
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0358TS168_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS168_3-D1.T0358_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:    47        24 - 70          4.94    11.45
  LCS_AVERAGE:     63.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        13 - 24          1.84    15.57
  LONGEST_CONTINUOUS_SEGMENT:    12        14 - 25          1.65    14.97
  LCS_AVERAGE:     13.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        14 - 24          0.28    14.98
  LCS_AVERAGE:      8.83

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:   65
LCS_GDT     G      10     G      10      3    3   18     3    3    3    3    4    5    6    8   10   15   18   22   25   30   33   35   36   37   40   42 
LCS_GDT     P      11     P      11      3    5   18     3    3    3    5    5    7   10   12   14   16   17   18   19   20   23   24   31   35   37   42 
LCS_GDT     F      12     F      12      3    5   20     3    3    3    5    6    7   11   13   15   17   17   19   22   22   24   32   34   37   40   42 
LCS_GDT     T      13     T      13      3   12   25     3    3    3    5    7   11   13   14   15   17   19   20   22   27   28   32   34   37   40   42 
LCS_GDT     R      14     R      14     11   12   29    11   11   11   14   16   18   18   19   19   20   21   26   27   28   29   30   34   37   39   42 
LCS_GDT     R      15     R      15     11   12   29    11   11   11   14   16   18   18   19   19   20   22   26   27   28   29   30   31   34   35   37 
LCS_GDT     Q      16     Q      16     11   12   29    11   11   11   14   16   18   18   19   19   20   22   26   27   28   29   32   34   37   40   42 
LCS_GDT     A      17     A      17     11   12   29    11   11   11   14   16   18   18   19   19   20   23   26   27   30   33   35   36   37   40   42 
LCS_GDT     Q      18     Q      18     11   12   29    11   11   11   14   16   18   18   19   19   20   23   26   27   28   29   32   34   37   40   42 
LCS_GDT     A      19     A      19     11   12   29    11   11   11   14   16   18   18   19   19   20   23   26   27   28   29   32   34   37   40   42 
LCS_GDT     V      20     V      20     11   12   29    11   11   11   14   16   18   18   19   21   23   24   26   29   31   33   35   36   37   42   45 
LCS_GDT     T      21     T      21     11   12   29    11   11   11   11   14   18   18   19   21   23   24   26   29   31   33   35   36   37   40   43 
LCS_GDT     T      22     T      22     11   12   29    11   11   11   12   16   18   18   19   21   23   24   26   29   31   32   33   35   37   40   42 
LCS_GDT     T      23     T      23     11   12   34    11   11   11   11   16   18   18   19   21   23   24   26   29   33   33   35   40   43   46   48 
LCS_GDT     Y      24     Y      24     11   12   47    11   11   11   11   11   16   18   19   21   27   29   33   37   43   44   46   46   47   47   48 
LCS_GDT     S      25     S      25      3   12   47     3    3    4    7    9   12   13   16   23   27   33   39   41   43   45   46   46   47   47   48 
LCS_GDT     N      26     N      26      4    7   47     3    6    7    8   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     I      27     I      27      4    7   47     3    4    6    9   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     T      28     T      28      4    7   47     3    6    7    9   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     L      29     L      29      4    7   47     3    6    7    8   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     E      30     E      30      4    7   47     3    4    6    9    9   12   17   22   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     D      31     D      31      3    7   47     3    3    5    7    9   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     D      32     D      32      3    7   47     3    3    6    7   10   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     Q      33     Q      33      3    7   47     3    6    7    8   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     G      34     G      34      3    6   47     3    4    6    8    9   13   16   21   25   28   35   40   42   43   45   46   46   47   47   48 
LCS_GDT     S      35     S      35      4    6   47     3    5    5    7    9   14   18   21   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     H      36     H      36      4    6   47     3    5    5    7    9   12   17   21   26   32   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     F      37     F      37      4    9   47     3    5    6    7    9   12   17   20   26   30   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     R      38     R      38      4    9   47     3    5    6    8    9   11   17   20   24   26   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     L      39     L      39      3    9   47     3    4    6    8    9   14   17   21   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     V      40     V      40      4    9   47     3    3    6    8   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     V      41     V      41      4    9   47     3    4    6    7   10   14   17   21   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     R      42     R      42      4    9   47     3    4    6    7   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     D      43     D      43      4    9   47     3    4    6    8   10   14   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     T      44     T      44      4    9   47     3    3    6    7   10   14   17   21   26   31   37   40   42   43   45   46   46   47   47   48 
