
#######################################################
#                                                     #
#                        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 T0358TS393_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS393_2-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:    37        23 - 59          4.96    15.50
  LONGEST_CONTINUOUS_SEGMENT:    37        24 - 60          4.95    15.45
  LCS_AVERAGE:     48.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        13 - 26          1.79    17.00
  LCS_AVERAGE:     15.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        13 - 24          0.80    18.07
  LCS_AVERAGE:      9.02

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    5   21     0    3    4    5    6    9   11   14   17   19   21   23   24   24   26   29   32   36   37   38 
LCS_GDT     P      11     P      11      4    5   21     0    3    4    5    6    6    7   12   17   18   20   23   23   23   26   28   30   36   37   38 
LCS_GDT     F      12     F      12      4   13   21     3    3    4    5    7   11   14   16   17   19   21   23   24   24   26   29   32   36   37   38 
LCS_GDT     T      13     T      13     12   14   21     3    4    9   14   14   14   15   17   18   19   21   23   24   26   29   30   32   36   37   38 
LCS_GDT     R      14     R      14     12   14   21    11   11   12   14   14   14   15   17   18   19   21   23   24   27   29   30   32   36   37   38 
LCS_GDT     R      15     R      15     12   14   21    11   11   12   14   14   14   15   17   18   19   22   24   26   28   29   30   32   34   35   37 
LCS_GDT     Q      16     Q      16     12   14   21    11   11   12   14   14   14   15   17   18   19   22   24   26   28   29   30   36   39   39   41 
LCS_GDT     A      17     A      17     12   14   21    11   11   12   14   14   14   15   17   18   20   22   24   26   28   32   34   39   42   46   47 
LCS_GDT     Q      18     Q      18     12   14   21    11   11   12   14   14   14   15   17   18   20   22   24   26   28   30   34   37   42   46   47 
LCS_GDT     A      19     A      19     12   14   21    11   11   12   14   14   14   15   17   18   20   21   24   28   31   33   34   40   42   46   47 
LCS_GDT     V      20     V      20     12   14   32    11   11   12   14   14   14   15   17   18   21   25   29   33   37   39   41   43   44   46   47 
LCS_GDT     T      21     T      21     12   14   32    11   11   12   14   14   14   15   17   18   21   26   29   33   37   39   41   43   44   46   47 
LCS_GDT     T      22     T      22     12   14   32    11   11   12   14   14   14   15   17   18   19   24   29   33   37   39   41   42   44   46   47 
LCS_GDT     T      23     T      23     12   14   37    11   11   12   14   14   14   15   17   18   19   24   28   33   37   39   41   43   44   46   47 
LCS_GDT     Y      24     Y      24     12   14   37    11   11   12   14   14   14   15   18   19   25   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     S      25     S      25      4   14   37     3    5    5    8   13   14   15   17   18   19   21   26   30   32   35   37   43   44   45   46 
LCS_GDT     N      26     N      26      4   14   37     3    5    5    9   13   14   15   17   18   19   21   23   26   30   31   35   43   44   45   46 
LCS_GDT     I      27     I      27      4    8   37     3    5    7    9   11   13   15   18   19   25   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     T      28     T      28      4    8   37     3    3    9   10   11   11   15   18   21   25   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     L      29     L      29      4    8   37     3    3    4    7   10   14   18   20   23   25   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     E      30     E      30      3    8   37     1    4    4    7   10   12   13   14   21   24   28   32   34   37   39   41   43   44   46   47 
LCS_GDT     D      31     D      31      3    6   37     0    4    4    5   10   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     D      32     D      32      4    5   37     3    4    5   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     Q      33     Q      33      4    5   37     3    4    6   10   14   18   19   21   24   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     G      34     G      34      4    6   37     3    4    4    5   12   17   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     S      35     S      35      5    6   37     2    4    5    5    7   11   18   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     H      36     H      36      5    7   37     3    4    5    7   10   16   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     F      37     F      37      5   12   37     3    4    5    8   12   16   19   21   23   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     R      38     R      38      5   12   37     3    4    7    9   12   16   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     L      39     L      39      5   12   37     3    5    5    8   10   11   14   17   19   22   26   30   34   37   39   41   43   44   46   47 
