
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS599_1-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:    31        27 - 72          4.86    15.50
  LCS_AVERAGE:     47.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        50 - 69          1.90    13.02
  LCS_AVERAGE:     26.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        12 - 26          0.84    13.29
  LONGEST_CONTINUOUS_SEGMENT:    15        13 - 27          0.96    13.27
  LCS_AVERAGE:     17.08

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    3    8     3    3    3    3    3    3    4    6    6    6    6    7   16   21   25   27   28   29   31   32 
LCS_GDT     R       2     R       2      3    3    8     3    3    3    3    3    3    4    6    6    6    6    7    7    8   10   11   12   17   18   32 
LCS_GDT     E       3     E       3      3    4   10     3    3    3    4    4    4    4    6    6    6    8   11   13   14   16   17   18   19   20   22 
LCS_GDT     L       4     L       4      3    4   12     3    3    3    4    4    4    4    6    6    6    7   11   13   14   16   17   18   23   30   32 
LCS_GDT     L       5     L       5      3    4   12     3    3    3    4    4    4    5    6    8    9   10   11   14   17   20   23   24   28   31   33 
LCS_GDT     R       6     R       6      6    6   24     0    3    6    6    6    6    6    7    8    9   10   11   13   17   18   23   23   28   32   35 
LCS_GDT     T       7     T       7      6    6   24     4    5    6    6    6    6    6    7    8    9   10   11   22   28   28   30   31   33   34   35 
LCS_GDT     N       8     N       8      6    6   26     4    5    6    6    6    6    6    7    8   15   19   24   26   28   28   30   31   33   34   35 
LCS_GDT     D       9     D       9      6    6   26     4    5    6    6    6    6    6   14   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     A      10     A      10      6    6   26     4    5    6    6    6    9   11   12   17   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     V      11     V      11      6   18   26     3    5    6    6    8   14   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     L      12     L      12     15   18   26     8   12   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     L      13     L      13     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     S      14     S      14     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     A      15     A      15     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     V      16     V      16     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     G      17     G      17     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     A      18     A      18     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     L      19     L      19     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     L      20     L      20     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     D      21     D      21     15   18   26     9   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     G      22     G      22     15   18   26     6   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     A      23     A      23     15   18   26     8   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     D      24     D      24     15   18   26     6   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     I      25     I      25     15   18   26     6   13   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     G      26     G      26     15   18   26     4    6   12   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     H      27     H      27     15   18   31     4    9   14   16   17   18   19   20   21   22   23   24   26   28   28   30   31   33   34   35 
LCS_GDT     L      28     L      28      8   18   31     4    6   14   16   17   18   19   20   21   22   24   24   26   28   28   30   31   33   34   35 
LCS_GDT     V      29     V      29      7   18   31     4    6    8    8   16   18   19   20   22   23   24   25   26   28   28   30   31   33   34   35 
LCS_GDT     P      45     P      45      5   13   31     0    4    8   10   12   13   15   18   18   20   22   23   25   27   28   30   30   31   31   32 
