
#######################################################
#                                                     #
#                        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 T0358TS599_1-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS599_1-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:    36        21 - 56          4.97    14.21
  LONGEST_CONTINUOUS_SEGMENT:    36        22 - 57          4.90    13.91
  LONGEST_CONTINUOUS_SEGMENT:    36        23 - 58          4.96    13.48
  LCS_AVERAGE:     46.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        36 - 53          1.97    14.37
  LCS_AVERAGE:     20.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        12 - 24          0.93    19.60
  LCS_AVERAGE:     12.92

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      4   14   19     0    4    4    6    8   10   12   12   14   15   15   17   20   22   23   24   24   27   34   36 
LCS_GDT     P      11     P      11     10   14   19     3    5    9   12   13   14   14   14   15   16   17   17   20   22   23   24   26   28   33   36 
LCS_GDT     F      12     F      12     13   14   19     3    5    9   12   13   14   14   14   15   16   17   17   20   22   23   24   26   31   34   36 
LCS_GDT     T      13     T      13     13   14   19     5   11   12   12   13   14   14   14   15   16   17   17   20   22   23   24   26   28   29   30 
LCS_GDT     R      14     R      14     13   14   19     8   11   12   12   13   14   14   14   15   16   17   17   20   22   23   24   26   28   29   30 
LCS_GDT     R      15     R      15     13   14   19     8   11   12   12   13   14   14   14   15   16   17   17   20   22   23   24   26   28   29   30 
LCS_GDT     Q      16     Q      16     13   14   19     8   11   12   12   13   14   14   14   15   16   17   17   20   22   23   24   29   32   34   37 
LCS_GDT     A      17     A      17     13   14   19     8   11   12   12   13   14   14   14   15   16   17   17   20   22   23   24   28   32   34   37 
LCS_GDT     Q      18     Q      18     13   14   19     8   11   12   12   13   14   14   14   15   16   17   17   20   22   23   24   26   29   31   32 
LCS_GDT     A      19     A      19     13   14   19     8   11   12   12   13   14   14   14   15   16   17   17   22   22   28   30   34   36   37   38 
LCS_GDT     V      20     V      20     13   14   19     8   11   12   12   13   14   14   14   16   20   22   25   28   31   34   35   37   37   38   38 
LCS_GDT     T      21     T      21     13   14   36     8   11   12   12   13   14   14   14   15   19   22   24   26   31   33   35   37   37   38   38 
LCS_GDT     T      22     T      22     13   14   36     8   11   12   12   13   14   14   14   15   16   18   20   22   27   30   34   35   37   38   38 
LCS_GDT     T      23     T      23     13   14   36     8   11   12   12   13   14   14   14   16   20   23   27   30   32   34   35   37   37   38   38 
LCS_GDT     Y      24     Y      24     13   14   36     8   11   12   12   13   14   17   21   22   27   29   31   32   33   34   35   37   39   45   47 
LCS_GDT     S      25     S      25      4   14   36     3    4    4    5    8   18   20   23   25   28   29   31   32   33   34   35   41   44   45   47 
LCS_GDT     N      26     N      26      5   14   36     4    5    9   10   12   13   17   22   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     I      27     I      27      5   10   36     4    5    6    8    9   12   17   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     T      28     T      28      5   10   36     4    5    6    8    9   12   18   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     L      29     L      29      5   10   36     4    5    6    8    9   12   18   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     E      30     E      30      5   10   36     3    5    6    8    9   10   17   22   24   27   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     D      31     D      31      4   10   36     3    4    4    7    8   10   10   15   17   21   24   27   30   33   34   35   37   37   42   45 
LCS_GDT     D      32     D      32      4   10   36     3    3    4    5    7   10   12   17   21   25   28   31   32   33   34   37   41   44   45   47 
LCS_GDT     Q      33     Q      33      4   10   36     3    5    6    8    9   10   17   22   24   27   29   31   32   33   34   35   37   40   44   47 
LCS_GDT     G      34     G      34      3   10   36     3    3    6    7    8   11   17   22   24   27   29   31   32   33   34   35   37   44   45   47 