LCS_GDT     V      40     V      40      4   13   37     3    4    7    9   13   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     V      41     V      41      4   13   37     1    4    7   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     R      42     R      42      4   13   37     3    4    6   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     D      43     D      43      4   13   37     3    4    7    9   14   18   19   21   25   26   29   32   34   37   39   41   43   44   45   46 
LCS_GDT     T      44     T      44      4   13   37     3    4    7    9   12   16   19   21   25   26   29   32   34   37   39   41   43   44   45   46 
LCS_GDT     E      45     E      45      4   13   37     3    4    7    9   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     G      46     G      46      4   13   37     3    4    6   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     R      47     R      47      4   13   37     3    4    7   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     M      48     M      48      3   13   37     1    4    7   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     V      49     V      49      4   13   37     3    4    6   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     W      50     W      50      4   13   37     3    4    7   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     R      51     R      51      4   13   37     3    4    5    6   10   16   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     A      52     A      52      4   13   37     3    4    7    9   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     W      53     W      53      4    7   37     0    3    5    5    9   10   13   18   23   26   28   31   34   37   39   40   41   43   46   47 
LCS_GDT     N      54     N      54      4    7   37     3    3    5    7    9   13   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     F      55     F      55      3    7   37     3    4    5    8   11   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     E      56     E      56      3    7   37     3    4    5    7   10   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     P      57     P      57      3    7   37     3    4    5   10   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     D      58     D      58      4    7   37     3    3    5    9   14   18   19   21   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     A      59     A      59      4   10   37     3    4    5    9   11   13   15   20   25   26   29   32   34   37   39   41   43   44   46   47 
LCS_GDT     G      60     G      60      4   10   37     3    4    5    7    9   13   14   15   18   20   24   29   33   37   39   41   43   44   46   47 
LCS_GDT     E      61     E      61      8   10   36     8    9    9   10   11   13   14   15   18   21   24   29   33   37   39   41   43   44   46   47 
LCS_GDT     G      62     G      62      8   10   36     8   11   12   14   14   14   14   17   18   20   22   25   30   32   36   40   43   44   46   47 
LCS_GDT     L      63     L      63      8   10   24     8    9   11   14   14   14   14   17   18   20   22   25   32   35   39   41   43   44   46   47 
LCS_GDT     N      64     N      64      8   10   24     8    9    9   10   11   13   14   17   18   20   22   26   32   35   38   41   43   44   46   47 
LCS_GDT     R      65     R      65      8   10   24     8    9    9   10   11   13   14   15   18   20   22   24   26   29   34   37   40   43   46   47 
LCS_GDT     Y      66     Y      66      8   10   24     8    9    9   10   11   13   14   15   18   20   22   24   26   28   31   37   39   41   46   47 
LCS_GDT     I      67     I      67      8   10   24     8    9    9   10   11   13   14   15   18   20   22   24   26   28   31   37   39   42   46   47 
LCS_GDT     R      68     R      68      8   10   24     8    9    9   10   11   13   14   15   18   20   22   24   26   28   30   37   39   42   46   47 
LCS_GDT     T      69     T      69      3    9   24     3    3    4    5    9   12   14   15   18   19   22   24   26   28   29   31   32   34   36   38 
LCS_GDT     S      70     S      70      3    4   24     3    3    4    5    6    8    9   13   15   18   19   22   24   27   29   30   32   34   35   37 
LCS_GDT     G      71     G      71      3    4   22     3    3    5    5    5    7   13   13   14   16   19   22   23   27   29   30   32   34   35   37 
