
#######################################################
#                                                     #
#                        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   76 (   76),  selected   62 , name T0309TS599_3
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS599_3.T0309.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        30 - 56          4.86    19.08
  LCS_AVERAGE:     32.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        34 - 47          2.00    20.69
  LONGEST_CONTINUOUS_SEGMENT:    14        35 - 48          1.98    20.83
  LONGEST_CONTINUOUS_SEGMENT:    14        41 - 54          1.96    19.87
  LCS_AVERAGE:     15.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        34 - 44          1.00    22.46
  LCS_AVERAGE:     10.15

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:   62
LCS_GDT     A       2     A       2      0    3    8     0    0    0    0    3    4    4    5    8    9   10   11   14   16   17   19   21   22   24   27 
LCS_GDT     S       3     S       3      0    3   10     0    0    3    3    3    4    4    7    8    9   10   11   14   16   17   19   21   22   24   26 
LCS_GDT     K       4     K       4      3    3   10     3    3    3    3    3    4    4    5    6    9   11   11   15   16   17   21   23   24   27   27 
LCS_GDT     K       5     K       5      3    3   10     3    3    3    3    3    4    4    5    6    7   11   11   12   16   17   19   23   24   27   27 
LCS_GDT     V       6     V       6      3    3   10     3    3    3    3    3    4    4    5    6    9   11   11   15   18   20   21   23   24   27   27 
LCS_GDT     H       7     H       7      3    3   12     3    3    3    3    3    5    7    8    9   10   12   14   17   19   20   21   23   24   27   31 
LCS_GDT     Q       8     Q       8      5    6   12     4    5    5    5    6    7    7    9   10   12   13   14   17   19   20   21   25   28   28   31 
LCS_GDT     I       9     I       9      5    6   12     4    5    5    5    6    7    7    9   10   12   13   14   17   19   20   21   25   28   30   31 
LCS_GDT     N      10     N      10      5    6   12     4    5    5    5    6    9   10   12   14   15   16   17   19   21   23   26   31   32   35   35 
LCS_GDT     V      11     V      11      5    6   13     4    5    5    5    6    9   10   12   14   15   16   17   19   21   23   25   29   32   35   35 
LCS_GDT     K      12     K      12      5    6   13     4    5    5    5    8    9   10   12   14   15   16   17   19   21   25   30   31   32   35   35 
LCS_GDT     G      13     G      13      5    6   14     3    3    5    5    6    6    7   11   14   15   16   17   19   21   23   25   26   28   32   34 
LCS_GDT     F      14     F      14      5    6   14     3    4    4    5    6    6    7    8   10   11   15   17   19   21   23   25   26   28   28   30 
LCS_GDT     F      15     F      15      5    6   16     3    4    4    5    6    6    6    8   10   11   14   15   17   18   23   25   26   28   28   29 
LCS_GDT     D      16     D      16      5    6   16     3    4    4    5    6    6    7    9   10   11   14   15   17   18   23   25   25   28   28   29 
LCS_GDT     M      17     M      17      5    6   16     3    4    4    5    6    6    7    8   10   11   14   15   17   19   20   25   25   28   28   29 
LCS_GDT     D      18     D      18      5    6   16     3    4    4    5    6    6    7    8    9   11   14   15   19   21   23   25   25   28   28   29 
LCS_GDT     V      19     V      19      3    6   16     3    4    4    5    6    6    6    7    9   13   15   17   19   21   23   25   25   28   28   29 
LCS_GDT     M      20     M      20      3    4   16     3    3    3    3    4    5    6    8   10   13   15   17   19   21   23   25   25   28   28   29 
LCS_GDT     E      21     E      21      3    4   16     3    3    4    5    8    9   10   12   14   15   16   17   18   21   22   25   25   28   28   29 
LCS_GDT     V      22     V      22      3    4   16     2    3    4    5    8    9   10   12   14   15   16   17   18   21   23   25   26   29   32   34 
