
#######################################################
#                                                     #
#                        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   67 (   67),  selected   64 , name T0379TS168_5-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS168_5-D2.T0379_D2.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:    64        17 - 83          4.37     4.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        17 - 34          2.00     6.03
  LONGEST_CONTINUOUS_SEGMENT:    18        51 - 68          1.98     8.95
  LONGEST_CONTINUOUS_SEGMENT:    18        52 - 69          1.78     6.46
  LONGEST_CONTINUOUS_SEGMENT:    18        53 - 70          1.83     5.53
  LONGEST_CONTINUOUS_SEGMENT:    18        54 - 71          1.90     5.22
  LCS_AVERAGE:     23.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        54 - 69          0.83     5.18
  LCS_AVERAGE:     17.04

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:   64
LCS_GDT     N      17     N      17     13   18   64    12   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     R      18     R      18     13   18   64    10   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      19     E      19     13   18   64    10   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      20     E      20     13   18   64    10   12   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     S      21     S      21     13   18   64    10   12   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     I      22     I      22     13   18   64    10   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     R      23     R      23     13   18   64    10   12   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     R      24     R      24     13   18   64    10   12   13   21   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     F      25     F      25     13   18   64    10   12   15   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     K      26     K      26     13   18   64    10   12   15   21   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     A      27     A      27     13   18   64    10   12   15   21   28   34   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     I      28     I      28     13   18   64     5   12   15   21   28   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     G      29     G      29     13   18   64     5    7   13   19   24   29   31   41   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     V      30     V      30     13   18   64     5    6   10   18   24   29   31   44   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     A      31     A      31      3   18   64     3    3   15   21   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     D      32     D      32      6   18   64     6    6   13   21   30   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     I      33     I      33      6   18   64     6    6    6   10   17   20   38   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      34     E      34      6   18   64     6    6    6    6    7    8   16   28   34   47   51   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      35     E      35      6    7   64     6    6    6    6    7    7   16   28   35   51   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     M      36     M      36      6    7   64     6   12   15   21   30   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      37     L      37      6    7   64     6    6   12   17   22   29   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     D      38     D      38      3    5   64     3    3    3    4    6    7   17   24   29   32   36   37   50   59   63   64   64   64   64   64 
LCS_GDT     P      39     P      39      0    5   64     0    0    3    4   11   13   23   28   34   35   42   53   57   60   63   64   64   64   64   64 
LCS_GDT     K      43     K      43      0    8   64     0    0    3   12   18   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     G      44     G      44      7    8   64     7    7    9   12   18   33   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      45     L      45      7    8   64     7    7   10   16   19   22   36   45   48   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     F      46     F      46      7    8   64     7    7    9   16   19   21   22   25   33   49   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      47     L      47      7    8   64     7    7    9   14   18   21   22   23   36   48   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     D      48     D      48      7    8   64     7    7    9   10   13   17   19   20   25   30   49   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      49     L      49      7    8   64     7    7    9   10   13   17   19   23   25   26   26   31   54   60   63   64   64   64   64   64 