LCS_GDT     I      72     I      72      3    4   21     3    3    5    5    8    8   13   13   14   16   18   22   23   27   29   30   32   34   35   37 
LCS_GDT     R      73     R      73      3    4   20     3    3    4    4    4    7    9    9   14   14   17   18   21   22   23   25   31   32   34   34 
LCS_GDT     T      74     T      74      3    4   20     3    3    4    4    8   10   13   13   14   16   18   22   23   27   29   30   31   34   34   37 
LCS_AVERAGE  LCS_A:  24.47  (   9.02   15.67   48.73 )

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     12     14     14     18     19     21     25     26     29     32     34     37     39     41     43     44     46     47 
GDT PERCENT_CA  16.92  16.92  18.46  21.54  21.54  27.69  29.23  32.31  38.46  40.00  44.62  49.23  52.31  56.92  60.00  63.08  66.15  67.69  70.77  72.31
GDT RMS_LOCAL    0.28   0.28   0.51   0.99   0.99   2.22   2.29   2.64   3.09   3.22   3.70   4.00   4.18   4.81   5.14   5.52   5.81   5.90   6.91   6.95
GDT RMS_ALL_CA  18.11  18.11  18.03  17.91  17.91  16.50  16.50  16.53  16.35  16.37  16.04  15.96  15.97  15.17  14.69  14.16  14.27  14.08  12.43  12.51

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10         26.526
LGA    P      11      P      11         24.569
LGA    F      12      F      12         24.812
LGA    T      13      T      13         25.430
LGA    R      14      R      14         24.563
LGA    R      15      R      15         25.634
LGA    Q      16      Q      16         20.520
LGA    A      17      A      17         16.192
LGA    Q      18      Q      18         18.841
LGA    A      19      A      19         17.334
LGA    V      20      V      20         11.797
LGA    T      21      T      21         11.426
LGA    T      22      T      22         12.789
LGA    T      23      T      23         10.277
LGA    Y      24      Y      24          7.857
LGA    S      25      S      25         13.313
LGA    N      26      N      26         11.488
LGA    I      27      I      27          7.454
LGA    T      28      T      28          6.943
LGA    L      29      L      29          7.352
LGA    E      30      E      30          7.359
LGA    D      31      D      31          3.633
LGA    D      32      D      32          3.593
LGA    Q      33      Q      33          4.697
LGA    G      34      G      34          2.660
LGA    S      35      S      35          3.883
LGA    H      36      H      36          3.513
LGA    F      37      F      37          6.051
LGA    R      38      R      38          5.075
LGA    L      39      L      39          7.469
LGA    V      40      V      40          2.310
LGA    V      41      V      41          2.136
LGA    R      42      R      42          1.801
LGA    D      43      D      43          2.252
LGA    T      44      T      44          4.477
LGA    E      45      E      45          2.492
LGA    G      46      G      46          2.175
LGA    R      47      R      47          1.177
LGA    M      48      M      48          0.899
LGA    V      49      V      49          2.433
LGA    W      50      W      50          2.181
LGA    R      51      R      51          3.956
LGA    A      52      A      52          1.633
LGA    W      53      W      53          5.521
LGA    N      54      N      54          4.183
LGA    F      55      F      55          2.635
LGA    E      56      E      56          3.850
LGA    P      57      P      57          1.867
LGA    D      58      D      58          2.275
LGA    A      59      A      59          5.362
LGA    G      60      G      60         11.424
LGA    E      61      E      61         11.150
LGA    G      62      G      62         13.990
LGA    L      63      L      63         12.857
LGA    N      64      N      64         15.636
LGA    R      65      R      65         19.199
LGA    Y      66      Y      66         20.308
LGA    I      67      I      67         20.490
LGA    R      68      R      68         24.523
LGA    T      69      T      69         30.530
LGA    S      70      S      70         33.448
LGA    G      71      G      71         34.098
LGA    I      72      I      72         34.751
LGA    R      73      R      73         41.002
LGA    T      74      T      74         45.774

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     21    2.64    33.462    29.025     0.766

LGA_LOCAL      RMSD =  2.643  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.427  Number of atoms =   65 
Std_ALL_ATOMS  RMSD = 11.467  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.490831 * X  +  -0.851775 * Y  +   0.183206 * Z  +  -3.544024
  Y_new =  -0.160896 * X  +   0.118046 * Y  +   0.979887 * Z  +   8.514614
  Z_new =  -0.856269 * X  +  -0.510436 * Y  +  -0.079106 * Z  +   9.118655 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.724551    1.417042  [ DEG:   -98.8095     81.1905 ]
