
#######################################################
#                                                     #
#                        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   66 (   66),  selected   66 , name T0356TS464_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected   66 , name T0356_D1.pdb
# PARAMETERS: T0356TS464_2-D1.T0356_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:    23        17 - 48          5.00    21.05
  LCS_AVERAGE:     16.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18         7 - 24          1.75    15.03
  LCS_AVERAGE:     10.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17         8 - 24          0.94    14.87
  LCS_AVERAGE:      7.21

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:  124
LCS_GDT     N       7     N       7      3   18   18     0    3    3    5    6   14   17   19   21   22   23   26   27   27   29   31   35   37   40   41 
LCS_GDT     D       8     D       8     17   18   18     3   11   15   17   18   18   19   20   21   22   23   27   31   32   34   35   36   38   40   42 
LCS_GDT     L       9     L       9     17   18   18     4   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     R      10     R      10     17   18   18     4   11   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     D      11     D      11     17   18   18    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     F      12     F      12     17   18   18    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      13     L      13     17   18   18    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     T      14     T      14     17   18   18    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      15     L      15     17   18   18    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      16     L      16     17   18   18    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     E      17     E      17     17   18   23    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     Q      18     Q      18     17   18   23    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     Q      19     Q      19     17   18   23    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     G      20     G      20     17   18   23    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     E      21     E      21     17   18   23     9   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      22     L      22     17   18   23    11   13   15   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     K      23     K      23     17   18   23     5   11   14   17   18   18   19   20   21   22   23   27   31   32   34   35   36   38   40   42 
LCS_GDT     R      24     R      24     17   18   23     5   11   14   17   18   18   19   20   21   22   23   27   31   32   34   35   36   38   40   42 
LCS_GDT     E      34     E      34      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   23   24   25   26   27   29   31 
LCS_GDT     I      35     I      35      9   17   23     9    9   11   13   15   18   19   19   19   19   20   21   21   23   24   25   26   29   30   33 
LCS_GDT     T      36     T      36      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   23   24   25   26   29   30   34 
LCS_GDT     E      37     E      37      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   23   24   25   26   29   30   34 
LCS_GDT     I      38     I      38      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   23   24   25   28   30   33   35 
LCS_GDT     A      39     A      39      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   23   24   27   31   33   34   36 
LCS_GDT     D      40     D      40      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   23   26   27   31   33   34   36 
LCS_GDT     R      41     R      41      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   21   24   26   29   31   33   34   36 
LCS_GDT     T      42     T      42      9   17   23     9    9   11   13   16   18   19   19   19   19   20   21   27   27   28   29   31   33   34   36 
LCS_GDT     L      43     L      43      6   17   23     4    6    9   13   16   18   19   19   19   19   20   21   21   24   28   29   31   33   34   38 
LCS_GDT     R      44     R      44      6   17   23     4    6    9   13   16   18   19   19   19   19   20   21   21   23   26   29   31   33   34   36 
LCS_GDT     A      45     A      45      6   17   23     4    6   10   13   16   18   19   19   19   19   20   22   27   27   28   29   31   33   34   38 
LCS_GDT     G      46     G      46      6   17   23     4    6   11   13   16   18   19   19   19   19   20   26   27   27   31   34   36   38   40   42 
LCS_GDT     G      47     G      47      6   17   23     3    6   11   13   16   18   19   19   19   19   22   26   27   27   28   30   31   33   39   40 
