
#######################################################
#                                                     #
#                        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 T0349TS168_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS168_5-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:    27         6 - 47          4.74    18.72
  LONGEST_CONTINUOUS_SEGMENT:    27         7 - 48          4.78    18.48
  LCS_AVERAGE:     45.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        49 - 68          1.85    17.65
  LONGEST_CONTINUOUS_SEGMENT:    20        50 - 69          1.90    18.02
  LCS_AVERAGE:     25.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         9 - 22          0.54    14.72
  LONGEST_CONTINUOUS_SEGMENT:    14        54 - 67          0.84    18.50
  LCS_AVERAGE:     15.45

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      3    5   15     3    3    5    5    6    6    7    8    9   10   12   13   14   15   15   18   18   19   21   21 
LCS_GDT     R       2     R       2      4    5   15     3    4    5    5    6    6    7    8    9   10   12   13   14   15   15   18   18   19   21   21 
LCS_GDT     E       3     E       3      4    5   15     3    4    5    5    6    6    7    8    9   10   12   13   14   15   15   18   24   27   30   33 
LCS_GDT     L       4     L       4      4    5   15     3    4    4    5    5    5    6    6    6    8   10   13   14   15   15   18   24   25   25   31 
LCS_GDT     L       5     L       5      4    5   22     3    4    5    5    6    6    7   10   10   13   15   17   20   21   23   27   28   30   32   34 
LCS_GDT     R       6     R       6      3    5   27     0    4    4    4    4    5    7   11   13   17   19   21   23   24   25   27   28   30   32   34 
LCS_GDT     T       7     T       7      3    4   27     3    4    4    4    9   10   10   14   17   20   23   24   25   25   26   27   28   30   32   34 
LCS_GDT     N       8     N       8      3   15   27     3    3    3    5    8   11   13   16   21   22   23   24   25   25   26   27   28   31   33   35 
LCS_GDT     D       9     D       9     14   16   27    10   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   27   30   31   34 
LCS_GDT     A      10     A      10     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   28   30   32   34 
LCS_GDT     V      11     V      11     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   28   30   32   35 
LCS_GDT     L      12     L      12     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   29   31   33   35 
LCS_GDT     L      13     L      13     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   29   31   33   35 
LCS_GDT     S      14     S      14     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   29   31   33   35 
LCS_GDT     A      15     A      15     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     V      16     V      16     14   16   27    11   14   14   15   15   16   16   18   19   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     G      17     G      17     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     A      18     A      18     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     L      19     L      19     14   16   27    11   14   14   15   15   16   16   18   21   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     L      20     L      20     14   16   27    11   14   14   15   15   16   16   18   18   19   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     D      21     D      21     14   16   27     9   14   14   15   15   16   16   18   21   22   23   24   25   25   26   27   31   32   33   35 
LCS_GDT     G      22     G      22     14   16   27     9   14   14   15   15   16   16   18   21   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     A      23     A      23      4   16   27     4    4    7   10   13   15   15   18   21   22   23   24   25   25   26   27   28   29   33   34 
LCS_GDT     D      24     D      24      4   16   27     4    4    6    8   10   14   15   17   21   22   23   24   25   25   26   27   27   28   30   33 
LCS_GDT     I      25     I      25      4   10   27     4    4    7    8   10   14   15   17   21   22   23   24   25   25   26   26   27   28   30   33 