LCS_GDT     E      45     E      45      4    9   47     3    4    6    7    9   14   16   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     G      46     G      46      4    7   47     3    3    5    6    7    8   13   21   22   26   36   40   42   43   45   46   46   47   47   48 
LCS_GDT     R      47     R      47      4    7   47     3    4    5    7   10   14   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     M      48     M      48      4    7   47     3    4    6    8   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     V      49     V      49      5    9   47     3    4    6    9    9   11   12   18   24   26   33   40   42   43   45   46   46   47   47   48 
LCS_GDT     W      50     W      50      5    9   47     3    4    6    9    9   11   14   20   28   31   36   40   42   43   45   46   46   47   47   48 
LCS_GDT     R      51     R      51      5    9   47     3    4    6    9   10   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     A      52     A      52      5    9   47     3    4    6    9   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     W      53     W      53      5    9   47     3    3    6    9   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     N      54     N      54      6    9   47     3    4    6    9   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     F      55     F      55      6    9   47     3    5    6    7   10   14   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     E      56     E      56      6    9   47     3    5    6    7    8   14   16   21   28   32   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     P      57     P      57      6    9   47     0    5    6    7    9   12   15   21   21   24   33   40   42   43   45   46   46   47   47   48 
LCS_GDT     D      58     D      58      6    8   47     3    5    6    7    9   11   15   21   21   23   27   31   40   42   44   45   46   47   47   48 
LCS_GDT     A      59     A      59      6    8   47     3    5    6    6    9   14   16   21   28   32   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     G      60     G      60      3    9   47     3    3    5    6    9   14   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     E      61     E      61      8    9   47     8   10   11   14   16   18   18   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     G      62     G      62      8    9   47     8   10   11   14   16   18   18   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     L      63     L      63      8    9   47     8   10   11   14   16   18   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     N      64     N      64      8    9   47     8   10   11   14   16   18   18   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     R      65     R      65      8    9   47     8   10   11   14   16   18   18   19   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     Y      66     Y      66      8    9   47     8   10   11   14   16   18   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     I      67     I      67      8    9   47     8   10   11   14   16   18   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     R      68     R      68      8    9   47     8   10   11   14   16   18   18   19   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     T      69     T      69      3    9   47     3    3    5    8   13   16   20   24   28   33   38   40   42   43   45   46   46   47   47   48 
LCS_GDT     S      70     S      70      3    5   47     3    4    5    7   10   16   20   24   28   33   38   39   42   43   45   46   46   47   47   48 
LCS_GDT     G      71     G      71      4    5   46     3    4    5    7    7   10   11   16   17   23   26   28   31   36   39   42   44   46   47   48 
LCS_GDT     I      72     I      72      4    5   22     3    4    4    5    7   10   11   12   14   14   16   22   25   32   34   36   41   43   46   47 
LCS_GDT     R      73     R      73      4    5   17     3    4    5    7    7   10   11   12   13   14   15   15   20   20   31   34   40   43   45   47 
LCS_GDT     T      74     T      74      4    5   17     0    4    4    4    7    8   10   12   13   14   15   15   20   20   21   32   39   43   45   47 
LCS_AVERAGE  LCS_A:  28.54  (   8.83   13.18   63.60 )

