
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS599_4-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:    43        15 - 57          4.82     9.05
  LONGEST_CONTINUOUS_SEGMENT:    43        16 - 58          4.94     8.66
  LCS_AVERAGE:     58.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        10 - 27          1.23    13.24
  LONGEST_CONTINUOUS_SEGMENT:    18        11 - 28          1.75    12.25
  LONGEST_CONTINUOUS_SEGMENT:    18        36 - 53          1.98     9.87
  LCS_AVERAGE:     22.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        11 - 27          0.95    12.96
  LCS_AVERAGE:     15.67

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     14   18   24     0    4    9   14   17   17   18   21   22   26   30   38   45   47   48   52   55   57   58   59 
LCS_GDT     P      11     P      11     17   18   24     3   14   16   17   17   20   22   24   25   26   30   32   41   45   48   51   51   54   58   59 
LCS_GDT     F      12     F      12     17   18   24     4   14   16   17   17   20   22   24   25   26   30   36   45   47   51   54   55   57   58   59 
LCS_GDT     T      13     T      13     17   18   24     6   14   16   17   17   20   22   24   25   26   30   31   34   42   47   51   51   53   56   59 
LCS_GDT     R      14     R      14     17   18   42     7   14   16   17   17   20   22   24   25   26   30   31   34   40   47   51   51   52   54   57 
LCS_GDT     R      15     R      15     17   18   43     7   14   16   17   17   19   22   24   25   26   30   31   34   40   47   51   51   53   56   58 
LCS_GDT     Q      16     Q      16     17   18   43     8   14   16   17   17   20   22   24   25   27   35   36   45   47   51   54   55   57   58   59 
LCS_GDT     A      17     A      17     17   18   43     8   14   16   17   17   20   22   24   25   27   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     Q      18     Q      18     17   18   43     8   14   16   17   17   20   22   24   25   26   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     A      19     A      19     17   18   43     8   14   16   17   17   22   23   25   27   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     V      20     V      20     17   18   43     8   14   16   17   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     T      21     T      21     17   18   43     8   14   16   17   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     T      22     T      22     17   18   43     8   14   16   17   17   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     T      23     T      23     17   18   43     8   14   16   17   17   20   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     Y      24     Y      24     17   18   43     8   14   16   17   17   20   23   24   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     S      25     S      25     17   18   43     4   12   16   17   17   20   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     N      26     N      26     17   18   43     4   14   16   17   17   19   22   24   28   31   35   37   45   49   51   54   55   57   58   59 
LCS_GDT     I      27     I      27     17   18   43     4   12   15   17   17   20   22   24   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     T      28     T      28      5   18   43     4    5    7    9   12   19   20   24   28   31   35   37   45   49   51   54   55   57   58   59 
LCS_GDT     L      29     L      29      5   10   43     4    5    7    7   10   14   21   24   28   31   35   37   42   49   51   54   55   57   58   59 
LCS_GDT     E      30     E      30      5   10   43     3    5    7    7   10   14   17   24   28   30   32   36   41   49   51   54   55   57   58   59 
LCS_GDT     D      31     D      31      4   10   43     3    3    7    7    9   12   15   17   20   28   29   34   37   40   42   54   55   57   58   59 
LCS_GDT     D      32     D      32      4   10   43     3    3    4    4    7   10   13   19   25   30   32   35   37   46   50   54   55   57   58   59 
LCS_GDT     Q      33     Q      33      4   10   43     3    5    6    7   10   12   17   24   28   31   32   36   37   39   41   52   55   57   58   59 
LCS_GDT     G      34     G      34      3   10   43     3    4    6    7    8   10   15   22   27   30   32   35   36   39   40   45   49   55   56   59 
LCS_GDT     S      35     S      35      8   15   43     3    5    8   13   18   19   23   25   28   31   33   36   41   46   50   54   55   57   58   59 
LCS_GDT     H      36     H      36      8   18   43     3    6   10   15   18   22   23   25   28   31   35   37   41   49   51   54   55   57   58   59 
LCS_GDT     F      37     F      37      8   18   43     3    3    9   13   17   22   23   25   28   31   35   36   41   49   51   54   55   57   58   59 