LCS_GDT     S      35     S      35      8   15   36     3    3    7   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     H      36     H      36      8   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     F      37     F      37      8   18   36     3    4    9   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     R      38     R      38      8   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     L      39     L      39      8   18   36     3    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     V      40     V      40      9   18   36     3    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     V      41     V      41      9   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     R      42     R      42      9   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     D      43     D      43      9   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   35   41   44   45   47 
LCS_GDT     T      44     T      44      9   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   35   38   44   45   47 
LCS_GDT     E      45     E      45      9   18   36     4    7    9   13   15   18   20   22   24   28   29   31   32   33   34   35   41   44   45   47 
LCS_GDT     G      46     G      46      9   18   36     4    7    9   13   15   18   20   22   24   28   29   31   32   33   34   35   41   44   45   47 
LCS_GDT     R      47     R      47      9   18   36     4    7   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     M      48     M      48      9   18   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     V      49     V      49      9   18   36     4    7    9   12   17   18   20   23   25   28   29   31   32   33   34   35   41   44   45   47 
LCS_GDT     W      50     W      50      9   18   36     4    5    9   10   14   18   20   23   25   28   29   31   32   33   34   35   41   44   45   47 
LCS_GDT     R      51     R      51      6   18   36     4    5   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     A      52     A      52      6   18   36     4    5    7   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     W      53     W      53      6   18   36     4    6   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     N      54     N      54      6    8   36     4    5    6    7   16   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     F      55     F      55      6    8   36     4    8   12   14   17   18   20   23   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     E      56     E      56      4    6   36     3    4    4    7    9   12   14   19   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     P      57     P      57      4    6   36     3    4    4    5    6   10   16   19   25   28   29   31   32   33   34   37   41   44   45   47 
LCS_GDT     D      58     D      58     11   11   36     4    5    8   11   11   12   14   16   19   22   23   24   27   31   33   37   41   44   45   47 
LCS_GDT     A      59     A      59     11   12   26     4   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     G      60     G      60     11   12   23     4   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     E      61     E      61     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     G      62     G      62     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     L      63     L      63     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     N      64     N      64     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     R      65     R      65     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     Y      66     Y      66     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     I      67     I      67     11   12   23     8   10   10   11   11   12   14   16   19   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     R      68     R      68     11   12   23     8   10   10   11   11   12   14   16   18   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     T      69     T      69      4   12   23     3    4    4    4    7    9   12   16   16   16   19   23   27   30   33   37   41   44   45   47 
LCS_GDT     S      70     S      70      4   12   23     3    4    4   10   11   11   12   16   17   19   22   24   26   30   33   37   41   44   45   47 
LCS_GDT     G      71     G      71      4    5   23     3    4    4    7    9   12   14   16   18   22   23   24   26   30   33   37   41   44   45   47 
LCS_GDT     I      72     I      72      3    5   23     2    3    3    4   10   12   14   16   19   22   23   24   26   30   33   35   36   37   39   41 
LCS_GDT     R      73     R      73      3    5   23     2    3    3    5   10   12   14   16   17   19   21   24   26   29   33   35   36   37   38   39 
LCS_GDT     T      74     T      74      3    4   23     2    3    3    3    4    5    5    6    7    8   12   18   19   25   29   32   34   35   37   38 
LCS_AVERAGE  LCS_A:  26.45  (  12.92   20.33   46.11 )

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      8     11     12     14     17     18     20     23     25     28     29     31     32     33     34     37     41     44     45     47 
GDT PERCENT_CA  12.31  16.92  18.46  21.54  26.15  27.69  30.77  35.38  38.46  43.08  44.62  47.69  49.23  50.77  52.31  56.92  63.08  67.69  69.23  72.31
