
#######################################################
#                                                     #
#                        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 T0379TS393_1-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS393_1-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          4.38     4.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23        17 - 39          1.91     6.63
  LCS_AVERAGE:     31.40

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        54 - 68          0.94     7.21
  LONGEST_CONTINUOUS_SEGMENT:    15        55 - 69          0.76     8.48
  LCS_AVERAGE:     18.04

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     14   23   64     4   14   16   22   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     R      18     R      18     14   23   64    11   14   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      19     E      19     14   23   64    11   14   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      20     E      20     14   23   64    11   14   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     S      21     S      21     14   23   64    11   14   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     I      22     I      22     14   23   64    11   14   16   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     R      23     R      23     14   23   64    11   14   16   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     R      24     R      24     14   23   64    11   14   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     F      25     F      25     14   23   64    11   14   16   22   28   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     K      26     K      26     14   23   64    11   14   16   22   26   31   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     A      27     A      27     14   23   64    11   14   16   22   26   32   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     I      28     I      28     14   23   64     5   14   16   22   26   30   31   43   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     G      29     G      29     14   23   64     4    9   16   22   26   30   31   34   45   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     V      30     V      30     14   23   64     4    7   16   22   26   30   31   40   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     A      31     A      31     12   23   64     3    8   14   22   26   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     D      32     D      32      7   23   64     6    6    9   14   20   28   31   39   42   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     I      33     I      33      7   23   64     6    8   14   22   26   30   39   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      34     E      34      7   23   64     6    6   11   18   26   30   31   42   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      35     E      35      7   23   64     6    6    9   18   22   30   31   36   40   45   50   57   60   62   63   63   64   64   64   64 
LCS_GDT     M      36     M      36      7   23   64     6    8   14   22   26   30   32   43   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      37     L      37      7   23   64     6    6    9   17   25   30   31   42   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     D      38     D      38      7   23   64     3    3   10   18   22   30   31   36   40   49   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     P      39     P      39      4   23   64     0    3   13   20   26   30   31   34   40   44   50   57   60   62   63   63   64   64   64   64 
LCS_GDT     K      43     K      43      0   12   64     0    0   14   19   25   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     G      44     G      44      9   12   64     7   10   10   12   18   21   33   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      45     L      45      9   12   64     7   10   10   21   26   32   39   44   47   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     F      46     F      46      9   12   64     7   10   10   10   14   20   22   24   27   36   46   55   59   62   63   63   64   64   64   64 
LCS_GDT     L      47     L      47      9   12   64     7   10   10   10   14   20   22   24   27   43   53   57   60   62   63   63   64   64   64   64 
LCS_GDT     D      48     D      48      9   12   64     7   10   10   10   14   20   29   38   47   49   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      49     L      49      9   12   64     7   10   10   10   11   19   22   24   25   26   45   54   59   62   63   63   64   64   64   64 