LCS_GDT     R      38     R      38      8   18   43     6    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     L      39     L      39      8   18   43     5    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     V      40     V      40      9   18   43     6    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     V      41     V      41     10   18   43     5    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     R      42     R      42     10   18   43     6    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     D      43     D      43     10   18   43     4    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     T      44     T      44     10   18   43     4    8   14   15   18   22   23   25   27   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     E      45     E      45     10   18   43     4    7   10   13   18   22   23   25   27   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     G      46     G      46     10   18   43     4    7   10   15   18   22   23   25   27   30   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     R      47     R      47     10   18   43     4    8   14   15   18   22   23   25   27   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     M      48     M      48     10   18   43     6    8   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     V      49     V      49     10   18   43     4    7   10   13   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     W      50     W      50     10   18   43     4    6   10   11   16   20   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     R      51     R      51      6   18   43     4    5   14   15   18   22   23   25   28   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     A      52     A      52      6   18   43     4    5    7   14   18   22   23   25   28   31   35   37   44   49   51   54   55   57   58   59 
LCS_GDT     W      53     W      53      6   18   43     3    5   14   15   18   22   23   25   28   31   35   37   41   49   51   54   55   57   58   59 
LCS_GDT     N      54     N      54      6    8   43     3    5    6    7   13   18   23   25   28   31   33   37   41   46   50   53   55   57   58   59 
LCS_GDT     F      55     F      55      6    8   43     3    7   14   15   18   22   23   25   28   31   35   37   41   49   51   54   55   57   58   59 
LCS_GDT     E      56     E      56      4   10   43     3    4    4    7    9   12   16   22   25   31   35   38   45   49   51   54   55   57   58   59 
LCS_GDT     P      57     P      57      4   12   43     3    4    5    6    7   12   17   22   25   31   35   37   45   49   51   54   55   57   58   59 
LCS_GDT     D      58     D      58     11   12   43     4    8   11   11   11   14   16   18   19   22   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     A      59     A      59     11   12   41     5   10   11   11   11   14   16   19   23   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     G      60     G      60     11   12   31     5   10   11   11   11   14   16   18   19   26   30   32   45   49   51   54   55   57   58   59 
LCS_GDT     E      61     E      61     11   12   31     8   10   11   11   14   19   21   24   25   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     G      62     G      62     11   12   31     8   10   14   15   17   19   22   24   25   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     L      63     L      63     11   12   31     8   10   11   14   17   20   22   24   25   26   30   36   45   49   51   54   55   57   58   59 
LCS_GDT     N      64     N      64     11   12   31     8   10   11   11   16   20   22   24   25   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     R      65     R      65     11   12   31     8   10   11   13   16   20   22   24   25   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     Y      66     Y      66     11   12   31     8   10   11   11   14   20   21   23   25   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     I      67     I      67     11   12   31     8   10   11   11   11   14   20   22   24   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     R      68     R      68     11   12   31     8   10   11   11   11   16   20   22   23   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     T      69     T      69      4   11   24     3    4    4   14   17   20   22   24   25   26   31   38   45   49   51   54   55   57   58   59 
LCS_GDT     S      70     S      70      4   11   24     3    4    6   10   11   12   12   18   21   26   30   38   45   49   51   54   55   57   58   59 
LCS_GDT     G      71     G      71      4    5   24     3    4    4    4    8   12   16   18   20   26   31   38   45   49   51   54   55   57   58   59 
LCS_GDT     I      72     I      72      3    5   23     3    3    3    4    8   11   13   16   16   20   25   29   33   34   42   46   49   51   53   58 
LCS_GDT     R      73     R      73      3    5   23     3    3    3    4    8   11   13   15   16   16   17   20   23   31   35   40   42   45   49   53 
LCS_GDT     T      74     T      74      3    4   20     2    3    3    3    4    5    5    6    7   13   17   20   23   24   26   28   38   40   45   48 
LCS_AVERAGE  LCS_A:  32.36  (  15.67   22.53   58.89 )