LCS_GDT     P      48     P      48      6   17   23     4    5   11   13   16   18   19   20   21   22   23   26   27   27   31   33   36   38   40   42 
LCS_GDT     A      49     A      49      5   17   22     4    5    8   10   13   18   19   20   21   22   23   26   27   27   29   33   34   37   40   42 
LCS_GDT     L      50     L      50      5   17   22     4    6    9   12   16   18   19   19   19   19   20   22   27   27   28   29   31   33   34   36 
LCS_GDT     L      51     L      51      5   16   22     4    5    9   10   13   18   19   19   19   19   20   22   27   27   28   29   31   33   34   36 
LCS_GDT     F      52     F      52      5   16   21     4    6    9   12   16   18   19   19   19   19   20   21   23   24   28   29   31   33   34   36 
LCS_GDT     V      62     V      62      3    5   21     3    3    3    4    6    7    7    8    9    9   11   13   14   17   22   23   26   27   34   36 
LCS_GDT     L      63     L      63      3    5   21     3    3    3    5    6    7    7    8    9   10   15   17   27   27   28   29   31   33   34   36 
LCS_GDT     C      64     C      64      3    5   20     3    3    3    5    6    7    9   10   13   15   20   22   27   27   28   29   31   33   34   36 
LCS_GDT     N      65     N      65      3    5   17     0    3    3    5    6    7    7    9   10   14   15   17   27   27   28   29   31   33   34   36 
LCS_GDT     L      66     L      66      3    5   17     1    3    3    4    6    8    9    9   12   14   15   16   16   20   24   29   31   31   33   36 
LCS_GDT     M      77     M      77      3    4   17     1    3    3    4    6    7    8   10   12   14   15   16   16   18   20   22   25   29   34   36 
LCS_GDT     G      78     G      78      3    4   17     3    3    3    4    6    7    8    9   12   14   15   16   16   21   23   24   33   36   39   40 
LCS_GDT     Q      79     Q      79      3    4   17     3    3    3    4    6    7    7    9   15   16   21   24   28   31   34   35   36   38   40   42 
LCS_GDT     E      80     E      80      3   10   17     3    3    3    4    6    9    9   10   12   14   15   16   18   22   25   30   33   37   40   42 
LCS_GDT     D      81     D      81      9   10   17     4    5    9    9    9    9    9   10   11   12   15   18   21   26   32   34   36   38   40   42 
LCS_GDT     V      82     V      82      9   10   19     4    5    9    9    9    9   18   20   21   22   23   26   28   31   33   35   36   38   40   42 
LCS_GDT     S      83     S      83      9   10   19     4   11   13   17   18   18   19   20   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     A      84     A      84      9   10   19     4    6    9    9    9    9   14   15   19   21   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      85     L      85      9   10   19     5    6    9   10   13   15   19   19   20   21   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     R      86     R      86      9   10   19     5    6    9    9    9   12   14   17   19   21   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     E      87     E      87      9   10   19     5    6    9    9    9    9   11   13   14   17   22   27   31   32   34   35   36   37   40   42 
LCS_GDT     V      88     V      88      9   10   19     5    6    9    9   10   10   11   13   15   20   22   27   31   32   34   35   36   38   40   42 
LCS_GDT     G      89     G      89      9   10   19     5    6    9    9    9   12   14   17   19   21   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     K      90     K      90      3    4   19     3    3    4    4    5    5    7    9   10   19   22   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      91     L      91      3    4   19     0    3    4    4    4    4    6   11   14   17   22   27   31   32   34   35   36   38   40   42 
LCS_GDT     L      92     L      92      3    3   19     0    3    3    3    3    4    5    7   14   16   17   17   24   26   29   32   35   37   40   42 
LCS_GDT     D     314     D     314      6    8   19     4    6   10   13   15   16   18   19   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     A     315     A     315      6    8   19     3    6    6    7   10   12   15   19   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     I     316     I     316      6    8   19     4    6    6    7   10   13   16   18   21   22   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     Y     317     Y     317      6    8   19     3    6    6    7   10   12   14   17   19   21   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     H     318     H     318      6    8   19     3    6    6    7   10   12   14   17   19   21   24   27   31   32   34   35   36   38   40   42 
LCS_GDT     S     319     S     319      6    8   19     3    6    6    7   10   11   13   15   18   20   23   27   28   32   34   35   36   38   40   42 