LCS_GDT     E      50     E      50      9   12   64     7   10   10   10   11   13   21   23   25   26   26   32   46   52   61   63   64   64   64   64 
LCS_GDT     S      51     S      51      9   12   64     3   10   10   10   14   19   22   24   25   26   33   46   56   61   63   63   64   64   64   64 
LCS_GDT     G      52     G      52      9   12   64     3   10   10   10   14   20   22   24   35   46   53   57   60   62   63   63   64   64   64   64 
LCS_GDT     R      53     R      53      3   17   64     3    3    5    9   11   16   24   42   43   48   53   57   60   62   63   63   64   64   64   64 
LCS_GDT     K      54     K      54     15   17   64     4   10   12   21   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     S      55     S      55     15   17   64     4    9   14   21   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      56     E      56     15   17   64     9   13   14   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      57     E      57     15   17   64    10   13   14   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      58     E      58     15   17   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     F      59     F      59     15   17   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     R      60     R      60     15   17   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     T      61     T      61     15   17   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      62     E      62     15   22   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      63     L      63     15   22   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     S      64     S      64     15   22   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     R      65     R      65     15   22   64    10   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     Y      66     Y      66     15   22   64    10   13   14   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     I      67     I      67     15   22   64     9   13   14   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     G      68     G      68     15   22   64     6   13   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     K      69     K      69     15   22   64     4   11   14   21   28   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     E      70     E      70      5   22   64     3    6   13   20   27   32   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      71     L      71      5   22   64     3    6   14   20   24   32   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     T      72     T      72     12   22   64     3    5   14   20   24   32   39   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     Y      73     Y      73     12   22   64     5    8   11   19   22   29   35   40   46   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     Q      74     Q      74     12   22   64     8    9   14   20   27   32   39   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     Q      75     Q      75     12   22   64     7    9   14   20   27   32   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     V      76     V      76     12   22   64    11   14   16   21   28   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     Y      77     Y      77     12   22   64     8   10   16   22   28   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     D      78     D      78     12   22   64     8    9   16   23   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     A      79     A      79     12   22   64     8   14   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      80     L      80     12   22   64     8    9   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     L      81     L      81     12   22   64     8    9   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     G      82     G      82     12   22   64     8    9   17   24   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_GDT     F      83     F      83     12   22   64     3    8   16   23   29   33   40   44   48   51   54   57   60   62   63   63   64   64   64   64 
LCS_AVERAGE  LCS_A:  49.81  (  18.04   31.40  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     11     14     17     24     29     33     40     44     48     51     54     57     60     62     63     63     64     64     64     64 
GDT PERCENT_CA  17.19  21.88  26.56  37.50  45.31  51.56  62.50  68.75  75.00  79.69  84.38  89.06  93.75  96.88  98.44  98.44 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.23   0.54   1.13   1.42   1.65   1.83   2.32   2.52   2.93   3.06   3.28   3.57   3.85   4.07   4.20   4.20   4.38   4.38   4.38   4.38
GDT RMS_ALL_CA   5.98   6.13   5.33   5.18   5.11   5.15   4.96   4.97   4.68   4.70   4.63   4.53   4.44   4.41   4.39   4.39   4.38   4.38   4.38   4.38

