
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS599_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:    31        27 - 72          4.75    14.22
  LCS_AVERAGE:     48.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        50 - 69          1.76    11.43
  LCS_AVERAGE:     26.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        12 - 27          0.96    12.21
  LCS_AVERAGE:     17.94

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    8     0    0    0    3    3    3    4    5    6    6    6    6    8    8   19   19   22   24   26   31 
LCS_GDT     R       2     R       2      0    3    8     0    0    1    3    3    3    5    5    6    8    8   10   10   11   19   19   25   25   29   32 
LCS_GDT     E       3     E       3      3    4   10     3    3    3    4    4    4    5    5    7    8    9   11   14   17   18   19   20   21   22   22 
LCS_GDT     L       4     L       4      3    4   13     3    3    3    4    4    4    5    5    7    8    8   10   10   17   18   19   20   22   31   32 
LCS_GDT     L       5     L       5      3    4   25     3    3    3    4    4    5    5    5    9   13   15   17   20   21   21   25   27   32   33   36 
LCS_GDT     R       6     R       6      6    7   25     0    3    6    6    6    6    8    8    9   11   14   17   19   19   21   25   29   32   33   36 
LCS_GDT     T       7     T       7      6    7   25     4    5    6    6    6    6    8    8    9   11   15   19   20   22   27   30   35   41   41   43 
LCS_GDT     N       8     N       8      6    7   25     4    5    6    6    6    6    8    8   14   20   21   23   27   30   32   34   37   41   41   43 
LCS_GDT     D       9     D       9      6    7   26     4    5    6    6    6    6    8   14   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     A      10     A      10      6    7   26     4    5    6    6    6    6    8    8   15   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     V      11     V      11      6   18   26     3    5    6    6    6    6   14   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      12     L      12     16   18   26     8   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      13     L      13     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     S      14     S      14     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     A      15     A      15     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     V      16     V      16     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     G      17     G      17     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     A      18     A      18     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      19     L      19     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      20     L      20     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     D      21     D      21     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     G      22     G      22     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     A      23     A      23     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     D      24     D      24     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     I      25     I      25     16   18   26     9   14   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     G      26     G      26     16   18   26     3    5   11   15   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     H      27     H      27     16   18   31     3    6   14   16   17   17   18   19   20   21   23   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      28     L      28      7   18   31     3    5   14   16   17   17   18   19   20   21   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     V      29     V      29      5   18   31     3    4    6    7   12   16   17   18   20   21   21   22   23   27   32   34   37   41   41   43 
LCS_GDT     P      45     P      45      3    3   31     0    3    3    3    3    3    5    7    9   14   18   22   25   27   28   29   31   31   31   31 
LCS_GDT     R      46     R      46      5   12   31     3    4    6    9   11   11   14   15   17   19   22   24   26   27   28   29   31   31   31   31 