LCS_GDT     R      46     R      46      5   13   31     3    4    6    7   12   13   14   16   16   18   22   23   25   27   28   30   30   31   31   32 
LCS_GDT     R      47     R      47      5   13   31     3    4    7   10   12   13   16   19   21   22   23   24   25   27   28   30   30   33   34   34 
LCS_GDT     V      48     V      48      5   13   31     4    6    8   10   12   15   19   20   21   23   24   25   26   28   28   30   31   33   34   35 
LCS_GDT     L      49     L      49      5   15   31     4    4    7   10   12   15   18   19   21   23   24   25   26   28   28   30   31   33   34   35 
LCS_GDT     V      50     V      50      8   20   31     4    7   10   14   16   18   19   20   22   23   24   25   25   27   28   30   31   33   34   35 
LCS_GDT     H      51     H      51      8   20   31     4    7   11   14   17   18   19   20   22   23   24   25   25   27   28   30   30   31   31   33 
LCS_GDT     E      52     E      52     13   20   31     4    7   11   14   17   18   19   20   22   23   24   25   25   27   28   30   30   31   31   32 
LCS_GDT     D      53     D      53     13   20   31     4    9   13   14   17   18   19   20   22   23   24   25   25   27   28   30   30   31   31   32 
LCS_GDT     D      54     D      54     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   30   31   31   32 
LCS_GDT     L      55     L      55     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   30   31   34   35 
LCS_GDT     A      56     A      56     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   31   33   34   35 
LCS_GDT     G      57     G      57     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   30   32   34   35 
LCS_GDT     A      58     A      58     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   31   33   34   35 
LCS_GDT     R      59     R      59     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   26   28   28   30   31   33   34   35 
LCS_GDT     R      60     R      60     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   26   28   28   30   31   33   34   35 
LCS_GDT     L      61     L      61     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   30   33   34   35 
LCS_GDT     L      62     L      62     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   26   28   28   30   31   33   34   35 
LCS_GDT     T      63     T      63     13   20   31    10   11   13   14   17   18   19   20   22   23   24   25   26   27   28   30   30   33   34   35 
LCS_GDT     D      64     D      64     13   20   31     6   11   13   14   17   18   19   20   22   23   24   25   25   27   28   30   30   33   34   34 
LCS_GDT     A      65     A      65     13   20   31     4    9   13   14   17   18   19   20   22   23   24   25   25   26   28   30   30   31   31   32 
LCS_GDT     G      66     G      66      4   20   31     3    4    6    6   13   18   19   20   22   23   24   25   25   26   28   30   30   33   34   34 
LCS_GDT     L      67     L      67      3   20   31     3    3   10   14   17   18   19   20   21   23   24   25   25   26   28   30   30   33   34   34 
LCS_GDT     A      68     A      68      4   20   31     3    4   11   14   17   18   19   20   22   23   24   25   26   27   28   30   30   33   34   34 
LCS_GDT     H      69     H      69      4   20   31     3    4    8   14   16   17   19   20   22   23   24   25   25   27   28   30   30   31   31   32 
LCS_GDT     E      70     E      70      4    5   31     3    4    4    8   13   16   18   20   22   23   24   25   25   27   28   30   30   31   31   32 
LCS_GDT     L      71     L      71      4    5   31     3    4    4    4    6    8   13   18   22   23   24   25   25   27   28   30   30   31   31   32 
LCS_GDT     R      72     R      72      3    5   31     0    3    3    3    4    7    8   11   12   15   19   21   25   27   28   30   30   31   31   32 
LCS_AVERAGE  LCS_A:  30.57  (  17.08   26.84   47.80 )

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     13     14     16     17     18     19     20     22     23     24     25     26     28     28     30     31     33     34     35 
GDT PERCENT_CA  17.54  22.81  24.56  28.07  29.82  31.58  33.33  35.09  38.60  40.35  42.11  43.86  45.61  49.12  49.12  52.63  54.39  57.89  59.65  61.40
GDT RMS_LOCAL    0.26   0.55   0.66   1.04   1.22   1.59   1.73   1.90   2.52   2.63   3.04   3.15   4.64   4.98   4.08   4.48   5.80   5.99   6.18   6.68