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          2.563
LGA    R      18      R      18          1.053
LGA    E      19      E      19          0.960
LGA    E      20      E      20          1.053
LGA    S      21      S      21          0.886
LGA    I      22      I      22          1.514
LGA    R      23      R      23          1.783
LGA    R      24      R      24          1.381
LGA    F      25      F      25          2.058
LGA    K      26      K      26          3.220
LGA    A      27      A      27          3.153
LGA    I      28      I      28          4.139
LGA    G      29      G      29          5.784
LGA    V      30      V      30          5.287
LGA    A      31      A      31          3.384
LGA    D      32      D      32          6.591
LGA    I      33      I      33          3.866
LGA    E      34      E      34          5.980
LGA    E      35      E      35          8.438
LGA    M      36      M      36          5.336
LGA    L      37      L      37          6.157
LGA    D      38      D      38          8.429
LGA    P      39      P      39          8.875
LGA    K      43      K      43          2.588
LGA    G      44      G      44          4.778
LGA    L      45      L      45          3.875
LGA    F      46      F      46          8.498
LGA    L      47      L      47          9.254
LGA    D      48      D      48          6.401
LGA    L      49      L      49          9.310
LGA    E      50      E      50         13.182
LGA    S      51      S      51         11.557
LGA    G      52      G      52          8.695
LGA    R      53      R      53          5.979
LGA    K      54      K      54          3.508
LGA    S      55      S      55          3.242
LGA    E      56      E      56          2.952
LGA    E      57      E      57          3.387
LGA    E      58      E      58          2.913
LGA    F      59      F      59          2.037
LGA    R      60      R      60          2.577
LGA    T      61      T      61          2.824
LGA    E      62      E      62          2.538
LGA    L      63      L      63          1.857
LGA    S      64      S      64          2.161
LGA    R      65      R      65          2.401
LGA    Y      66      Y      66          2.094
LGA    I      67      I      67          2.399
LGA    G      68      G      68          2.188
LGA    K      69      K      69          3.331
LGA    E      70      E      70          3.204
LGA    L      71      L      71          3.357
LGA    T      72      T      72          3.756
LGA    Y      73      Y      73          4.912
LGA    Q      74      Q      74          3.881
LGA    Q      75      Q      75          3.344
LGA    V      76      V      76          1.812
LGA    Y      77      Y      77          1.904
LGA    D      78      D      78          1.319
LGA    A      79      A      79          1.150
LGA    L      80      L      80          1.320
LGA    L      81      L      81          1.265
LGA    G      82      G      82          1.476
LGA    F      83      F      83          2.032

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67   64    4.0     44    2.52    56.641    53.031     1.679

LGA_LOCAL      RMSD =  2.521  Number of atoms =   44  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.817  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  4.384  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.985980 * X  +  -0.124154 * Y  +  -0.111484 * Z  +  58.628029
  Y_new =  -0.120261 * X  +  -0.991894 * Y  +   0.041024 * Z  +   7.798385
  Z_new =  -0.115674 * X  +  -0.027042 * Y  +  -0.992919 * Z  +   8.189504 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.114365    0.027228  [ DEG:  -178.4400      1.5600 ]
  Theta =   0.115933    3.025660  [ DEG:     6.6425    173.3575 ]
  Phi   =  -0.121371    3.020222  [ DEG:    -6.9540    173.0460 ]
 
# 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: T0379TS393_1-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0379TS393_1-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   44   2.52  53.031     4.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS393_1-D2
PFRMAT TS
TARGET T0379
MODEL 1
PARENT N/A
ATOM     17  CA  ASN    17      66.139   6.517  12.825  1.00 25.00           C
ATOM     18  CA  ARG    18      66.074   3.867  15.605  1.00 25.00           C
ATOM     19  CA  GLU    19      69.618   2.845  16.636  1.00 25.00           C
ATOM     20  CA  GLU    20      70.267   6.369  17.990  1.00 25.00           C
ATOM     21  CA  SER    21      66.993   6.235  19.973  1.00 25.00           C
ATOM     22  CA  ILE    22      67.978   2.828  21.416  1.00 25.00           C
ATOM     23  CA  ARG    23      71.406   4.213  22.417  1.00 25.00           C