LCS_GDT     G      26     G      26      4    5   27     3    4    5    7    8   11   13   16   21   22   23   24   25   25   26   26   27   28   28   29 
LCS_GDT     H      27     H      27      4    5   27     3    4    5    7    8   10   13   16   21   22   23   24   25   25   26   26   27   27   30   34 
LCS_GDT     L      28     L      28      4    5   27     3    4    5    7    7    9   13   16   21   22   23   24   25   25   26   26   27   29   33   34 
LCS_GDT     V      29     V      29      4    5   27     3    4    5    7    7    9   10   14   20   22   23   24   25   25   26   31   31   32   33   34 
LCS_GDT     P      45     P      45      3    5   27     2    3    3    5    7   11   13   16   21   22   23   24   25   25   26   27   30   32   33   35 
LCS_GDT     R      46     R      46      3    5   27     3    3    3    5    7   11   15   16   21   22   23   24   25   25   26   31   31   32   33   35 
LCS_GDT     R      47     R      47      3    5   27     3    3    3    5   10   11   15   16   19   20   22   23   24   25   26   31   31   32   33   35 
LCS_GDT     V      48     V      48      3    5   27     3    3    3    5    5    6   10   16   21   22   22   22   23   24   26   31   31   32   33   35 
LCS_GDT     L      49     L      49      4   20   26     0    3    4   13   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     V      50     V      50      4   20   26     3    4    5   11   17   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     H      51     H      51      5   20   26     3   10   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     E      52     E      52      5   20   26     4   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     D      53     D      53      5   20   26     3    4    9   14   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     D      54     D      54     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     L      55     L      55     14   20   26     9   11   14   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     A      56     A      56     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     G      57     G      57     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     A      58     A      58     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     R      59     R      59     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     R      60     R      60     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     L      61     L      61     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     L      62     L      62     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     T      63     T      63     14   20   26     9   11   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     D      64     D      64     14   20   26     7   11   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     A      65     A      65     14   20   26     4    6   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     G      66     G      66     14   20   26     0    4   15   16   18   19   20   21   21   22   22   23   24   24   26   31   31   32   33   35 
LCS_GDT     L      67     L      67     14   20   26     3   11   15   16   18   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     A      68     A      68      4   20   26     3    3    6    8   17   19   20   21   21   22   22   23   23   24   26   31   31   32   33   35 
LCS_GDT     H      69     H      69      4   20   26     3    3    6    8   11   19   19   21   21   22   22   23   23   24   25   27   29   31   33   34 
LCS_GDT     E      70     E      70      4   17   26     0    3    6    7   12   17   19   20   21   21   22   23   23   23   24   24   25   26   30   33 
LCS_GDT     L      71     L      71      4   11   26     0    3    6    7   11   12   15   19   21   21   21   23   23   23   24   25   26   28   30   32 
LCS_GDT     R      72     R      72      3   10   26     0    3    6    7    9   12   13   13   15   17   18   21   22   22   24   25   26   28   28   28 
LCS_AVERAGE  LCS_A:  28.49  (  15.45   25.02   45.00 )

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     11     14     15     16     18     19     20     21     21     22     23     24     25     25     26     31     31     32     33     35 
GDT PERCENT_CA  19.30  24.56  26.32  28.07  31.58  33.33  35.09  36.84  36.84  38.60  40.35  42.11  43.86  43.86  45.61  54.39  54.39  56.14  57.89  61.40