LCS_GDT     T      23     T      23      3    3   19     2    3    4    5    7    9   10   12   14   15   16   17   18   19   21   23   26   29   32   34 
LCS_GDT     E      24     E      24      3    3   22     3    4    4    5    6    8    8   11   11   12   16   17   19   21   24   30   31   32   35   35 
LCS_GDT     Q      25     Q      25      3    4   22     3    4    4    4    5    9   11   13   15   16   16   18   19   21   22   30   31   32   35   35 
LCS_GDT     T      26     T      26      4   11   22     3    4    5    9   11   13   14   15   18   18   18   19   20   21   27   30   31   32   35   35 
LCS_GDT     K      27     K      27      4   11   22     3    4    5    9   11   13   14   15   18   18   18   19   20   21   27   30   31   32   35   35 
LCS_GDT     E      28     E      28      4   11   22     3    4    5    9   11   13   14   15   18   18   18   19   20   21   27   30   31   32   35   35 
LCS_GDT     A      29     A      29      6   11   26     3    4    5    9   11   13   14   15   18   18   18   19   20   21   24   29   31   32   35   35 
LCS_GDT     E      30     E      30      6   11   27     3    4    5    6    7   13   14   15   18   18   18   19   20   24   27   30   31   32   35   35 
LCS_GDT     Y      31     Y      31      6   11   27     4    4    5    9   11   13   14   15   18   18   18   19   21   24   27   30   31   32   35   35 
LCS_GDT     T      32     T      32      6   12   27     4    4    5    9   11   13   14   15   18   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     Y      33     Y      33      9   13   27     4    5    8    9   11   13   14   17   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     D      34     D      34     11   14   27     4    8   10   11   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     F      35     F      35     11   14   27     7    9   10   11   12   16   17   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     K      36     K      36     11   14   27     7    9   10   11   12   16   18   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     E      37     E      37     11   14   27     7    9   10   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     I      38     I      38     11   14   27     7    9   10   11   12   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     L      39     L      39     11   14   27     7    9   10   11   12   16   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     S      40     S      40     11   14   27     7    9   10   11   13   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     E      41     E      41     11   14   27     7    9   10   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     F      42     F      42     11   14   27     4    9   10   11   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     N      43     N      43     11   14   27     4    9   10   11   12   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     G      44     G      44     11   14   27     4    6   10   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     K      45     K      45      9   14   27     4    6    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     N      46     N      46      9   14   27     4    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     V      47     V      47      9   14   27     5    8    8    9   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     S      48     S      48      9   14   27     5    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     I      49     I      49      9   14   27     5    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     T      50     T      50      9   14   27     5    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     V      51     V      51      9   14   27     5    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     K      52     K      52      9   14   27     4    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     E      53     E      53      9   14   27     4    8    8   12   14   17   19   21   21   22   23   23   24   24   27   30   31   32   35   35 
LCS_GDT     E      54     E      54      7   14   27     3    5    7   12   14   17   19   21   21   22   23   23   24   24   26   28   31   32   35   35 