GDT RMS_ALL_CA  13.20  13.33  13.38  13.30  13.37  12.89  12.90  13.02  13.65  13.53  14.25  14.02  13.09  12.58  15.16  15.56  12.30  13.10  13.04  12.15

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         12.783
LGA    R       2      R       2         14.089
LGA    E       3      E       3         17.963
LGA    L       4      L       4         16.730
LGA    L       5      L       5         18.469
LGA    R       6      R       6         21.397
LGA    T       7      T       7         22.999
LGA    N       8      N       8         21.835
LGA    D       9      D       9         21.458
LGA    A      10      A      10         17.828
LGA    V      11      V      11         17.907
LGA    L      12      L      12         13.879
LGA    L      13      L      13          8.786
LGA    S      14      S      14         11.626
LGA    A      15      A      15         14.293
LGA    V      16      V      16          9.377
LGA    G      17      G      17          9.997
LGA    A      18      A      18         16.048
LGA    L      19      L      19         16.425
LGA    L      20      L      20         14.909
LGA    D      21      D      21         18.531
LGA    G      22      G      22         23.148
LGA    A      23      A      23         23.649
LGA    D      24      D      24         24.200
LGA    I      25      I      25         19.591
LGA    G      26      G      26         18.591
LGA    H      27      H      27         12.495
LGA    L      28      L      28          9.891
LGA    V      29      V      29          5.406
LGA    P      45      P      45         17.446
LGA    R      46      R      46         16.141
LGA    R      47      R      47         14.176
LGA    V      48      V      48          8.991
LGA    L      49      L      49          8.787
LGA    V      50      V      50          3.123
LGA    H      51      H      51          2.053
LGA    E      52      E      52          2.074
LGA    D      53      D      53          2.144
LGA    D      54      D      54          1.317
LGA    L      55      L      55          0.650
LGA    A      56      A      56          0.894
LGA    G      57      G      57          0.716
LGA    A      58      A      58          0.926
LGA    R      59      R      59          1.042
LGA    R      60      R      60          0.674
LGA    L      61      L      61          0.688
LGA    L      62      L      62          0.799
LGA    T      63      T      63          0.764
LGA    D      64      D      64          1.599
LGA    A      65      A      65          2.382
LGA    G      66      G      66          3.002
LGA    L      67      L      67          2.924
LGA    A      68      A      68          1.870
LGA    H      69      H      69          3.555
LGA    E      70      E      70          6.770
LGA    L      71      L      71          7.035
LGA    R      72      R      72         10.604

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     20    1.90    34.649    32.972     0.999

LGA_LOCAL      RMSD =  1.902  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.015  Number of atoms =   57 
Std_ALL_ATOMS  RMSD = 11.200  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.492417 * X  +  -0.406509 * Y  +  -0.769595 * Z  +  -2.031752
  Y_new =   0.851233 * X  +   0.409285 * Y  +   0.328463 * Z  +   3.288928
  Z_new =   0.181460 * X  +  -0.816846 * Y  +   0.547572 * Z  +   2.637898 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.980248    2.161345  [ DEG:   -56.1641    123.8359 ]
  Theta =  -0.182471   -2.959121  [ DEG:   -10.4548   -169.5452 ]
  Phi   =   1.046355   -2.095238  [ DEG:    59.9517   -120.0483 ]
 
# 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_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_1-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   20   1.90  32.972    11.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_1-D1
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -7.079   2.476  -9.797  1.00  0.00              
ATOM      2  CA  ARG     2      -8.065   5.934  -9.804  1.00  0.00              
ATOM      3  CA  GLU     3     -10.641   7.457 -12.753  1.00  0.00              
ATOM      4  CA  LEU     4      -7.592   6.775 -10.621  1.00  0.00              
ATOM      5  CA  LEU     5      -5.291   6.763 -13.713  1.00  0.00              