LCS_GDT     R      47     R      47      5   12   31     3    4    6    8   11   11   12   15   16   16   19   22   23   27   28   29   31   31   31   31 
LCS_GDT     V      48     V      48      5   17   31     3    6    8   11   13   16   17   20   21   22   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      49     L      49      5   17   31     3    4    7    9   14   17   18   20   21   22   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     V      50     V      50     11   20   31     5    7   12   15   18   19   19   20   21   22   24   25   26   30   32   34   37   41   41   43 
LCS_GDT     H      51     H      51     14   20   31     5   10   14   16   18   19   19   20   21   22   24   25   26   27   30   32   37   41   41   43 
LCS_GDT     E      52     E      52     14   20   31     5    7   14   16   18   19   19   20   21   22   24   25   26   27   30   32   34   37   40   43 
LCS_GDT     D      53     D      53     14   20   31     5    7   14   15   18   19   19   20   21   22   24   25   26   27   28   29   32   33   36   39 
LCS_GDT     D      54     D      54     14   20   31     5   11   14   16   18   19   19   20   21   22   24   25   26   27   30   32   34   37   40   43 
LCS_GDT     L      55     L      55     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   26   27   31   33   37   41   41   43 
LCS_GDT     A      56     A      56     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   26   27   31   34   37   41   41   43 
LCS_GDT     G      57     G      57     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   26   27   31   34   37   41   41   43 
LCS_GDT     A      58     A      58     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   26   30   32   34   37   41   41   43 
LCS_GDT     R      59     R      59     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     R      60     R      60     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     L      61     L      61     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   26   30   32   34   37   41   41   43 
LCS_GDT     L      62     L      62     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     T      63     T      63     14   20   31     9   11   14   16   18   19   19   20   21   22   24   25   27   30   32   34   37   41   41   43 
LCS_GDT     D      64     D      64     14   20   31     7   11   14   16   18   19   19   20   21   22   24   25   26   27   32   34   37   41   41   43 
LCS_GDT     A      65     A      65     14   20   31     4    9   14   16   18   19   19   20   21   22   24   25   26   27   30   34   37   41   41   43 
LCS_GDT     G      66     G      66      4   20   31     3    4    4    6   14   17   19   20   21   22   24   25   26   27   32   34   37   41   41   43 
LCS_GDT     L      67     L      67      3   20   31     3   10   14   16   18   19   19   20   21   22   24   25   26   27   30   34   37   41   41   43 
LCS_GDT     A      68     A      68      4   20   31     3    4   12   16   18   19   19   20   21   22   24   25   26   29   32   34   37   41   41   43 
LCS_GDT     H      69     H      69      4   20   31     3    4   11   14   17   19   19   20   21   22   24   25   26   27   29   30   32   35   37   41 
LCS_GDT     E      70     E      70      4    5   31     3    4    5    5    5    7   10   17   20   22   24   25   26   27   28   29   31   33   34   37 
LCS_GDT     L      71     L      71      4    5   31     3    4    5    5    5    7   10   12   16   20   24   25   26   27   28   29   31   33   34   37 
LCS_GDT     R      72     R      72      3    5   31     0    3    3    3    4    5    9   12   16   19   22   23   25   26   28   29   31   31   31   32 
LCS_AVERAGE  LCS_A:  31.00  (  17.94   26.81   48.26 )

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      9     14     14     16     18     19     19     20     21     22     24     25     27     30     32     34     37     41     41     43 
GDT PERCENT_CA  15.79  24.56  24.56  28.07  31.58  33.33  33.33  35.09  36.84  38.60  42.11  43.86  47.37  52.63  56.14  59.65  64.91  71.93  71.93  75.44
GDT RMS_LOCAL    0.21   0.50   0.50   1.08   1.34   1.55   1.55   1.76   2.46   2.61   3.31   3.37   4.53   5.08   5.39   5.60   6.02   6.56   6.56   6.88