LCS_GDT     N      55     N      55      4   10   27     3    4    7    7    9   10   10   10   10   15   22   23   24   24   25   27   31   32   35   35 
LCS_GDT     E      56     E      56      4   10   27     3    4    5    6    9   10   10   10   10   10   11   11   18   22   24   25   26   30   32   33 
LCS_GDT     L      57     L      57      4   10   25     3    4    6    8    9   10   10   10   10   10   11   11   11   13   13   16   18   19   21   26 
LCS_GDT     P      58     P      58      6   10   12     3    6    7    8    9   10   10   10   10   10   11   11   11   13   13   16   18   18   22   26 
LCS_GDT     V      59     V      59      6   10   12     3    6    7    8    9   10   10   10   10   10   11   11   11   12   13   16   18   19   21   24 
LCS_GDT     K      60     K      60      6   10   12     3    6    7    8    9   10   10   10   10   10   11   11   11   12   13   16   18   19   21   24 
LCS_GDT     G      61     G      61      6   10   12     3    6    7    8    9   10   10   10   10   10   11   11   11   12   13   16   18   18   21   24 
LCS_GDT     V      62     V      62      6   10   12     3    6    7    8    9   10   10   10   10   10   11   11   11   12   13   13   16   18   19   20 
LCS_GDT     E      63     E      63      6   10   12     3    6    7    8    9   10   10   10   10   10   10   11   11   12   13   13   13   13   13   14 
LCS_AVERAGE  LCS_A:  19.39  (  10.15   15.27   32.75 )

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      7      9     10     12     14     17     19     21     21     22     23     23     24     24     27     30     31     32     35     35 
GDT PERCENT_CA  11.29  14.52  16.13  19.35  22.58  27.42  30.65  33.87  33.87  35.48  37.10  37.10  38.71  38.71  43.55  48.39  50.00  51.61  56.45  56.45
GDT RMS_LOCAL    0.30   0.61   0.75   1.62   1.82   2.09   2.37   2.63   2.63   2.79   3.08   3.08   3.40   3.40   5.44   6.09   6.14   6.25   6.67   6.67
GDT RMS_ALL_CA  23.11  22.78  22.49  19.59  19.68  19.65  19.77  19.82  19.82  19.80  19.62  19.62  19.62  19.62  18.21  18.03  17.96  17.96  17.78  17.78

#      Molecule1      Molecule2       DISTANCE
LGA    A       2      A       2         31.080
LGA    S       3      S       3         34.232
LGA    K       4      K       4         32.294
LGA    K       5      K       5         30.934
LGA    V       6      V       6         25.520
LGA    H       7      H       7         24.281
LGA    Q       8      Q       8         20.459
LGA    I       9      I       9         17.419
LGA    N      10      N      10         14.874
LGA    V      11      V      11         15.443
LGA    K      12      K      12         16.323
LGA    G      13      G      13         22.247
LGA    F      14      F      14         24.988
LGA    F      15      F      15         24.189
LGA    D      16      D      16         29.259
LGA    M      17      M      17         26.774
LGA    D      18      D      18         31.692
LGA    V      19      V      19         32.251
LGA    M      20      M      20         28.129
LGA    E      21      E      21         23.476
LGA    V      22      V      22         19.797
LGA    T      23      T      23         21.700
LGA    E      24      E      24         18.338
LGA    Q      25      Q      25         17.953
LGA    T      26      T      26         17.089
LGA    K      27      K      27         17.975
LGA    E      28      E      28         17.239
LGA    A      29      A      29         16.636
LGA    E      30      E      30         13.713
LGA    Y      31      Y      31         11.437
LGA    T      32      T      32          7.382
LGA    Y      33      Y      33          5.229
LGA    D      34      D      34          1.330
LGA    F      35      F      35          3.935
LGA    K      36      K      36          3.936
LGA    E      37      E      37          1.995
LGA    I      38      I      38          2.969
LGA    L      39      L      39          3.933
LGA    S      40      S      40          2.494
LGA    E      41      E      41          1.950
LGA    F      42      F      42          2.436
LGA    N      43      N      43          2.279
LGA    G      44      G      44          0.984