ATOM      6  CA  ARG     6      -6.658   9.994 -15.038  1.00  0.00              
ATOM      7  CA  THR     7      -6.364  12.010 -11.875  1.00  0.00              
ATOM      8  CA  ASN     8      -2.948  10.608 -10.821  1.00  0.00              
ATOM      9  CA  ASP     9      -4.257   9.800  -7.401  1.00  0.00              
ATOM     10  CA  ALA    10      -3.466   6.103  -6.837  1.00  0.00              
ATOM     11  CA  VAL    11      -6.553   4.014  -5.979  1.00  0.00              
ATOM     12  CA  LEU    12      -6.044   0.537  -4.465  1.00  0.00              
ATOM     13  CA  LEU    13      -8.615  -0.518  -1.875  1.00  0.00              
ATOM     14  CA  SER    14      -8.776  -4.259  -2.602  1.00  0.00              
ATOM     15  CA  ALA    15      -4.975  -4.606  -2.843  1.00  0.00              
ATOM     16  CA  VAL    16      -4.496  -2.745   0.426  1.00  0.00              
ATOM     17  CA  GLY    17      -7.014  -4.925   2.200  1.00  0.00              
ATOM     18  CA  ALA    18      -5.656  -8.236   1.142  1.00  0.00              
ATOM     19  CA  LEU    19      -2.140  -7.350   2.110  1.00  0.00              
ATOM     20  CA  LEU    20      -3.031  -5.984   5.492  1.00  0.00              
ATOM     21  CA  ASP    21      -5.152  -8.896   6.522  1.00  0.00              
ATOM     22  CA  GLY    22      -2.624 -11.504   5.622  1.00  0.00              
ATOM     23  CA  ALA    23       0.225  -9.897   7.448  1.00  0.00              
ATOM     24  CA  ASP    24      -1.736  -9.098  10.639  1.00  0.00              
ATOM     25  CA  ILE    25      -1.077  -5.363  10.229  1.00  0.00              
ATOM     26  CA  GLY    26      -3.932  -2.911  10.537  1.00  0.00              
ATOM     27  CA  HIS    27      -2.602   0.046   8.568  1.00  0.00              
ATOM     28  CA  LEU    28      -4.810   2.423   6.524  1.00  0.00              
ATOM     29  CA  VAL    29      -3.210   4.403   3.790  1.00  0.00              
ATOM     45  CA  PRO    45      -4.937   0.975  12.319  1.00  0.00              
ATOM     46  CA  ARG    46      -2.347   3.614  12.136  1.00  0.00              
ATOM     47  CA  ARG    47      -3.506   5.948   9.474  1.00  0.00              
ATOM     48  CA  VAL    48      -1.047   7.127   6.985  1.00  0.00              
ATOM     49  CA  LEU    49      -1.753  10.024   4.748  1.00  0.00              
ATOM     50  CA  VAL    50       0.313  10.397   1.601  1.00  0.00              
ATOM     51  CA  HIS    51      -0.274  13.039  -1.060  1.00  0.00              
ATOM     52  CA  GLU    52       2.800  12.699  -3.304  1.00  0.00              
ATOM     53  CA  ASP    53       3.749  16.416  -3.125  1.00  0.00              
ATOM     54  CA  ASP    54       3.790  16.117   0.623  1.00  0.00              
ATOM     55  CA  LEU    55       6.012  12.995   0.173  1.00  0.00              
ATOM     56  CA  ALA    56       8.426  14.015   2.824  1.00  0.00              
ATOM     57  CA  GLY    57       5.597  14.661   5.278  1.00  0.00              
ATOM     58  CA  ALA    58       3.949  11.331   4.440  1.00  0.00              
ATOM     59  CA  ARG    59       7.260   9.478   4.980  1.00  0.00              
ATOM     60  CA  ARG    60       7.820  11.216   8.282  1.00  0.00              
ATOM     61  CA  LEU    61       4.341  10.290   9.469  1.00  0.00              
ATOM     62  CA  LEU    62       4.853   6.701   8.466  1.00  0.00              
ATOM     63  CA  THR    63       8.178   6.579  10.345  1.00  0.00              
ATOM     64  CA  ASP    64       6.712   8.093  13.457  1.00  0.00              
ATOM     65  CA  ALA    65       3.843   5.546  13.308  1.00  0.00              
ATOM     66  CA  GLY    66       6.004   2.476  12.858  1.00  0.00              
ATOM     67  CA  LEU    67       5.087   1.425   9.352  1.00  0.00              
ATOM     68  CA  ALA    68       8.552   0.211   8.194  1.00  0.00              
ATOM     69  CA  HIS    69       8.881  -1.918  11.358  1.00  0.00              
ATOM     70  CA  GLU    70       5.419  -3.414  10.793  1.00  0.00              
ATOM     71  CA  LEU    71       6.086  -4.282   7.114  1.00  0.00              
ATOM     72  CA  ARG    72       9.524  -5.570   7.927  1.00  0.00              
TER                                                                             
END