ATOM     24  CA  ARG    24      69.727   7.209  24.112  1.00 25.00           C
ATOM     25  CA  PHE    25      67.379   4.852  26.008  1.00 25.00           C
ATOM     26  CA  LYS    26      70.370   2.744  27.139  1.00 25.00           C
ATOM     27  CA  ALA    27      72.175   5.902  28.335  1.00 25.00           C
ATOM     28  CA  ILE    28      70.310   7.967  30.949  1.00 25.00           C
ATOM     29  CA  GLY    29      70.272   4.921  33.225  1.00 25.00           C
ATOM     30  CA  VAL    30      67.186   3.873  31.356  1.00 25.00           C
ATOM     31  CA  ALA    31      65.924   0.329  31.162  1.00 25.00           C
ATOM     32  CA  ASP    32      62.445   1.911  31.410  1.00 25.00           C
ATOM     33  CA  ILE    33      62.381   2.421  27.614  1.00 25.00           C
ATOM     34  CA  GLU    34      63.388  -1.236  27.081  1.00 25.00           C
ATOM     35  CA  GLU    35      60.608  -2.373  29.458  1.00 25.00           C
ATOM     36  CA  MET    36      58.071  -0.218  27.562  1.00 25.00           C
ATOM     37  CA  LEU    37      59.237  -1.726  24.241  1.00 25.00           C
ATOM     38  CA  ASP    38      56.217  -4.029  24.497  1.00 25.00           C
ATOM     39  CA  PRO    39      54.075  -1.338  22.867  1.00 25.00           C
ATOM     40  CA  TYR    40      51.799  -0.955  25.922  1.00 25.00           C
ATOM     41  CA  LEU    41      52.214   2.850  25.786  1.00 25.00           C
ATOM     42  CA  GLN    42      51.344   2.836  22.056  1.00 25.00           C
ATOM     43  CA  LYS    43      48.227   0.726  22.767  1.00 25.00           C
ATOM     44  CA  GLY    44      47.177   3.164  25.528  1.00 25.00           C
ATOM     45  CA  LEU    45      47.655   6.117  23.138  1.00 25.00           C
ATOM     46  CA  PHE    46      45.536   4.344  20.484  1.00 25.00           C
ATOM     47  CA  LEU    47      42.791   3.697  23.075  1.00 25.00           C
ATOM     48  CA  ASP    48      42.860   7.385  24.106  1.00 25.00           C
ATOM     49  CA  LEU    49      42.579   8.442  20.436  1.00 25.00           C
ATOM     50  CA  GLU    50      39.604   6.078  19.958  1.00 25.00           C
ATOM     51  CA  SER    51      37.804   8.412  22.286  1.00 25.00           C
ATOM     52  CA  GLY    52      39.256  11.936  22.797  1.00 25.00           C
ATOM     53  CA  ARG    53      41.106  14.970  24.225  1.00 25.00           C
ATOM     54  CA  LYS    54      44.483  13.220  23.646  1.00 25.00           C
ATOM     55  CA  SER    55      46.212  16.505  24.328  1.00 25.00           C
ATOM     56  CA  GLU    56      49.906  15.869  25.246  1.00 25.00           C
ATOM     57  CA  GLU    57      48.755  15.279  28.849  1.00 25.00           C
ATOM     58  CA  GLU    58      47.529  11.774  27.911  1.00 25.00           C
ATOM     59  CA  PHE    59      50.896  11.016  26.249  1.00 25.00           C
ATOM     60  CA  ARG    60      52.740  12.218  29.382  1.00 25.00           C
ATOM     61  CA  THR    61      50.522   9.993  31.572  1.00 25.00           C
ATOM     62  CA  GLU    62      51.236   6.998  29.295  1.00 25.00           C
ATOM     63  CA  LEU    63      54.996   7.697  29.513  1.00 25.00           C
ATOM     64  CA  SER    64      54.764   7.884  33.331  1.00 25.00           C
ATOM     65  CA  ARG    65      52.874   4.554  33.404  1.00 25.00           C
ATOM     66  CA  TYR    66      55.550   2.958  31.178  1.00 25.00           C
ATOM     67  CA  ILE    67      58.300   4.276  33.495  1.00 25.00           C
ATOM     68  CA  GLY    68      56.433   2.366  36.248  1.00 25.00           C
ATOM     69  CA  LYS    69      57.081   5.386  38.372  1.00 25.00           C
ATOM     70  CA  GLU    70      60.582   6.952  38.669  1.00 25.00           C
ATOM     71  CA  LEU    71      62.077   8.707  35.645  1.00 25.00           C
ATOM     72  CA  THR    72      62.205  12.509  35.708  1.00 25.00           C
ATOM     73  CA  TYR    73      62.428  12.965  31.996  1.00 25.00           C
ATOM     74  CA  GLN    74      65.785  14.313  30.739  1.00 25.00           C
ATOM     75  CA  GLN    75      66.576  10.925  29.138  1.00 25.00           C
ATOM     76  CA  VAL    76      63.143  10.899  27.439  1.00 25.00           C
ATOM     77  CA  TYR    77      63.744  14.443  26.118  1.00 25.00           C
ATOM     78  CA  ASP    78      67.166  13.385  24.763  1.00 25.00           C
ATOM     79  CA  ALA    79      65.575  10.355  23.043  1.00 25.00           C
ATOM     80  CA  LEU    80      62.905  12.613  21.482  1.00 25.00           C
ATOM     81  CA  LEU    81      65.622  15.005  20.233  1.00 25.00           C
ATOM     82  CA  GLY    82      67.548  12.064  18.715  1.00 25.00           C
ATOM     83  CA  PHE    83      64.360  10.840  16.979  1.00 25.00           C
TER
END