LCS_GDT     T     320     T     320      4    8   19     3    4    5    7   10   12   14   17   18   20   23   27   28   32   34   35   36   38   40   42 
LCS_GDT     Y     321     Y     321      4    8   19     3    4    4    7   10   11   13   14   17   20   22   24   26   29   32   35   36   38   40   42 
LCS_AVERAGE  LCS_A:  11.34  (   7.21   10.47   16.35 )

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     13     15     17     18     18     19     20     21     22     24     27     31     32     34     35     36     38     40     42 
GDT PERCENT_CA   8.87  10.48  12.10  13.71  14.52  14.52  15.32  16.13  16.94  17.74  19.35  21.77  25.00  25.81  27.42  28.23  29.03  30.65  32.26  33.87
GDT RMS_LOCAL    0.27   0.42   0.63   0.94   1.10   1.10   1.66   1.76   1.96   2.31   3.74   4.02   4.51   4.65   4.90   5.07   5.23   5.66   5.87   6.18
GDT RMS_ALL_CA  14.71  14.77  14.79  14.87  14.61  14.61  14.62  14.53  14.52  14.57  14.89  14.86  15.24  15.11  14.88  14.71  14.56  14.16  14.27  14.12

#      Molecule1      Molecule2       DISTANCE
LGA    N       7      N       7          7.511
LGA    D       8      D       8          2.039
LGA    L       9      L       9          1.809
LGA    R      10      R      10          1.982
LGA    D      11      D      11          0.897
LGA    F      12      F      12          0.627
LGA    L      13      L      13          0.533
LGA    T      14      T      14          0.297
LGA    L      15      L      15          0.520
LGA    L      16      L      16          0.361
LGA    E      17      E      17          0.145
LGA    Q      18      Q      18          0.417
LGA    Q      19      Q      19          0.325
LGA    G      20      G      20          0.648
LGA    E      21      E      21          1.126
LGA    L      22      L      22          0.514
LGA    K      23      K      23          2.157
LGA    R      24      R      24          2.460
LGA    E      34      E      34         34.081
LGA    I      35      I      35         27.451
LGA    T      36      T      36         29.671
LGA    E      37      E      37         32.469
LGA    I      38      I      38         26.641
LGA    A      39      A      39         22.344
LGA    D      40      D      40         26.777
LGA    R      41      R      41         25.678
LGA    T      42      T      42         18.625
LGA    L      43      L      43         15.309
LGA    R      44      R      44         19.665
LGA    A      45      A      45         15.393
LGA    G      46      G      46          8.479
LGA    G      47      G      47          8.244
LGA    P      48      P      48          3.861
LGA    A      49      A      49          4.052
LGA    L      50      L      50         10.146
LGA    L      51      L      51         13.782
LGA    F      52      F      52         18.771
LGA    V      62      V      62         21.295
LGA    L      63      L      63         15.978
LGA    C      64      C      64         16.618
LGA    N      65      N      65         14.917
LGA    L      66      L      66         14.734
LGA    M      77      M      77         12.801
LGA    G      78      G      78         12.197
LGA    Q      79      Q      79          7.228
LGA    E      80      E      80         11.505
LGA    D      81      D      81          9.194
LGA    V      82      V      82          3.710
LGA    S      83      S      83          3.023
LGA    A      84      A      84          9.108
LGA    L      85      L      85          8.170
LGA    R      86      R      86         11.226
LGA    E      87      E      87         16.693
LGA    V      88      V      88         16.943
LGA    G      89      G      89         16.953
LGA    K      90      K      90         17.286
LGA    L      91      L      91         16.829
LGA    L      92      L      92         12.786
LGA    D     314      D     314          6.920
LGA    A     315      A     315          9.860
LGA    I     316      I     316          9.708
LGA    Y     317      Y     317         11.140
LGA    H     318      H     318         13.365
LGA    S     319      S     319         14.496
LGA    T     320      T     320         17.398
LGA    Y     321      Y     321         20.393

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   66  124    4.0     20    1.76    17.137    15.337     1.073

LGA_LOCAL      RMSD =  1.763  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.519  Number of atoms =   66 
Std_ALL_ATOMS  RMSD = 12.009  (standard rmsd on all 66 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.482499 * X  +  -0.499343 * Y  +   0.719619 * Z  +  79.250351
  Y_new =   0.684483 * X  +   0.727580 * Y  +   0.045926 * Z  +  37.767197
  Z_new =  -0.546514 * X  +   0.470408 * Y  +   0.692849 * Z  +  63.140598 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.596456   -2.545136  [ DEG:    34.1744   -145.8256 ]