LGA    K      45      K      45          1.619
LGA    N      46      N      46          2.466
LGA    V      47      V      47          2.780
LGA    S      48      S      48          1.618
LGA    I      49      I      49          1.700
LGA    T      50      T      50          1.798
LGA    V      51      V      51          2.951
LGA    K      52      K      52          3.284
LGA    E      53      E      53          3.268
LGA    E      54      E      54          2.997
LGA    N      55      N      55          8.908
LGA    E      56      E      56         11.758
LGA    L      57      L      57         17.247
LGA    P      58      P      58         22.503
LGA    V      59      V      59         29.028
LGA    K      60      K      60         33.930
LGA    G      61      G      61         38.324
LGA    V      62      V      62         36.951
LGA    E      63      E      63         42.998

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   76   62    4.0     21    2.63    29.032    25.549     0.770

LGA_LOCAL      RMSD =  2.627  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 19.857  Number of atoms =   62 
Std_ALL_ATOMS  RMSD = 15.414  (standard rmsd on all 62 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.602447 * X  +  -0.539744 * Y  +   0.587991 * Z  +  -0.539795
  Y_new =   0.549628 * X  +  -0.814728 * Y  +  -0.184736 * Z  + -19.149395
  Z_new =   0.578763 * X  +   0.211883 * Y  +   0.787489 * Z  +   2.095102 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.262837   -2.878756  [ DEG:    15.0594   -164.9406 ]
  Theta =  -0.617211   -2.524381  [ DEG:   -35.3636   -144.6364 ]
  Phi   =   2.402009   -0.739583  [ DEG:   137.6250    -42.3750 ]
 
# 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: T0309TS599_3                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309TS599_3.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   76   62   4.0   21   2.63  25.549    15.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS599_3
PFRMAT TS                                                                       
TARGET T0309                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      17.584 -14.994   9.009  1.00  0.00              
ATOM      2  CA  ALA     2      14.511 -17.499  10.319  1.00  0.00              
ATOM      3  CA  SER     3      16.684 -21.028   9.565  1.00  0.00              
ATOM      4  CA  LYS     4      15.558 -17.729   8.702  1.00  0.00              
ATOM      5  CA  LYS     5      14.531 -18.584   5.194  1.00  0.00              
ATOM      6  CA  VAL     6      12.515 -21.661   6.264  1.00  0.00              
ATOM      7  CA  HIS     7      10.568 -19.896   8.985  1.00  0.00              
ATOM      8  CA  GLN     8       9.891 -16.759   6.858  1.00  0.00              
ATOM      9  CA  ILE     9       8.554 -18.720   3.959  1.00  0.00              
ATOM     10  CA  ASN    10       6.141 -21.253   4.931  1.00  0.00              
ATOM     11  CA  VAL    11       5.675 -24.287   2.777  1.00  0.00              
ATOM     12  CA  LYS    12       2.626 -26.312   3.449  1.00  0.00              
ATOM     13  CA  GLY    13       4.227 -29.654   4.315  1.00  0.00              
ATOM     14  CA  PHE    14       6.455 -28.007   6.930  1.00  0.00              
ATOM     15  CA  PHE    15       3.607 -26.124   8.669  1.00  0.00              
ATOM     16  CA  ASP    16       0.730 -28.561   8.714  1.00  0.00              
ATOM     17  CA  MET    17      -2.117 -26.065   8.468  1.00  0.00              
ATOM     18  CA  ASP    18      -4.927 -27.653   6.469  1.00  0.00              
ATOM     19  CA  VAL    19      -2.749 -29.830   4.325  1.00  0.00              
ATOM     20  CA  MET    20      -5.049 -29.957   1.314  1.00  0.00              
ATOM     21  CA  GLU    21      -5.551 -26.152   1.065  1.00  0.00              
ATOM     22  CA  VAL    22      -1.828 -25.390   1.298  1.00  0.00              
ATOM     23  CA  THR    23      -0.950 -28.068  -1.328  1.00  0.00              
ATOM     24  CA  GLU    24      -3.502 -27.436  -4.041  1.00  0.00              
ATOM     25  CA  GLN    25      -2.948 -23.731  -4.374  1.00  0.00              