GDT RMS_ALL_CA  11.50  12.12  12.12  11.30  11.55  11.50  11.50  11.43  12.88  12.62  13.10  12.84  11.80  11.58  11.55  11.54  11.34  10.83  10.83  10.61

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         19.103
LGA    R       2      R       2         15.009
LGA    E       3      E       3         16.729
LGA    L       4      L       4         15.219
LGA    L       5      L       5         14.525
LGA    R       6      R       6         15.922
LGA    T       7      T       7         17.615
LGA    N       8      N       8         17.407
LGA    D       9      D       9         19.159
LGA    A      10      A      10         16.878
LGA    V      11      V      11         16.490
LGA    L      12      L      12         12.489
LGA    L      13      L      13          7.925
LGA    S      14      S      14         10.605
LGA    A      15      A      15         13.120
LGA    V      16      V      16          8.982
LGA    G      17      G      17          8.649
LGA    A      18      A      18         13.878
LGA    L      19      L      19         14.589
LGA    L      20      L      20         12.647
LGA    D      21      D      21         15.245
LGA    G      22      G      22         19.332
LGA    A      23      A      23         19.787
LGA    D      24      D      24         19.634
LGA    I      25      I      25         15.780
LGA    G      26      G      26         14.572
LGA    H      27      H      27          9.732
LGA    L      28      L      28          7.370
LGA    V      29      V      29          6.843
LGA    P      45      P      45         14.822
LGA    R      46      R      46         14.825
LGA    R      47      R      47         14.442
LGA    V      48      V      48          8.895
LGA    L      49      L      49          7.575
LGA    V      50      V      50          2.986
LGA    H      51      H      51          1.072
LGA    E      52      E      52          1.566
LGA    D      53      D      53          2.371
LGA    D      54      D      54          1.392
LGA    L      55      L      55          0.373
LGA    A      56      A      56          0.579
LGA    G      57      G      57          0.551
LGA    A      58      A      58          0.568
LGA    R      59      R      59          0.739
LGA    R      60      R      60          0.797
LGA    L      61      L      61          0.615
LGA    L      62      L      62          0.319
LGA    T      63      T      63          0.843
LGA    D      64      D      64          1.525
LGA    A      65      A      65          2.020
LGA    G      66      G      66          3.758
LGA    L      67      L      67          1.783
LGA    A      68      A      68          2.023
LGA    H      69      H      69          3.225
LGA    E      70      E      70          7.791
LGA    L      71      L      71          8.533
LGA    R      72      R      72         10.173

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     20    1.76    36.842    33.903     1.077

LGA_LOCAL      RMSD =  1.757  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.433  Number of atoms =   57 
Std_ALL_ATOMS  RMSD = 10.016  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.666656 * X  +   0.618100 * Y  +  -0.416561 * Z  +   0.210454
  Y_new =   0.715457 * X  +  -0.373919 * Y  +   0.590175 * Z  +   1.942758
  Z_new =   0.209027 * X  +  -0.691474 * Y  +  -0.691499 * Z  +   1.737092 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.356213    0.785380  [ DEG:  -135.0010     44.9990 ]
  Theta =  -0.210580   -2.931013  [ DEG:   -12.0653   -167.9347 ]
  Phi   =   0.820692   -2.320900  [ DEG:    47.0222   -132.9778 ]
 
# 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_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_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   20   1.76  33.903    10.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_5-D1
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -3.185  -7.661  -9.177  1.00  0.00              
ATOM      2  CA  ARG     2      -2.301  -4.030 -10.091  1.00  0.00              
ATOM      3  CA  GLU     3      -3.629  -6.933 -12.826  1.00  0.00              
ATOM      4  CA  LEU     4      -1.532  -4.390 -11.107  1.00  0.00              
ATOM      5  CA  LEU     5       1.794  -5.945 -12.230  1.00  0.00              