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     14     16     17     18     22     23     25     28     31     35     38     45     49     51     54     55     57     58     59 
GDT PERCENT_CA  12.31  21.54  24.62  26.15  27.69  33.85  35.38  38.46  43.08  47.69  53.85  58.46  69.23  75.38  78.46  83.08  84.62  87.69  89.23  90.77
GDT RMS_LOCAL    0.28   0.67   0.78   0.95   1.61   1.96   2.12   2.30   3.21   3.34   3.84   5.01   5.28   5.50   5.64   5.91   5.94   6.13   6.23   6.34
GDT RMS_ALL_CA  10.72  13.55  13.25  12.96   9.05   9.45   9.57   9.62   9.95   9.73   8.67   8.04   7.84   7.46   7.42   7.36   7.40   7.38   7.38   7.37

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10         16.795
LGA    P      11      P      11         17.111
LGA    F      12      F      12         13.144
LGA    T      13      T      13         13.419
LGA    R      14      R      14         13.141
LGA    R      15      R      15         10.826
LGA    Q      16      Q      16          7.526
LGA    A      17      A      17          7.557
LGA    Q      18      Q      18          6.071
LGA    A      19      A      19          3.788
LGA    V      20      V      20          2.336
LGA    T      21      T      21          1.947
LGA    T      22      T      22          2.970
LGA    T      23      T      23          3.759
LGA    Y      24      Y      24          4.953
LGA    S      25      S      25          4.347
LGA    N      26      N      26          6.957
LGA    I      27      I      27          6.434
LGA    T      28      T      28          6.671
LGA    L      29      L      29          6.353
LGA    E      30      E      30          8.224
LGA    D      31      D      31         10.142
LGA    D      32      D      32          8.920
LGA    Q      33      Q      33          8.948
LGA    G      34      G      34          8.505
LGA    S      35      S      35          3.106
LGA    H      36      H      36          1.498
LGA    F      37      F      37          2.696
LGA    R      38      R      38          0.884
LGA    L      39      L      39          0.210
LGA    V      40      V      40          1.380
LGA    V      41      V      41          1.403
LGA    R      42      R      42          1.748
LGA    D      43      D      43          0.956
LGA    T      44      T      44          1.143
LGA    E      45      E      45          3.563
LGA    G      46      G      46          3.063
LGA    R      47      R      47          2.056
LGA    M      48      M      48          1.468
LGA    V      49      V      49          2.482
LGA    W      50      W      50          3.644
LGA    R      51      R      51          1.752
LGA    A      52      A      52          2.429
LGA    W      53      W      53          1.307
LGA    N      54      N      54          4.120
LGA    F      55      F      55          1.232
LGA    E      56      E      56          8.063
LGA    P      57      P      57          8.654
LGA    D      58      D      58         14.626
LGA    A      59      A      59         13.961
LGA    G      60      G      60         15.274
LGA    E      61      E      61         15.739
LGA    G      62      G      62         15.154
LGA    L      63      L      63         14.344
LGA    N      64      N      64         15.045
LGA    R      65      R      65         15.416
LGA    Y      66      Y      66         14.408
LGA    I      67      I      67         13.564
LGA    R      68      R      68         14.235
LGA    T      69      T      69         10.342
LGA    S      70      S      70         11.502
LGA    G      71      G      71         11.538
LGA    I      72      I      72         16.689
LGA    R      73      R      73         17.480
LGA    T      74      T      74         22.588

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     25    2.30    42.308    36.854     1.041

LGA_LOCAL      RMSD =  2.301  Number of atoms =   25  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.712  Number of atoms =   65 
Std_ALL_ATOMS  RMSD =  7.293  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.762389 * X  +  -0.610127 * Y  +  -0.215659 * Z  +   5.333170
  Y_new =   0.116073 * X  +  -0.456787 * Y  +   0.881971 * Z  +   1.781574
  Z_new =  -0.636624 * X  +   0.647372 * Y  +   0.419068 * Z  +  -5.822101 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.996295   -2.145298  [ DEG:    57.0835   -122.9165 ]
  Theta =   0.690113    2.451479  [ DEG:    39.5406    140.4594 ]
  Phi   =   2.990504   -0.151089  [ DEG:   171.3433     -8.6567 ]
 
# 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_4-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS599_4-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   25   2.30  36.854     7.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS599_4-D1
PFRMAT TS                                                                       
TARGET T0358                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM     10  CA  GLY    10      10.433   4.841 -11.607  1.00  0.00              
ATOM     11  CA  PRO    11      11.442   2.459 -14.349  1.00  0.00              
ATOM     12  CA  PHE    12       9.482  -0.674 -13.365  1.00  0.00              