GDT RMS_LOCAL    0.17   0.46   0.57   1.35   1.68   1.79   2.06   2.75   3.39   3.49   3.57   3.75   3.92   4.10   4.40   6.08   6.51   6.78   6.88   7.11
GDT RMS_ALL_CA  19.37  19.55  19.42  13.83  14.09  14.03  14.20  14.25  13.34  13.39  13.37  14.15  13.90  14.00  13.73  14.27  13.84  13.58  13.59  13.42

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10         19.157
LGA    P      11      P      11         21.092
LGA    F      12      F      12         21.091
LGA    T      13      T      13         24.289
LGA    R      14      R      14         25.859
LGA    R      15      R      15         24.956
LGA    Q      16      Q      16         19.528
LGA    A      17      A      17         17.698
LGA    Q      18      Q      18         18.860
LGA    A      19      A      19         16.529
LGA    V      20      V      20         10.923
LGA    T      21      T      21         11.296
LGA    T      22      T      22         14.069
LGA    T      23      T      23         10.277
LGA    Y      24      Y      24          5.864
LGA    S      25      S      25          3.843
LGA    N      26      N      26          4.242
LGA    I      27      I      27          3.917
LGA    T      28      T      28          3.826
LGA    L      29      L      29          3.763
LGA    E      30      E      30          5.340
LGA    D      31      D      31          7.665
LGA    D      32      D      32          5.725
LGA    Q      33      Q      33          5.628
LGA    G      34      G      34          6.479
LGA    S      35      S      35          2.595
LGA    H      36      H      36          3.169
LGA    F      37      F      37          3.359
LGA    R      38      R      38          2.854
LGA    L      39      L      39          2.629
LGA    V      40      V      40          2.936
LGA    V      41      V      41          2.975
LGA    R      42      R      42          3.208
LGA    D      43      D      43          2.567
LGA    T      44      T      44          3.563
LGA    E      45      E      45          5.697
LGA    G      46      G      46          5.641
LGA    R      47      R      47          3.832
LGA    M      48      M      48          3.144
LGA    V      49      V      49          1.588
LGA    W      50      W      50          3.490
LGA    R      51      R      51          1.244
LGA    A      52      A      52          2.566
LGA    W      53      W      53          1.988
LGA    N      54      N      54          3.520
LGA    F      55      F      55          2.348
LGA    E      56      E      56          6.114
LGA    P      57      P      57          7.378
LGA    D      58      D      58         13.578
LGA    A      59      A      59         14.736
LGA    G      60      G      60         17.896
LGA    E      61      E      61         18.608
LGA    G      62      G      62         17.088
LGA    L      63      L      63         17.001
LGA    N      64      N      64         19.986
LGA    R      65      R      65         20.378
LGA    Y      66      Y      66         18.488
LGA    I      67      I      67         19.444
LGA    R      68      R      68         22.201
LGA    T      69      T      69         16.531
LGA    S      70      S      70         18.040
LGA    G      71      G      71         19.127
LGA    I      72      I      72         22.055
LGA    R      73      R      73         23.125
LGA    T      74      T      74         28.894

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     23    2.75    32.692    30.245     0.806

LGA_LOCAL      RMSD =  2.755  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.661  Number of atoms =   65 
Std_ALL_ATOMS  RMSD = 12.136  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.913041 * X  +  -0.227502 * Y  +   0.338524 * Z  +   1.862076
  Y_new =   0.054344 * X  +   0.754728 * Y  +   0.653783 * Z  +   0.976854
  Z_new =  -0.404231 * X  +   0.615327 * Y  +  -0.676735 * Z  +  -6.102771 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.403685   -0.737907  [ DEG:   137.7210    -42.2790 ]
  Theta =   0.416138    2.725455  [ DEG:    23.8429    156.1571 ]
  Phi   =   3.082143   -0.059450  [ DEG:   176.5938     -3.4062 ]
 
# 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: T0358TS599_1-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS599_1-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   23   2.75  30.245    12.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS599_1-D1
PFRMAT TS                                                                       
TARGET T0358                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     10  CA  GLY    10       3.292  -9.870  -5.229  1.00  0.00              
ATOM     11  CA  PRO    11       4.267 -12.180  -8.005  1.00  0.00              
ATOM     12  CA  PHE    12       2.020 -15.151  -7.394  1.00  0.00              
ATOM     13  CA  THR    13       2.904 -18.850  -7.195  1.00  0.00              
ATOM     14  CA  ARG    14      -0.327 -20.851  -6.807  1.00  0.00              