ATOM      6  CA  ARG     6       0.598  -6.135 -15.821  1.00  0.00              
ATOM      7  CA  THR     7      -0.582  -2.532 -16.046  1.00  0.00              
ATOM      8  CA  ASN     8       2.298  -0.899 -14.120  1.00  0.00              
ATOM      9  CA  ASP     9       0.077   1.125 -11.784  1.00  0.00              
ATOM     10  CA  ALA    10       0.864  -0.180  -8.252  1.00  0.00              
ATOM     11  CA  VAL    11      -2.152  -1.533  -6.488  1.00  0.00              
ATOM     12  CA  LEU    12      -2.757  -4.587  -4.267  1.00  0.00              
ATOM     13  CA  LEU    13      -5.730  -3.678  -2.035  1.00  0.00              
ATOM     14  CA  SER    14      -6.188  -7.010  -0.252  1.00  0.00              
ATOM     15  CA  ALA    15      -2.494  -7.660   0.294  1.00  0.00              
ATOM     16  CA  VAL    16      -1.960  -4.210   1.730  1.00  0.00              
ATOM     17  CA  GLY    17      -5.110  -4.356   3.896  1.00  0.00              
ATOM     18  CA  ALA    18      -4.308  -7.718   5.330  1.00  0.00              
ATOM     19  CA  LEU    19      -0.714  -6.911   6.129  1.00  0.00              
ATOM     20  CA  LEU    20      -1.569  -3.683   7.848  1.00  0.00              
ATOM     21  CA  ASP    21      -4.277  -5.209   9.982  1.00  0.00              
ATOM     22  CA  GLY    22      -2.147  -8.068  11.182  1.00  0.00              
ATOM     23  CA  ALA    23       0.618  -5.758  12.333  1.00  0.00              
ATOM     24  CA  ASP    24      -1.793  -3.278  13.993  1.00  0.00              
ATOM     25  CA  ILE    25      -0.601  -0.404  11.865  1.00  0.00              
ATOM     26  CA  GLY    26      -3.003   1.837  10.143  1.00  0.00              
ATOM     27  CA  HIS    27      -0.702   3.897   7.814  1.00  0.00              
ATOM     28  CA  LEU    28      -1.522   4.364   4.162  1.00  0.00              
ATOM     29  CA  VAL    29       0.791   6.114   1.795  1.00  0.00              
ATOM     45  CA  PRO    45      -6.796   3.961   6.062  1.00  0.00              
ATOM     46  CA  ARG    46      -6.054   4.679   9.675  1.00  0.00              
ATOM     47  CA  ARG    47      -3.485   7.453   8.867  1.00  0.00              
ATOM     48  CA  VAL    48      -3.519   8.251   5.192  1.00  0.00              
ATOM     49  CA  LEU    49      -0.833  10.096   3.511  1.00  0.00              
ATOM     50  CA  VAL    50      -1.449  11.156  -0.045  1.00  0.00              
ATOM     51  CA  HIS    51       0.009  13.576  -2.339  1.00  0.00              
ATOM     52  CA  GLU    52       3.213  13.425  -4.318  1.00  0.00              
ATOM     53  CA  ASP    53       4.284  16.900  -3.208  1.00  0.00              
ATOM     54  CA  ASP    54       3.800  15.931   0.429  1.00  0.00              
ATOM     55  CA  LEU    55       5.804  12.692   0.191  1.00  0.00              
ATOM     56  CA  ALA    56       8.234  13.712   2.944  1.00  0.00              
ATOM     57  CA  GLY    57       5.417  14.492   5.367  1.00  0.00              
ATOM     58  CA  ALA    58       3.747  11.141   4.678  1.00  0.00              
ATOM     59  CA  ARG    59       6.978   9.258   5.223  1.00  0.00              
ATOM     60  CA  ARG    60       7.516  11.119   8.471  1.00  0.00              
ATOM     61  CA  LEU    61       4.104  10.042   9.812  1.00  0.00              
ATOM     62  CA  LEU    62       4.759   6.417   8.906  1.00  0.00              
ATOM     63  CA  THR    63       8.240   6.566  10.575  1.00  0.00              
ATOM     64  CA  ASP    64       6.858   8.120  13.728  1.00  0.00              
ATOM     65  CA  ALA    65       4.306   5.396  14.009  1.00  0.00              
ATOM     66  CA  GLY    66       6.875   2.628  13.500  1.00  0.00              
ATOM     67  CA  LEU    67       5.240   1.161  10.485  1.00  0.00              
ATOM     68  CA  ALA    68       8.034  -0.009   8.271  1.00  0.00              
ATOM     69  CA  HIS    69       9.926  -1.954  10.842  1.00  0.00              
ATOM     70  CA  GLU    70       6.872  -3.765  12.037  1.00  0.00              
ATOM     71  CA  LEU    71       5.414  -4.745   8.627  1.00  0.00              
ATOM     72  CA  ARG    72       8.839  -5.639   7.257  1.00  0.00              
TER                                                                             
END