ATOM     26  CA  THR    26       0.780 -24.187  -4.240  1.00  0.00              
ATOM     27  CA  LYS    27       0.960 -26.962  -6.894  1.00  0.00              
ATOM     28  CA  GLU    28      -0.905 -24.870  -9.402  1.00  0.00              
ATOM     29  CA  ALA    29       1.212 -21.717  -8.743  1.00  0.00              
ATOM     30  CA  GLU    30      -1.702 -19.239  -9.075  1.00  0.00              
ATOM     31  CA  TYR    31      -0.551 -16.080  -7.413  1.00  0.00              
ATOM     32  CA  THR    32      -1.198 -12.537  -8.737  1.00  0.00              
ATOM     33  CA  TYR    33      -2.341  -9.595  -6.706  1.00  0.00              
ATOM     34  CA  ASP    34      -4.427  -6.584  -7.837  1.00  0.00              
ATOM     35  CA  PHE    35      -4.405  -4.053  -5.018  1.00  0.00              
ATOM     36  CA  LYS    36      -8.178  -3.580  -4.867  1.00  0.00              
ATOM     37  CA  GLU    37      -8.581  -7.382  -4.804  1.00  0.00              
ATOM     38  CA  ILE    38      -6.023  -7.813  -2.089  1.00  0.00              
ATOM     39  CA  LEU    39      -7.633  -5.064  -0.019  1.00  0.00              
ATOM     40  CA  SER    40     -11.104  -6.623  -0.490  1.00  0.00              
ATOM     41  CA  GLU    41      -9.804 -10.028   0.553  1.00  0.00              
ATOM     42  CA  PHE    42      -8.202  -8.484   3.673  1.00  0.00              
ATOM     43  CA  ASN    43     -11.214  -6.574   4.943  1.00  0.00              
ATOM     44  CA  GLY    44     -11.265  -8.286   8.341  1.00  0.00              
ATOM     45  CA  LYS    45     -10.474 -11.744   7.089  1.00  0.00              
ATOM     46  CA  ASN    46      -7.224 -13.431   7.901  1.00  0.00              
ATOM     47  CA  VAL    47      -5.091 -14.162   4.795  1.00  0.00              
ATOM     48  CA  SER    48      -2.389 -16.730   4.915  1.00  0.00              
ATOM     49  CA  ILE    49       0.573 -16.347   2.644  1.00  0.00              
ATOM     50  CA  THR    50       3.004 -19.167   1.896  1.00  0.00              
ATOM     51  CA  VAL    51       6.074 -18.499  -0.158  1.00  0.00              
ATOM     52  CA  LYS    52       7.867 -21.422  -1.710  1.00  0.00              
ATOM     53  CA  GLU    53      10.672 -20.506  -4.030  1.00  0.00              
ATOM     54  CA  GLU    54      10.242 -22.961  -6.819  1.00  0.00              
ATOM     55  CA  ASN    55       6.483 -22.844  -7.012  1.00  0.00              
ATOM     56  CA  GLU    56       6.266 -19.126  -7.490  1.00  0.00              
ATOM     57  CA  LEU    57       4.813 -17.406  -4.502  1.00  0.00              
ATOM     58  CA  PRO    58       3.046 -14.115  -5.456  1.00  0.00              
ATOM     59  CA  VAL    59       0.318 -12.979  -3.167  1.00  0.00              
ATOM     60  CA  LYS    60       0.619  -9.246  -3.166  1.00  0.00              
ATOM     61  CA  GLY    61      -0.118  -7.986   0.386  1.00  0.00              
ATOM     62  CA  VAL    62       0.012 -11.184   2.307  1.00  0.00              
ATOM     63  CA  GLU    63      -1.434 -11.296   5.812  1.00  0.00              
ATOM     64  CA  MET    64      -0.339 -14.040   8.037  1.00  0.00              
ATOM     65  CA  ALA    65      -2.450 -15.129  10.804  1.00  0.00              
ATOM     66  CA  GLY    66      -0.882 -18.207  12.253  1.00  0.00              
ATOM     67  CA  ASP    67      -3.985 -20.092  13.175  1.00  0.00              
ATOM     68  CA  PRO    68      -4.088 -22.847  10.498  1.00  0.00              
ATOM     69  CA  LEU    69      -7.757 -23.558  10.164  1.00  0.00              
ATOM     70  CA  GLU    70      -8.142 -27.331  10.551  1.00  0.00              
ATOM     71  CA  HIS    71     -11.433 -28.429   8.977  1.00  0.00              
ATOM     72  CA  HIS    72     -12.056 -31.658  10.789  1.00  0.00              
ATOM     73  CA  HIS    73     -13.901 -34.155   8.576  1.00  0.00              
ATOM     74  CA  HIS    74     -12.474 -31.894   5.874  1.00  0.00              
ATOM     75  CA  HIS    75     -11.593 -32.563   2.301  1.00  0.00              
ATOM     76  CA  HIS    76     -10.835 -29.290  -0.016  1.00  0.00              
TER                                                                             
END