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     11     11     14     16     18     20     24     28     33     38     40     42     43     45     46     46     47     47     48 
GDT PERCENT_CA  16.92  16.92  16.92  21.54  24.62  27.69  30.77  36.92  43.08  50.77  58.46  61.54  64.62  66.15  69.23  70.77  70.77  72.31  72.31  73.85
GDT RMS_LOCAL    0.28   0.28   0.28   1.07   1.39   1.61   2.69   2.98   3.29   3.61   3.99   4.18   4.28   4.37   4.62   4.78   4.78   4.94   4.94   5.16
GDT RMS_ALL_CA  14.98  14.98  14.98  15.52  15.34  15.31  10.89  11.29  11.12  11.27  11.39  11.42  11.39  11.38  11.42  11.33  11.33  11.45  11.45  11.41

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10         21.746
LGA    P      11      P      11         23.374
LGA    F      12      F      12         22.890
LGA    T      13      T      13         25.114
LGA    R      14      R      14         23.485
LGA    R      15      R      15         26.624
LGA    Q      16      Q      16         21.444
LGA    A      17      A      17         17.438
LGA    Q      18      Q      18         22.400
LGA    A      19      A      19         21.939
LGA    V      20      V      20         15.167
LGA    T      21      T      21         15.849
LGA    T      22      T      22         20.000
LGA    T      23      T      23         15.716
LGA    Y      24      Y      24         10.185
LGA    S      25      S      25          7.476
LGA    N      26      N      26          1.249
LGA    I      27      I      27          1.410
LGA    T      28      T      28          2.132
LGA    L      29      L      29          2.999
LGA    E      30      E      30          4.036
LGA    D      31      D      31          3.247
LGA    D      32      D      32          2.940
LGA    Q      33      Q      33          2.059
LGA    G      34      G      34          6.357
LGA    S      35      S      35          4.783
LGA    H      36      H      36          5.441
LGA    F      37      F      37          5.539
LGA    R      38      R      38          5.859
LGA    L      39      L      39          4.564
LGA    V      40      V      40          2.109
LGA    V      41      V      41          5.380
LGA    R      42      R      42          3.422
LGA    D      43      D      43          5.567
LGA    T      44      T      44          8.936
LGA    E      45      E      45          7.110
LGA    G      46      G      46          9.528
LGA    R      47      R      47          5.416
LGA    M      48      M      48          2.939
LGA    V      49      V      49          7.165
LGA    W      50      W      50          5.891
LGA    R      51      R      51          1.866
LGA    A      52      A      52          2.166
LGA    W      53      W      53          3.106
LGA    N      54      N      54          3.773
LGA    F      55      F      55          3.487
LGA    E      56      E      56          7.406
LGA    P      57      P      57         11.264
LGA    D      58      D      58         12.464
LGA    A      59      A      59          7.514
LGA    G      60      G      60          3.140
LGA    E      61      E      61          3.845
LGA    G      62      G      62          3.978
LGA    L      63      L      63          3.120
LGA    N      64      N      64          3.982
LGA    R      65      R      65          4.883
LGA    Y      66      Y      66          3.148
LGA    I      67      I      67          3.275
LGA    R      68      R      68          5.525
LGA    T      69      T      69          3.292
LGA    S      70      S      70          2.817
LGA    G      71      G      71          8.494
LGA    I      72      I      72         12.140
LGA    R      73      R      73         13.691
LGA    T      74      T      74         14.992

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     24    2.98    36.538    31.562     0.779

LGA_LOCAL      RMSD =  2.983  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.338  Number of atoms =   65 
Std_ALL_ATOMS  RMSD = 10.240  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.746206 * X  +   0.487737 * Y  +   0.453090 * Z  +  -0.652902
  Y_new =   0.265988 * X  +   0.405480 * Y  +  -0.874549 * Z  +  -1.513923
  Z_new =  -0.610268 * X  +   0.773110 * Y  +   0.172839 * Z  +   8.096195 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.350850   -1.790743  [ DEG:    77.3980   -102.6020 ]
  Theta =   0.656399    2.485193  [ DEG:    37.6089    142.3911 ]
  Phi   =   0.342413   -2.799180  [ DEG:    19.6188   -160.3812 ]
 
# 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: T0358TS168_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS168_3-D1.T0358_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   65   65   4.0   24   2.98  31.562    10.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS168_3-D1
PFRMAT TS
TARGET T0358
MODEL 3
PARENT N/A
ATOM     10  CA  GLY    10      -5.632   9.568  18.611  1.00 25.00           C
ATOM     11  CA  PRO    11      -7.226   6.248  19.357  1.00 25.00           C