GDT RMS_LOCAL    0.30   0.54   0.89   1.00   1.56   1.70   1.85   2.03   2.03   2.53   3.65   3.80   3.98   3.98   4.23   6.01   6.01   6.14   6.30   6.78
GDT RMS_ALL_CA  14.69  14.72  18.54  18.56  17.82  17.60  17.65  17.70  17.70  17.13  19.42  19.35  19.26  19.26  18.92  12.20  12.20  12.10  11.95  11.79

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         24.744
LGA    R       2      R       2         23.689
LGA    E       3      E       3         24.009
LGA    L       4      L       4         23.912
LGA    L       5      L       5         23.365
LGA    R       6      R       6         26.596
LGA    T       7      T       7         31.128
LGA    N       8      N       8         30.260
LGA    D       9      D       9         28.575
LGA    A      10      A      10         30.965
LGA    V      11      V      11         28.739
LGA    L      12      L      12         22.559
LGA    L      13      L      13         23.113
LGA    S      14      S      14         25.499
LGA    A      15      A      15         19.851
LGA    V      16      V      16         16.134
LGA    G      17      G      17         21.463
LGA    A      18      A      18         20.955
LGA    L      19      L      19         14.706
LGA    L      20      L      20         17.549
LGA    D      21      D      21         23.602
LGA    G      22      G      22         21.005
LGA    A      23      A      23         17.742
LGA    D      24      D      24         22.908
LGA    I      25      I      25         19.222
LGA    G      26      G      26         21.397
LGA    H      27      H      27         20.740
LGA    L      28      L      28         22.204
LGA    V      29      V      29         21.891
LGA    P      45      P      45         23.795
LGA    R      46      R      46         19.540
LGA    R      47      R      47         13.588
LGA    V      48      V      48          7.751
LGA    L      49      L      49          3.311
LGA    V      50      V      50          3.793
LGA    H      51      H      51          2.038
LGA    E      52      E      52          1.096
LGA    D      53      D      53          2.359
LGA    D      54      D      54          2.000
LGA    L      55      L      55          2.172
LGA    A      56      A      56          1.834
LGA    G      57      G      57          1.380
LGA    A      58      A      58          0.955
LGA    R      59      R      59          0.493
LGA    R      60      R      60          0.699
LGA    L      61      L      61          0.546
LGA    L      62      L      62          0.569
LGA    T      63      T      63          0.907
LGA    D      64      D      64          0.908
LGA    A      65      A      65          2.143
LGA    G      66      G      66          2.002
LGA    L      67      L      67          1.876
LGA    A      68      A      68          3.172
LGA    H      69      H      69          3.889
LGA    E      70      E      70          7.191
LGA    L      71      L      71          8.145
LGA    R      72      R      72         12.276

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     21    2.03    35.965    32.649     0.987

LGA_LOCAL      RMSD =  2.028  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.498  Number of atoms =   57 
Std_ALL_ATOMS  RMSD = 11.201  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.748552 * X  +   0.151218 * Y  +  -0.645603 * Z  +   3.447337
  Y_new =  -0.235493 * X  +   0.970803 * Y  +  -0.045656 * Z  +  12.409190
  Z_new =   0.619850 * X  +   0.186211 * Y  +   0.762307 * Z  +   7.973721 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.239581   -2.902012  [ DEG:    13.7270   -166.2730 ]
  Theta =  -0.668551   -2.473042  [ DEG:   -38.3052   -141.6948 ]
  Phi   =  -0.304795    2.836798  [ DEG:   -17.4635    162.5365 ]
 
# 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: T0349TS168_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS168_5-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   21   2.03  32.649    11.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS168_5-D1
PFRMAT TS
TARGET T0349
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       1.296  34.417  -0.897  1.00 25.00           C
ATOM      2  CA  ARG     2       0.787  31.301  -3.039  1.00 25.00           C