LCS_GDT     E      50     E      50      7    8   64     7    7    9   10   13   20   22   23   25   26   26   31   43   54   63   64   64   64   64   64 
LCS_GDT     S      51     S      51      5   18   64     4    4    7   12   18   21   22   23   25   26   37   53   58   60   63   64   64   64   64   64 
LCS_GDT     G      52     G      52      5   18   64     4    5   10   14   19   21   33   45   48   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     R      53     R      53      7   18   64     3    5   11   16   19   29   34   40   45   51   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     K      54     K      54     16   18   64     3   10   15   22   31   37   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     S      55     S      55     16   18   64     3   12   15   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      56     E      56     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      57     E      57     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      58     E      58     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     F      59     F      59     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     R      60     R      60     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     T      61     T      61     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      62     E      62     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      63     L      63     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     S      64     S      64     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     R      65     R      65     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     Y      66     Y      66     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     I      67     I      67     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     G      68     G      68     16   18   64    13   16   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     K      69     K      69     16   18   64    11   15   20   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     E      70     E      70      4   18   64     3    3    7   18   22   25   38   45   48   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      71     L      71      4   18   64     3    3    9   19   24   29   34   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     T      72     T      72     12   16   64     3    6   15   19   24   31   36   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     Y      73     Y      73     12   14   64     5   10   12   16   22   27   30   39   44   51   53   55   58   60   62   64   64   64   64   64 
LCS_GDT     Q      74     Q      74     12   14   64     9   10   15   21   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     Q      75     Q      75     12   14   64     9   10   15   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     V      76     V      76     12   14   64     9   10   15   23   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     Y      77     Y      77     12   14   64     9   10   15   19   30   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     D      78     D      78     12   14   64     9   10   17   25   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     A      79     A      79     12   14   64     9   15   19   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      80     L      80     12   14   64     9   10   17   26   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     L      81     L      81     12   14   64     9   10   15   19   24   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     G      82     G      82     12   14   64     9   10   15   19   22   32   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_GDT     F      83     F      83     12   14   64     3    7   15   20   31   39   42   45   49   52   53   55   58   60   63   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  46.88  (  17.04   23.61  100.00 )

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     13     16     20     26     31     39     42     45     49     52     53     55     58     60     63     64     64     64     64     64 
GDT PERCENT_CA  20.31  25.00  31.25  40.62  48.44  60.94  65.62  70.31  76.56  81.25  82.81  85.94  90.62  93.75  98.44 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.51   0.76   1.19   1.57   2.07   2.19   2.46   2.73   2.97   3.01   3.18   3.53   3.79   4.34   4.37   4.37   4.37   4.37   4.37
GDT RMS_ALL_CA   5.16   5.21   5.23   5.21   5.19   4.91   4.87   4.85   4.71   4.59   4.65   4.58   4.48   4.43   4.37   4.37   4.37   4.37   4.37   4.37