ATOM     12  CA  PHE    12      -6.326   3.974  16.492  1.00 25.00           C
ATOM     13  CA  THR    13      -7.836   6.780  14.409  1.00 25.00           C
ATOM     14  CA  ARG    14      -7.101   9.142  11.519  1.00 25.00           C
ATOM     15  CA  ARG    15     -10.242   7.805   9.784  1.00 25.00           C
ATOM     16  CA  GLN    16      -8.200   7.009   6.644  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.597   5.175   8.773  1.00 25.00           C
ATOM     18  CA  GLN    18      -8.373   3.161  10.477  1.00 25.00           C
ATOM     19  CA  ALA    19      -9.842   2.247   7.060  1.00 25.00           C
ATOM     20  CA  VAL    20      -6.385   1.132   5.845  1.00 25.00           C
ATOM     21  CA  THR    21      -5.947  -1.014   8.987  1.00 25.00           C
ATOM     22  CA  THR    22      -9.384  -2.601   8.413  1.00 25.00           C
ATOM     23  CA  THR    23      -8.458  -3.351   4.774  1.00 25.00           C
ATOM     24  CA  TYR    24      -5.171  -4.951   5.915  1.00 25.00           C
ATOM     25  CA  SER    25      -4.787  -7.040   2.817  1.00 25.00           C
ATOM     26  CA  ASN    26      -4.398  -5.874  -0.828  1.00 25.00           C
ATOM     27  CA  ILE    27      -1.749  -3.262  -1.739  1.00 25.00           C
ATOM     28  CA  THR    28      -2.879   0.205  -2.967  1.00 25.00           C
ATOM     29  CA  LEU    29      -4.083   3.781  -3.095  1.00 25.00           C
ATOM     30  CA  GLU    30      -1.473   5.724  -5.172  1.00 25.00           C
ATOM     31  CA  ASP    31      -4.402   7.211  -7.153  1.00 25.00           C
ATOM     32  CA  ASP    32      -4.725   9.764  -9.878  1.00 25.00           C
ATOM     33  CA  GLN    33      -3.911  12.685  -7.510  1.00 25.00           C
ATOM     34  CA  GLY    34      -1.786  13.442  -4.449  1.00 25.00           C
ATOM     35  CA  SER    35       0.327  10.354  -3.755  1.00 25.00           C
ATOM     36  CA  HIS    36      -0.453   8.637  -0.518  1.00 25.00           C
ATOM     37  CA  PHE    37       0.276   4.936  -0.193  1.00 25.00           C
ATOM     38  CA  ARG    38       0.460   1.277   0.922  1.00 25.00           C
ATOM     39  CA  LEU    39      -2.692  -0.218   2.482  1.00 25.00           C
ATOM     40  CA  VAL    40      -6.141  -0.523   0.772  1.00 25.00           C
ATOM     41  CA  VAL    41      -9.061  -2.759  -0.230  1.00 25.00           C
ATOM     42  CA  ARG    42      -9.817  -6.340   0.814  1.00 25.00           C
ATOM     43  CA  ASP    43     -13.514  -6.779   1.484  1.00 25.00           C
ATOM     44  CA  THR    44     -16.370  -6.251  -0.996  1.00 25.00           C
ATOM     45  CA  GLU    45     -18.672  -5.886   1.993  1.00 25.00           C
ATOM     46  CA  GLY    46     -20.156  -2.575   0.793  1.00 25.00           C
ATOM     47  CA  ARG    47     -16.734  -1.003   1.601  1.00 25.00           C
ATOM     48  CA  MET    48     -13.005  -1.044   2.511  1.00 25.00           C
ATOM     49  CA  VAL    49     -10.878   1.832   1.186  1.00 25.00           C
ATOM     50  CA  TRP    50      -7.862   4.054   2.039  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.112   4.630   2.319  1.00 25.00           C
ATOM     52  CA  ALA    52      -2.040   4.023   5.459  1.00 25.00           C
ATOM     53  CA  TRP    53       0.208   6.956   4.686  1.00 25.00           C
ATOM     54  CA  ASN    54       3.645   6.399   3.260  1.00 25.00           C
ATOM     55  CA  PHE    55       6.447   7.425   0.923  1.00 25.00           C
ATOM     56  CA  GLU    56       8.182   4.080   0.767  1.00 25.00           C
ATOM     57  CA  PRO    57       9.890   1.332  -1.309  1.00 25.00           C
ATOM     58  CA  ASP    58       7.751  -1.532  -2.706  1.00 25.00           C
ATOM     59  CA  ALA    59       5.255  -0.401  -0.068  1.00 25.00           C
ATOM     60  CA  GLY    60       7.569  -0.524   2.985  1.00 25.00           C
ATOM     61  CA  GLU    61       5.967   2.107   5.228  1.00 25.00           C
ATOM     62  CA  GLY    62       6.345   0.144   8.494  1.00 25.00           C
ATOM     63  CA  LEU    63       2.536  -0.026   8.862  1.00 25.00           C
ATOM     64  CA  ASN    64       2.219  -1.284   5.258  1.00 25.00           C
ATOM     65  CA  ARG    65       4.877  -3.959   5.934  1.00 25.00           C
ATOM     66  CA  TYR    66       3.010  -5.052   9.092  1.00 25.00           C
ATOM     67  CA  ILE    67      -0.261  -5.279   7.112  1.00 25.00           C
ATOM     68  CA  ARG    68       1.483  -7.388   4.431  1.00 25.00           C
ATOM     69  CA  THR    69       2.886  -9.709   7.134  1.00 25.00           C
ATOM     70  CA  SER    70       5.148 -11.851   5.003  1.00 25.00           C
ATOM     71  CA  GLY    71       7.848 -11.775   7.752  1.00 25.00           C
ATOM     72  CA  ILE    72       5.617 -12.159  10.802  1.00 25.00           C
ATOM     73  CA  ARG    73       6.465 -15.869  10.915  1.00 25.00           C
ATOM     74  CA  THR    74       8.940 -18.371  12.488  1.00 25.00           C
TER
END