ATOM     15  CA  ARG    15      -0.100 -21.644  -3.074  1.00  0.00              
ATOM     16  CA  GLN    16       1.208 -18.191  -2.188  1.00  0.00              
ATOM     17  CA  ALA    17      -1.284 -16.539  -4.585  1.00  0.00              
ATOM     18  CA  GLN    18      -4.148 -18.142  -2.645  1.00  0.00              
ATOM     19  CA  ALA    19      -2.648 -16.712   0.564  1.00  0.00              
ATOM     20  CA  VAL    20      -2.321 -13.276  -1.053  1.00  0.00              
ATOM     21  CA  THR    21      -5.962 -13.456  -2.262  1.00  0.00              
ATOM     22  CA  THR    22      -6.936 -13.806   1.354  1.00  0.00              
ATOM     23  CA  THR    23      -4.908 -10.701   2.272  1.00  0.00              
ATOM     24  CA  TYR    24      -5.792  -8.226  -0.492  1.00  0.00              
ATOM     25  CA  SER    25      -2.730  -6.095  -1.130  1.00  0.00              
ATOM     26  CA  ASN    26      -3.525  -3.854  -3.871  1.00  0.00              
ATOM     27  CA  ILE    27      -1.536  -0.875  -3.994  1.00  0.00              
ATOM     28  CA  THR    28      -2.849   2.177  -5.749  1.00  0.00              
ATOM     29  CA  LEU    29      -0.556   4.985  -6.675  1.00  0.00              
ATOM     30  CA  GLU    30      -1.922   8.236  -7.601  1.00  0.00              
ATOM     31  CA  ASP    31       0.226  10.777  -9.301  1.00  0.00              
ATOM     32  CA  ASP    32      -0.773  14.225  -8.617  1.00  0.00              
ATOM     33  CA  GLN    33       2.417  16.089  -7.972  1.00  0.00              
ATOM     34  CA  GLY    34       2.929  15.061  -4.299  1.00  0.00              
ATOM     35  CA  SER    35       2.463  11.375  -4.571  1.00  0.00              
ATOM     36  CA  HIS    36      -0.558   9.734  -3.097  1.00  0.00              
ATOM     37  CA  PHE    37      -0.390   6.176  -1.990  1.00  0.00              
ATOM     38  CA  ARG    38      -3.361   4.153  -1.337  1.00  0.00              
ATOM     39  CA  LEU    39      -3.259   0.768   0.164  1.00  0.00              
ATOM     40  CA  VAL    40      -6.115  -1.508   0.207  1.00  0.00              
ATOM     41  CA  VAL    41      -6.172  -4.404   2.390  1.00  0.00              
ATOM     42  CA  ARG    42      -8.834  -7.063   2.115  1.00  0.00              
ATOM     43  CA  ASP    43      -9.203  -9.478   4.953  1.00  0.00              
ATOM     44  CA  THR    44     -10.364 -13.028   4.289  1.00  0.00              
ATOM     45  CA  GLU    45     -13.785 -12.106   5.703  1.00  0.00              
ATOM     46  CA  GLY    46     -14.380  -9.311   3.252  1.00  0.00              
ATOM     47  CA  ARG    47     -13.501  -6.490   5.609  1.00  0.00              
ATOM     48  CA  MET    48     -11.831  -3.659   3.874  1.00  0.00              
ATOM     49  CA  VAL    49      -9.006  -1.959   5.375  1.00  0.00              
ATOM     50  CA  TRP    50      -7.808   1.217   3.827  1.00  0.00              
ATOM     51  CA  ARG    51      -4.389   2.438   4.459  1.00  0.00              
ATOM     52  CA  ALA    52      -3.404   5.690   3.298  1.00  0.00              
ATOM     53  CA  TRP    53       0.160   6.166   2.763  1.00  0.00              
ATOM     54  CA  ASN    54       1.660   9.583   1.876  1.00  0.00              
ATOM     55  CA  PHE    55       4.579   9.284  -0.547  1.00  0.00              
ATOM     56  CA  GLU    56       6.678  12.387  -0.790  1.00  0.00              
ATOM     57  CA  PRO    57      10.344  11.232  -0.689  1.00  0.00              
ATOM     58  CA  ASP    58      11.717  13.790  -3.169  1.00  0.00              
ATOM     59  CA  ALA    59       9.206  13.333  -5.989  1.00  0.00              
ATOM     60  CA  GLY    60      11.556  11.663  -8.492  1.00  0.00              
ATOM     61  CA  GLU    61      13.476   9.326  -6.172  1.00  0.00              
ATOM     62  CA  GLY    62      10.574   7.659  -4.337  1.00  0.00              
ATOM     63  CA  LEU    63       8.501   7.222  -7.520  1.00  0.00              
ATOM     64  CA  ASN    64      11.494   5.691  -9.237  1.00  0.00              
ATOM     65  CA  ARG    65      12.076   3.253  -6.324  1.00  0.00              
ATOM     66  CA  TYR    66       8.467   2.214  -6.264  1.00  0.00              
ATOM     67  CA  ILE    67       8.328   1.573  -9.978  1.00  0.00              
ATOM     68  CA  ARG    68      11.452  -0.491  -9.936  1.00  0.00              
ATOM     69  CA  THR    69      10.355  -2.703  -7.089  1.00  0.00              
ATOM     70  CA  SER    70       7.070  -3.383  -8.777  1.00  0.00              
ATOM     71  CA  GLY    71       8.569  -4.384 -12.076  1.00  0.00              
ATOM     72  CA  ILE    72       7.967  -1.183 -14.116  1.00  0.00              
ATOM     73  CA  ARG    73      10.621  -0.741 -16.747  1.00  0.00              
ATOM     74  CA  THR    74      13.065   2.054 -17.341  1.00  0.00              
TER                                                                             
END