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          3.097
LGA    R      18      R      18          3.313
LGA    E      19      E      19          2.771
LGA    E      20      E      20          2.827
LGA    S      21      S      21          2.515
LGA    I      22      I      22          1.214
LGA    R      23      R      23          1.298
LGA    R      24      R      24          2.365
LGA    F      25      F      25          1.649
LGA    K      26      K      26          1.785
LGA    A      27      A      27          2.903
LGA    I      28      I      28          2.893
LGA    G      29      G      29          5.136
LGA    V      30      V      30          4.685
LGA    A      31      A      31          2.856
LGA    D      32      D      32          3.565
LGA    I      33      I      33          5.439
LGA    E      34      E      34          7.294
LGA    E      35      E      35          6.239
LGA    M      36      M      36          3.259
LGA    L      37      L      37          4.295
LGA    D      38      D      38         10.315
LGA    P      39      P      39          9.738
LGA    K      43      K      43          2.892
LGA    G      44      G      44          5.003
LGA    L      45      L      45          5.635
LGA    F      46      F      46          8.223
LGA    L      47      L      47          8.869
LGA    D      48      D      48          9.172
LGA    L      49      L      49         10.820
LGA    E      50      E      50         12.615
LGA    S      51      S      51         10.745
LGA    G      52      G      52          6.447
LGA    R      53      R      53          5.610
LGA    K      54      K      54          3.520
LGA    S      55      S      55          3.337
LGA    E      56      E      56          2.749
LGA    E      57      E      57          2.715
LGA    E      58      E      58          2.432
LGA    F      59      F      59          2.386
LGA    R      60      R      60          2.470
LGA    T      61      T      61          2.504
LGA    E      62      E      62          2.503
LGA    L      63      L      63          1.975
LGA    S      64      S      64          2.199
LGA    R      65      R      65          2.539
LGA    Y      66      Y      66          2.004
LGA    I      67      I      67          2.154
LGA    G      68      G      68          2.416
LGA    K      69      K      69          3.037
LGA    E      70      E      70          3.658
LGA    L      71      L      71          3.630
LGA    T      72      T      72          3.559
LGA    Y      73      Y      73          4.859
LGA    Q      74      Q      74          2.283
LGA    Q      75      Q      75          1.177
LGA    V      76      V      76          2.062
LGA    Y      77      Y      77          2.285
LGA    D      78      D      78          1.676
LGA    A      79      A      79          1.028
LGA    L      80      L      80          0.993
LGA    L      81      L      81          2.883
LGA    G      82      G      82          3.204
LGA    F      83      F      83          1.673

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67   64    4.0     45    2.46    58.984    52.763     1.757

LGA_LOCAL      RMSD =  2.461  Number of atoms =   45  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.790  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  4.372  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.212335 * X  +   0.929211 * Y  +  -0.302457 * Z  +  59.561634
  Y_new =   0.703854 * X  +  -0.360136 * Y  +  -0.612284 * Z  +   4.107239
  Z_new =  -0.677867 * X  +  -0.082877 * Y  +  -0.730498 * Z  +   8.948233 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.028623    0.112969  [ DEG:  -173.5273      6.4727 ]
  Theta =   0.744857    2.396735  [ DEG:    42.6772    137.3228 ]
  Phi   =   1.277804   -1.863788  [ DEG:    73.2128   -106.7872 ]
 
# 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: T0379TS168_5-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0379TS168_5-D2.T0379_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   67   64   4.0   45   2.46  52.763     4.37
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS168_5-D2
PFRMAT TS
TARGET T0379
MODEL 5
PARENT N/A
ATOM     17  CA  ASN    17      68.229   4.029  13.243  1.00 25.00           C
ATOM     18  CA  ARG    18      66.130   1.618  15.325  1.00 25.00           C
ATOM     19  CA  GLU    19      69.060   0.159  17.314  1.00 25.00           C
ATOM     20  CA  GLU    20      70.609   3.647  17.637  1.00 25.00           C
ATOM     21  CA  SER    21      67.261   5.048  18.861  1.00 25.00           C
ATOM     22  CA  ILE    22      66.994   2.227  21.437  1.00 25.00           C
ATOM     23  CA  ARG    23      70.554   2.959  22.644  1.00 25.00           C
