   3.08   4.56   4.71   5.02   5.54   5.78   5.86   5.98   6.10   6.10
GDT RMS_ALL_CA  14.01  13.94  13.89  13.65  13.78  13.78  13.85  13.85  13.32  14.06  12.85  10.78  11.82  11.66  10.99  11.09  11.08  11.09  11.05  11.05

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         27.678
LGA    R       2      R       2         27.008
LGA    E       3      E       3         23.339
LGA    L       4      L       4         17.606
LGA    L       5      L       5         12.933
LGA    R       6      R       6         12.917
LGA    T       7      T       7          7.670
LGA    N       8      N       8          3.956
LGA    D       9      D       9          2.297
LGA    A      10      A      10          1.047
LGA    V      11      V      11          0.931
LGA    L      12      L      12          1.122
LGA    L      13      L      13          1.218
LGA    S      14      S      14          1.291
LGA    A      15      A      15          0.947
LGA    V      16      V      16          0.859
LGA    G      17      G      17          0.984
LGA    A      18      A      18          0.440
LGA    L      19      L      19          0.237
LGA    L      20      L      20          0.505
LGA    D      21      D      21          1.133
LGA    G      22      G      22          1.150
LGA    A      23      A      23          1.005
LGA    D      24      D      24          1.475
LGA    I      25      I      25          0.563
LGA    G      26      G      26          2.199
LGA    H      27      H      27          0.691
LGA    L      28      L      28          1.883
LGA    V      29      V      29          2.384
LGA    P      45      P      45         19.549
LGA    R      46      R      46         19.541
LGA    R      47      R      47         16.094
LGA    V      48      V      48         10.084
LGA    L      49      L      49          7.895
LGA    V      50      V      50          6.593
LGA    H      51      H      51         10.934
LGA    E      52      E      52         16.281
LGA    D      53      D      53         19.469
LGA    D      54      D      54         17.828
LGA    L      55      L      55         15.339
LGA    A      56      A      56         19.321
LGA    G      57      G      57         19.375
LGA    A      58      A      58         14.570
LGA    R      59      R      59         15.343
LGA    R      60      R      60         20.128
LGA    L      61      L      61         19.062
LGA    L      62      L      62         16.426
LGA    T      63      T      63         19.923
LGA    D      64      D      64         23.715
LGA    A      65      A      65         21.881
LGA    G      66      G      66         21.325
LGA    L      67      L      67         19.230
LGA    A      68      A      68         16.140
LGA    H      69      H      69         19.463
LGA    E      70      E      70         18.349
LGA    L      71      L      71         10.932
LGA    R      72      R      72         10.796

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     22    1.41    43.421    38.735     1.460

LGA_LOCAL      RMSD =  1.407  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.924  Number of atoms =   57 
Std_ALL_ATOMS  RMSD = 10.275  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.802894 * X  +  -0.389501 * Y  +  -0.451276 * Z  +   0.295049
  Y_new =   0.530271 * X  +  -0.812512 * Y  +  -0.242152 * Z  +   5.587264
  Z_new =  -0.272349 * X  +  -0.433721 * Y  +   0.858902 * Z  +  -0.020215 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.467617    2.673975  [ DEG:   -26.7925    153.2075 ]
  Theta =   0.275833    2.865759  [ DEG:    15.8041    164.1959 ]
  Phi   =   2.557907   -0.583686  [ DEG:   146.5573    -33.4427 ]
 