  Theta =   0.578195    2.563397  [ DEG:    33.1282    146.8718 ]
  Phi   =   0.956783   -2.184810  [ DEG:    54.8196   -125.1804 ]
 
# 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: T0356TS464_2-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_2-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   66  124   4.0   20   1.76  15.337    12.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_2-D1
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM      4  CA  ASN     7      76.379  80.500  88.384  1.00  0.00
ATOM      5  CA  ASP     8      74.727  79.112  85.263  1.00  0.00
ATOM      6  CA  LEU     9      71.837  77.216  86.786  1.00  0.00
ATOM      7  CA  ARG    10      71.370  80.065  89.184  1.00  0.00
ATOM      8  CA  ASP    11      72.547  82.545  86.494  1.00  0.00
ATOM      9  CA  PHE    12      69.750  80.740  84.678  1.00  0.00
ATOM     10  CA  LEU    13      67.883  80.294  87.957  1.00  0.00
ATOM     11  CA  THR    14      68.517  83.962  88.704  1.00  0.00
ATOM     12  CA  LEU    15      66.973  84.729  85.315  1.00  0.00
ATOM     13  CA  LEU    16      63.884  82.574  85.918  1.00  0.00
ATOM     14  CA  GLU    17      63.510  83.902  89.470  1.00  0.00
ATOM     15  CA  GLN    18      63.606  87.405  88.036  1.00  0.00
ATOM     16  CA  GLN    19      60.675  86.430  85.825  1.00  0.00
ATOM     17  CA  GLY    20      58.722  85.007  88.749  1.00  0.00
ATOM     18  CA  GLU    21      58.786  81.489  87.307  1.00  0.00
ATOM     19  CA  LEU    22      60.998  79.979  89.972  1.00  0.00
ATOM     20  CA  LYS    23      61.344  80.539  93.697  1.00  0.00
ATOM     21  CA  ARG    24      63.974  79.461  96.199  1.00  0.00
ATOM     22  CA  GLU    34      73.899  85.211  76.341  1.00  0.00
ATOM     23  CA  ILE    35      72.016  85.179  79.673  1.00  0.00
ATOM     24  CA  THR    36      69.977  88.314  79.012  1.00  0.00
ATOM     25  CA  GLU    37      69.162  87.541  75.368  1.00  0.00
ATOM     26  CA  ILE    38      67.884  84.200  76.747  1.00  0.00
ATOM     27  CA  ALA    39      65.682  85.871  79.361  1.00  0.00
ATOM     28  CA  ASP    40      64.352  88.307  76.754  1.00  0.00
ATOM     29  CA  ARG    41      63.332  85.394  74.544  1.00  0.00
ATOM     30  CA  THR    42      61.412  83.784  77.419  1.00  0.00
ATOM     31  CA  LEU    43      61.986  83.220  81.271  1.00  0.00
ATOM     32  CA  ARG    44      59.951  86.213  80.077  1.00  0.00
ATOM     33  CA  ALA    45      57.727  83.924  78.015  1.00  0.00
ATOM     34  CA  GLY    46      56.928  81.893  81.126  1.00  0.00
ATOM     35  CA  GLY    47      59.255  78.852  81.144  1.00  0.00
ATOM     36  CA  PRO    48      60.288  77.780  84.657  1.00  0.00
ATOM     37  CA  ALA    49      61.990  74.403  84.082  1.00  0.00
ATOM     38  CA  LEU    50      65.222  74.829  82.123  1.00  0.00
ATOM     39  CA  LEU    51      67.015  71.974  80.392  1.00  0.00
ATOM     40  CA  PHE    52      70.518  72.959  79.287  1.00  0.00
ATOM     41  CA  VAL    62      58.666  74.460  75.423  1.00  0.00
ATOM     42  CA  LEU    63      62.338  75.237  76.126  1.00  0.00
ATOM     43  CA  CYS    64      64.631  76.961  73.656  1.00  0.00
ATOM     44  CA  ASN    65      67.961  75.128  73.805  1.00  0.00
ATOM     45  CA  LEU    66      71.119  76.951  72.714  1.00  0.00
ATOM     46  CA  MET    77      63.892  78.242  61.992  1.00  0.00
ATOM     47  CA  GLY    78      62.778  81.594  63.471  1.00  0.00
ATOM     48  CA  GLN    79      61.028  83.022  66.535  1.00  0.00
ATOM     49  CA  GLU    80      57.736  82.857  64.657  1.00  0.00
ATOM     50  CA  ASP    81      58.175  79.120  64.247  1.00  0.00
ATOM     51  CA  VAL    82      58.468  78.744  67.998  1.00  0.00
ATOM     52  CA  SER    83      55.310  80.821  68.497  1.00  0.00
ATOM     53  CA  ALA    84      53.502  78.507  66.127  1.00  0.00
ATOM     54  CA  LEU    85      54.871  75.470  67.960  1.00  0.00
ATOM     55  CA  ARG    86      53.289  76.764  71.209  1.00  0.00
ATOM     56  CA  GLU    87      49.883  76.527  69.551  1.00  0.00
ATOM     57  CA  VAL    88      50.696  73.275  68.117  1.00  0.00
ATOM     58  CA  GLY    89      51.243  72.077  71.667  1.00  0.00
ATOM     59  CA  LYS    90      54.807  70.939  71.127  1.00  0.00
ATOM     60  CA  LEU    91      58.321  71.690  72.328  1.00  0.00
ATOM     61  CA  LEU    92      61.490  73.399  71.202  1.00  0.00
ATOM     99  CA  ASP   314      71.240  74.522 100.725  1.00  0.00
ATOM    100  CA  ALA   315      68.193  75.982  98.955  1.00  0.00
ATOM    101  CA  ILE   316      64.649  74.941  98.208  1.00  0.00
ATOM    102  CA  TYR   317      63.412  76.120  94.804  1.00  0.00
ATOM    103  CA  HIS   318      59.663  76.353  94.123  1.00  0.00
ATOM    104  CA  SER   319      57.683  77.014  90.911  1.00  0.00
ATOM    105  CA  THR   320      54.814  79.204  92.082  1.00  0.00
ATOM    106  CA  TYR   321      51.868  80.034  89.901  1.00  0.00
TER
END