ATOM     13  CA  THR    13      10.365  -4.146 -14.649  1.00  0.00              
ATOM     14  CA  ARG    14       7.264  -6.339 -15.157  1.00  0.00              
ATOM     15  CA  ARG    15       7.914  -8.839 -12.430  1.00  0.00              
ATOM     16  CA  GLN    16       8.555  -6.129  -9.920  1.00  0.00              
ATOM     17  CA  ALA    17       5.456  -4.155 -10.727  1.00  0.00              
ATOM     18  CA  GLN    18       3.230  -7.201 -10.450  1.00  0.00              
ATOM     19  CA  ALA    19       4.765  -8.139  -7.063  1.00  0.00              
ATOM     20  CA  VAL    20       4.413  -4.659  -5.606  1.00  0.00              
ATOM     21  CA  THR    21       0.789  -4.422  -6.768  1.00  0.00              
ATOM     22  CA  THR    22      -0.101  -7.762  -5.286  1.00  0.00              
ATOM     23  CA  THR    23       1.487  -6.933  -1.899  1.00  0.00              
ATOM     24  CA  TYR    24      -0.291  -3.545  -1.547  1.00  0.00              
ATOM     25  CA  SER    25      -3.847  -3.996  -2.750  1.00  0.00              
ATOM     26  CA  ASN    26      -4.259  -1.031  -5.005  1.00  0.00              
ATOM     27  CA  ILE    27      -1.334   1.174  -5.594  1.00  0.00              
ATOM     28  CA  THR    28      -1.923   4.712  -6.710  1.00  0.00              
ATOM     29  CA  LEU    29       0.878   7.162  -7.043  1.00  0.00              
ATOM     30  CA  GLU    30       0.046  10.627  -7.735  1.00  0.00              
ATOM     31  CA  ASP    31       2.569  12.911  -9.189  1.00  0.00              
ATOM     32  CA  ASP    32       1.874  16.434  -8.607  1.00  0.00              
ATOM     33  CA  GLN    33       5.102  18.006  -7.543  1.00  0.00              
ATOM     34  CA  GLY    34       4.787  16.988  -3.853  1.00  0.00              
ATOM     35  CA  SER    35       4.380  13.286  -4.212  1.00  0.00              
ATOM     36  CA  HIS    36       1.244  11.650  -3.016  1.00  0.00              
ATOM     37  CA  PHE    37       1.151   7.983  -2.330  1.00  0.00              
ATOM     38  CA  ARG    38      -1.987   6.116  -1.911  1.00  0.00              
ATOM     39  CA  LEU    39      -1.960   2.550  -0.942  1.00  0.00              
ATOM     40  CA  VAL    40      -4.993   0.431  -0.754  1.00  0.00              
ATOM     41  CA  VAL    41      -4.829  -2.689   1.128  1.00  0.00              
ATOM     42  CA  ARG    42      -7.432  -5.344   0.773  1.00  0.00              
ATOM     43  CA  ASP    43      -7.541  -8.019   3.397  1.00  0.00              
ATOM     44  CA  THR    44      -8.643 -11.528   2.450  1.00  0.00              
ATOM     45  CA  GLU    45     -12.024 -10.758   4.079  1.00  0.00              
ATOM     46  CA  GLY    46     -12.744  -7.793   1.904  1.00  0.00              
ATOM     47  CA  ARG    47     -11.875  -5.153   4.533  1.00  0.00              
ATOM     48  CA  MET    48     -10.335  -2.140   3.052  1.00  0.00              
ATOM     49  CA  VAL    49      -7.387  -0.629   4.579  1.00  0.00              
ATOM     50  CA  TRP    50      -6.204   2.671   3.267  1.00  0.00              
ATOM     51  CA  ARG    51      -2.667   3.791   3.674  1.00  0.00              
ATOM     52  CA  ALA    52      -1.785   7.117   2.782  1.00  0.00              
ATOM     53  CA  TRP    53       1.716   7.772   2.314  1.00  0.00              
ATOM     54  CA  ASN    54       2.974  11.307   1.617  1.00  0.00              
ATOM     55  CA  PHE    55       6.237  11.214  -0.068  1.00  0.00              
ATOM     56  CA  GLU    56       7.886  14.106  -1.719  1.00  0.00              
ATOM     57  CA  PRO    57      11.559  13.739  -0.707  1.00  0.00              
ATOM     58  CA  ASP    58      13.243  13.546  -4.069  1.00  0.00              
ATOM     59  CA  ALA    59      10.883  11.035  -5.728  1.00  0.00              
ATOM     60  CA  GLY    60      13.451   8.309  -6.410  1.00  0.00              
ATOM     61  CA  GLU    61      14.429   7.911  -2.732  1.00  0.00              
ATOM     62  CA  GLY    62      10.755   7.450  -1.771  1.00  0.00              
ATOM     63  CA  LEU    63      10.051   4.884  -4.526  1.00  0.00              
ATOM     64  CA  ASN    64      13.150   2.885  -3.571  1.00  0.00              
ATOM     65  CA  ARG    65      12.056   2.966   0.078  1.00  0.00              
ATOM     66  CA  TYR    66       8.564   1.756  -0.858  1.00  0.00              
ATOM     67  CA  ILE    67       9.898  -1.018  -3.007  1.00  0.00              
ATOM     68  CA  ARG    68      12.247  -2.186  -0.170  1.00  0.00              
ATOM     69  CA  THR    69       9.355  -2.202   2.288  1.00  0.00              
ATOM     70  CA  SER    70       7.504  -4.453  -0.197  1.00  0.00              
ATOM     71  CA  GLY    71      10.289  -6.964  -0.424  1.00  0.00              
ATOM     72  CA  ILE    72      11.858  -6.074  -3.807  1.00  0.00              
ATOM     73  CA  ARG    73      15.568  -6.658  -3.733  1.00  0.00              
ATOM     74  CA  THR    74      18.453  -4.465  -4.727  1.00  0.00              
TER                                                                             
END