# 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: T0349TS599_4-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_4-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   57   57   4.0   22   1.41  38.735    10.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_4-D1
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -4.706  -8.669  11.817  1.00  0.00              
ATOM      2  CA  ARG     2      -1.659 -10.164  13.243  1.00  0.00              
ATOM      3  CA  GLU     3      -3.899 -11.753  10.062  1.00  0.00              
ATOM      4  CA  LEU     4      -3.265  -8.743   8.218  1.00  0.00              
ATOM      5  CA  LEU     5       0.543  -8.763   8.800  1.00  0.00              
ATOM      6  CA  ARG     6       0.890 -12.427   7.921  1.00  0.00              
ATOM      7  CA  THR     7      -1.069 -12.214   4.648  1.00  0.00              
ATOM      8  CA  ASN     8       0.346  -8.932   3.512  1.00  0.00              
ATOM      9  CA  ASP     9      -2.694  -6.872   2.822  1.00  0.00              
ATOM     10  CA  ALA    10      -5.710  -6.094   4.963  1.00  0.00              
ATOM     11  CA  VAL    11      -4.831  -4.910   8.471  1.00  0.00              
ATOM     12  CA  LEU    12      -1.803  -3.005   7.145  1.00  0.00              
ATOM     13  CA  LEU    13      -3.669  -1.078   4.410  1.00  0.00              
ATOM     14  CA  SER    14      -6.348  -0.034   6.880  1.00  0.00              
ATOM     15  CA  ALA    15      -3.807   1.094   9.515  1.00  0.00              
ATOM     16  CA  VAL    16      -1.885   3.156   6.923  1.00  0.00              
ATOM     17  CA  GLY    17      -5.149   4.754   5.756  1.00  0.00              
ATOM     18  CA  ALA    18      -6.141   5.610   9.337  1.00  0.00              
ATOM     19  CA  LEU    19      -2.716   7.173   9.998  1.00  0.00              
ATOM     20  CA  LEU    20      -3.001   9.241   6.782  1.00  0.00              
ATOM     21  CA  ASP    21      -6.512  10.391   7.774  1.00  0.00              
ATOM     22  CA  GLY    22      -5.389  11.467  11.262  1.00  0.00              
ATOM     23  CA  ALA    23      -2.529  13.506   9.785  1.00  0.00              
ATOM     24  CA  ASP    24      -4.665  15.264   7.213  1.00  0.00              
ATOM     25  CA  ILE    25      -3.031  13.593   4.207  1.00  0.00              
ATOM     26  CA  GLY    26      -5.372  11.989   1.773  1.00  0.00              
ATOM     27  CA  HIS    27      -3.641   9.025   0.381  1.00  0.00              
ATOM     28  CA  LEU    28      -5.488   6.239  -1.508  1.00  0.00              
ATOM     29  CA  VAL    29      -3.441   3.625  -3.251  1.00  0.00              
ATOM     45  CA  PRO    45       2.980  11.108   1.499  1.00  0.00              
ATOM     46  CA  ARG    46       2.614  14.775   2.561  1.00  0.00              
ATOM     47  CA  ARG    47      -0.861  15.029   0.964  1.00  0.00              
ATOM     48  CA  VAL    48      -0.982  12.566  -1.910  1.00  0.00              
ATOM     49  CA  LEU    49      -4.366  11.620  -3.274  1.00  0.00              
ATOM     50  CA  VAL    50      -4.576   8.501  -5.323  1.00  0.00              
ATOM     51  CA  HIS    51      -7.818   7.025  -6.786  1.00  0.00              
ATOM     52  CA  GLU    52      -7.242   4.126  -9.116  1.00  0.00              
ATOM     53  CA  ASP    53      -8.572   5.609 -12.312  1.00  0.00              
ATOM     54  CA  ASP    54      -6.514   8.656 -11.745  1.00  0.00              
ATOM     55  CA  LEU    55      -3.197   6.842 -11.063  1.00  0.00              
ATOM     56  CA  ALA    56      -1.352   9.009 -13.515  1.00  0.00              
ATOM     57  CA  GLY    57      -2.839  12.177 -11.963  1.00  0.00              
ATOM     58  CA  ALA    58      -1.901  11.028  -8.467  1.00  0.00              
ATOM     59  CA  ARG    59       1.674  10.230  -9.386  1.00  0.00              
ATOM     60  CA  ARG    60       2.053  13.604 -11.007  1.00  0.00              
ATOM     61  CA  LEU    61       0.622  15.376  -7.930  1.00  0.00              
ATOM     62  CA  LEU    62       2.954  13.588  -5.541  1.00  0.00              
ATOM     63  CA  THR    63       6.015  14.445  -7.712  1.00  0.00              
ATOM     64  CA  ASP    64       4.884  18.068  -8.033  1.00  0.00              
ATOM     65  CA  ALA    65       4.595  18.276  -4.243  1.00  0.00              
ATOM     66  CA  GLY    66       8.273  17.211  -3.863  1.00  0.00              
ATOM     67  CA  LEU    67       7.935  14.167  -1.850  1.00  0.00              
ATOM     68  CA  ALA    68      10.626  11.674  -2.983  1.00  0.00              
ATOM     69  CA  HIS    69      13.379  14.158  -2.372  1.00  0.00              
ATOM     70  CA  GLU    70      12.077  14.976   1.095  1.00  0.00              
ATOM     71  CA  LEU    71      11.681  11.353   2.218  1.00  0.00              
ATOM     72  CA  ARG    72      15.012  10.295   0.779  1.00  0.00              
TER                                                                             
END