ATOM     24  CA  ARG    24      69.704   6.679  22.973  1.00 25.00           C
ATOM     25  CA  PHE    25      66.559   5.809  24.977  1.00 25.00           C
ATOM     26  CA  LYS    26      68.621   3.544  27.277  1.00 25.00           C
ATOM     27  CA  ALA    27      71.170   6.355  27.798  1.00 25.00           C
ATOM     28  CA  ILE    28      68.957   7.741  30.541  1.00 25.00           C
ATOM     29  CA  GLY    29      69.738   4.681  32.662  1.00 25.00           C
ATOM     30  CA  VAL    30      66.321   3.286  31.900  1.00 25.00           C
ATOM     31  CA  ALA    31      64.203   0.175  31.486  1.00 25.00           C
ATOM     32  CA  ASP    32      61.626  -2.328  30.158  1.00 25.00           C
ATOM     33  CA  ILE    33      59.246   0.545  29.293  1.00 25.00           C
ATOM     34  CA  GLU    34      62.074   2.370  27.463  1.00 25.00           C
ATOM     35  CA  GLU    35      62.896  -0.817  25.505  1.00 25.00           C
ATOM     36  CA  MET    36      59.207  -1.215  24.555  1.00 25.00           C
ATOM     37  CA  LEU    37      59.090   2.429  23.385  1.00 25.00           C
ATOM     38  CA  ASP    38      56.448   3.213  25.964  1.00 25.00           C
ATOM     39  CA  PRO    39      54.698   0.742  23.605  1.00 25.00           C
ATOM     40  CA  TYR    40      51.727  -1.629  24.073  1.00 25.00           C
ATOM     41  CA  LEU    41      50.507   0.448  27.051  1.00 25.00           C
ATOM     42  CA  GLN    42      50.796   3.649  24.968  1.00 25.00           C
ATOM     43  CA  LYS    43      48.808   2.012  22.132  1.00 25.00           C
ATOM     44  CA  GLY    44      46.104   0.931  24.619  1.00 25.00           C
ATOM     45  CA  LEU    45      45.924   4.495  26.010  1.00 25.00           C
ATOM     46  CA  PHE    46      45.584   5.889  22.459  1.00 25.00           C
ATOM     47  CA  LEU    47      42.775   3.392  21.720  1.00 25.00           C
ATOM     48  CA  ASP    48      40.983   4.417  24.946  1.00 25.00           C
ATOM     49  CA  LEU    49      41.308   8.110  23.982  1.00 25.00           C
ATOM     50  CA  GLU    50      39.880   7.354  20.510  1.00 25.00           C
ATOM     51  CA  SER    51      37.917  10.600  21.217  1.00 25.00           C
ATOM     52  CA  GLY    52      41.128  12.687  21.547  1.00 25.00           C
ATOM     53  CA  ARG    53      42.339  15.807  23.414  1.00 25.00           C
ATOM     54  CA  LYS    54      45.934  14.645  23.604  1.00 25.00           C
ATOM     55  CA  SER    55      48.488  17.431  23.125  1.00 25.00           C
ATOM     56  CA  GLU    56      51.806  15.581  23.598  1.00 25.00           C
ATOM     57  CA  GLU    57      51.559  16.223  27.365  1.00 25.00           C
ATOM     58  CA  GLU    58      48.868  13.514  27.675  1.00 25.00           C
ATOM     59  CA  PHE    59      51.082  11.060  25.738  1.00 25.00           C
ATOM     60  CA  ARG    60      54.034  11.869  28.039  1.00 25.00           C
ATOM     61  CA  THR    61      51.827  11.288  31.115  1.00 25.00           C
ATOM     62  CA  GLU    62      50.672   7.929  29.683  1.00 25.00           C
ATOM     63  CA  LEU    63      54.312   6.924  29.043  1.00 25.00           C
ATOM     64  CA  SER    64      55.234   7.879  32.636  1.00 25.00           C
ATOM     65  CA  ARG    65      52.305   5.800  33.966  1.00 25.00           C
ATOM     66  CA  TYR    66      53.432   2.814  31.849  1.00 25.00           C
ATOM     67  CA  ILE    67      57.001   3.177  33.192  1.00 25.00           C
ATOM     68  CA  GLY    68      56.029   3.632  36.837  1.00 25.00           C
ATOM     69  CA  LYS    69      57.552   7.148  37.106  1.00 25.00           C
ATOM     70  CA  GLU    70      60.865   6.681  38.944  1.00 25.00           C
ATOM     71  CA  LEU    71      62.162   9.310  36.524  1.00 25.00           C
ATOM     72  CA  THR    72      62.375  12.964  35.681  1.00 25.00           C
ATOM     73  CA  TYR    73      61.060  12.486  32.184  1.00 25.00           C
ATOM     74  CA  GLN    74      62.732  15.565  30.636  1.00 25.00           C
ATOM     75  CA  GLN    75      65.695  13.418  29.504  1.00 25.00           C
ATOM     76  CA  VAL    76      63.289  10.880  27.942  1.00 25.00           C
ATOM     77  CA  TYR    77      61.457  13.703  26.115  1.00 25.00           C
ATOM     78  CA  ASP    78      64.793  15.056  24.809  1.00 25.00           C
ATOM     79  CA  ALA    79      65.762  11.558  23.588  1.00 25.00           C
ATOM     80  CA  LEU    80      62.384  11.214  21.815  1.00 25.00           C
ATOM     81  CA  LEU    81      62.885  14.627  20.149  1.00 25.00           C
ATOM     82  CA  GLY    82      66.384  13.580  18.997  1.00 25.00           C
ATOM     83  CA  PHE    83      64.963  10.326  17.561  1.00 25.00           C
TER
END