ATOM      3  CA  GLU     3      -0.454  27.884  -1.936  1.00 25.00           C
ATOM      4  CA  LEU     4      -2.583  26.475   0.919  1.00 25.00           C
ATOM      5  CA  LEU     5      -1.590  22.911  -0.066  1.00 25.00           C
ATOM      6  CA  ARG     6       2.103  23.925  -0.110  1.00 25.00           C
ATOM      7  CA  THR     7       1.736  25.506   3.359  1.00 25.00           C
ATOM      8  CA  ASN     8       0.079  22.310   4.667  1.00 25.00           C
ATOM      9  CA  ASP     9       2.929  20.208   3.212  1.00 25.00           C
ATOM     10  CA  ALA    10       5.504  22.501   4.878  1.00 25.00           C
ATOM     11  CA  VAL    11       3.667  22.177   8.223  1.00 25.00           C
ATOM     12  CA  LEU    12       3.639  18.364   7.864  1.00 25.00           C
ATOM     13  CA  LEU    13       7.393  18.381   7.112  1.00 25.00           C
ATOM     14  CA  SER    14       8.026  20.556  10.200  1.00 25.00           C
ATOM     15  CA  ALA    15       5.960  18.151  12.348  1.00 25.00           C
ATOM     16  CA  VAL    16       7.953  15.180  10.982  1.00 25.00           C
ATOM     17  CA  GLY    17      11.236  16.985  11.777  1.00 25.00           C
ATOM     18  CA  ALA    18      10.010  17.697  15.335  1.00 25.00           C
ATOM     19  CA  LEU    19       9.061  14.013  15.773  1.00 25.00           C
ATOM     20  CA  LEU    20      12.524  12.948  14.531  1.00 25.00           C
ATOM     21  CA  ASP    21      14.179  15.370  16.993  1.00 25.00           C
ATOM     22  CA  GLY    22      12.080  15.248  20.208  1.00 25.00           C
ATOM     23  CA  ALA    23       8.996  13.935  22.035  1.00 25.00           C
ATOM     24  CA  ASP    24      10.615  10.498  22.144  1.00 25.00           C
ATOM     25  CA  ILE    25       8.623   9.340  19.178  1.00 25.00           C
ATOM     26  CA  GLY    26       5.402  11.198  19.779  1.00 25.00           C
ATOM     27  CA  HIS    27       3.250  14.230  18.971  1.00 25.00           C
ATOM     28  CA  LEU    28      -0.405  13.583  18.133  1.00 25.00           C
ATOM     29  CA  VAL    29      -1.364  16.286  15.708  1.00 25.00           C
ATOM     45  CA  PRO    45      -3.692  15.090   5.701  1.00 25.00           C
ATOM     46  CA  ARG    46      -0.691  13.415   7.461  1.00 25.00           C
ATOM     47  CA  ARG    47      -1.165  10.130   5.585  1.00 25.00           C
ATOM     48  CA  VAL    48      -1.235   9.832   1.792  1.00 25.00           C
ATOM     49  CA  LEU    49      -0.349   8.776  -1.730  1.00 25.00           C
ATOM     50  CA  VAL    50      -1.522  12.291  -2.649  1.00 25.00           C
ATOM     51  CA  HIS    51       1.659  12.797  -4.646  1.00 25.00           C
ATOM     52  CA  GLU    52       4.933  14.640  -3.952  1.00 25.00           C
ATOM     53  CA  ASP    53       4.708  16.736  -0.755  1.00 25.00           C
ATOM     54  CA  ASP    54       1.759  14.614   0.458  1.00 25.00           C
ATOM     55  CA  LEU    55       3.739  11.413  -0.250  1.00 25.00           C
ATOM     56  CA  ALA    56       6.731  12.805   1.694  1.00 25.00           C
ATOM     57  CA  GLY    57       4.442  13.681   4.637  1.00 25.00           C
ATOM     58  CA  ALA    58       2.975  10.143   4.581  1.00 25.00           C
ATOM     59  CA  ARG    59       6.504   8.655   4.568  1.00 25.00           C
ATOM     60  CA  ARG    60       7.476  10.867   7.539  1.00 25.00           C
ATOM     61  CA  LEU    61       4.340   9.746   9.431  1.00 25.00           C
ATOM     62  CA  LEU    62       5.187   6.081   8.713  1.00 25.00           C
ATOM     63  CA  THR    63       8.760   6.632   9.981  1.00 25.00           C
ATOM     64  CA  ASP    64       7.402   8.265  13.168  1.00 25.00           C
ATOM     65  CA  ALA    65       5.032   5.304  13.705  1.00 25.00           C
ATOM     66  CA  GLY    66       3.160   2.578  11.729  1.00 25.00           C
ATOM     67  CA  LEU    67       6.731   1.674  10.648  1.00 25.00           C
ATOM     68  CA  ALA    68       9.492  -0.933  11.001  1.00 25.00           C
ATOM     69  CA  HIS    69       9.411  -4.714  10.320  1.00 25.00           C
ATOM     70  CA  GLU    70      12.810  -4.142   8.711  1.00 25.00           C
ATOM     71  CA  LEU    71      14.798  -1.035   7.754  1.00 25.00           C
ATOM     72  CA  ARG    72      17.738  -3.398   7.921  1.00 25.00           C
TER
END