  Theta =   1.028004    2.113589  [ DEG:    58.9003    121.0997 ]
  Phi   =  -0.316765    2.824828  [ DEG:   -18.1493    161.8507 ]
 
# 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: T0358TS393_2-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_2-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   21   2.64  29.025    11.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_2-D1
PFRMAT TS
TARGET T0358
MODEL 2
PARENT N/A
ATOM     10  CA  GLY    10     -11.486   0.379  19.186  1.00 25.00           C
ATOM     11  CA  PRO    11      -7.978  -1.070  18.962  1.00 25.00           C
ATOM     12  CA  PHE    12      -6.742   2.516  18.559  1.00 25.00           C
ATOM     13  CA  THR    13      -3.035   2.213  17.847  1.00 25.00           C
ATOM     14  CA  ARG    14      -0.074   0.706  15.994  1.00 25.00           C
ATOM     15  CA  ARG    15      -2.944  -1.242  14.371  1.00 25.00           C
ATOM     16  CA  GLN    16      -3.287   1.459  11.678  1.00 25.00           C
ATOM     17  CA  ALA    17       0.481   1.304  11.007  1.00 25.00           C
ATOM     18  CA  GLN    18       0.294  -2.510  10.703  1.00 25.00           C
ATOM     19  CA  ALA    19      -2.630  -2.195   8.249  1.00 25.00           C
ATOM     20  CA  VAL    20      -0.650   0.343   6.176  1.00 25.00           C
ATOM     21  CA  THR    21       2.365  -2.019   6.120  1.00 25.00           C
ATOM     22  CA  THR    22       0.115  -4.903   4.983  1.00 25.00           C
ATOM     23  CA  THR    23      -1.339  -2.705   2.204  1.00 25.00           C
ATOM     24  CA  TYR    24       2.194  -1.750   1.076  1.00 25.00           C
ATOM     25  CA  SER    25       3.694   1.675   1.539  1.00 25.00           C
ATOM     26  CA  ASN    26       1.353   2.698  -1.256  1.00 25.00           C
ATOM     27  CA  ILE    27      -1.780   3.317   0.756  1.00 25.00           C
ATOM     28  CA  THR    28      -3.182   5.631  -1.967  1.00 25.00           C
ATOM     29  CA  LEU    29      -4.865   8.961  -2.955  1.00 25.00           C
ATOM     30  CA  GLU    30      -5.322  12.454  -4.490  1.00 25.00           C
ATOM     31  CA  ASP    31      -4.487  10.539  -7.704  1.00 25.00           C
ATOM     32  CA  ASP    32      -4.557   8.194 -10.670  1.00 25.00           C
ATOM     33  CA  GLN    33      -1.336   9.762 -11.969  1.00 25.00           C
ATOM     34  CA  GLY    34       0.563   9.505  -8.655  1.00 25.00           C
ATOM     35  CA  SER    35       0.395  10.847  -5.106  1.00 25.00           C
ATOM     36  CA  HIS    36      -0.123  10.883  -1.301  1.00 25.00           C
ATOM     37  CA  PHE    37      -2.476  10.601   1.693  1.00 25.00           C
ATOM     38  CA  ARG    38      -5.082   7.871   2.146  1.00 25.00           C
ATOM     39  CA  LEU    39      -7.790   5.292   2.502  1.00 25.00           C
ATOM     40  CA  VAL    40      -7.065   1.936   0.953  1.00 25.00           C
ATOM     41  CA  VAL    41      -6.199  -1.759   1.239  1.00 25.00           C
ATOM     42  CA  ARG    42      -7.019  -4.502   3.746  1.00 25.00           C
ATOM     43  CA  ASP    43      -7.039  -7.625   1.659  1.00 25.00           C
ATOM     44  CA  THR    44      -7.284  -9.057  -1.902  1.00 25.00           C
ATOM     45  CA  GLU    45     -10.902  -9.858  -0.930  1.00 25.00           C
ATOM     46  CA  GLY    46     -13.242  -6.828  -0.543  1.00 25.00           C
ATOM     47  CA  ARG    47     -12.024  -4.165   1.839  1.00 25.00           C
ATOM     48  CA  MET    48     -10.432  -1.634   4.280  1.00 25.00           C
ATOM     49  CA  VAL    49      -7.404   0.276   5.658  1.00 25.00           C
ATOM     50  CA  TRP    50      -4.455   2.569   5.357  1.00 25.00           C
ATOM     51  CA  ARG    51      -3.470   6.093   6.546  1.00 25.00           C
ATOM     52  CA  ALA    52      -0.498   6.666   4.243  1.00 25.00           C
ATOM     53  CA  TRP    53       2.254   4.617   5.888  1.00 25.00           C
ATOM     54  CA  ASN    54       4.612   6.434   3.612  1.00 25.00           C
ATOM     55  CA  PHE    55       6.526   8.340   0.960  1.00 25.00           C
ATOM     56  CA  GLU    56       7.719  11.719   2.311  1.00 25.00           C
ATOM     57  CA  PRO    57       9.744   9.595   4.758  1.00 25.00           C
ATOM     58  CA  ASP    58       9.976   6.974   7.585  1.00 25.00           C
ATOM     59  CA  ALA    59       6.744   7.621   9.500  1.00 25.00           C
ATOM     60  CA  GLY    60       7.150  10.912  11.368  1.00 25.00           C
ATOM     61  CA  GLU    61       5.290  12.317   8.389  1.00 25.00           C
ATOM     62  CA  GLY    62       3.364  14.521   5.919  1.00 25.00           C
ATOM     63  CA  LEU    63       0.865  11.686   5.300  1.00 25.00           C
ATOM     64  CA  ASN    64       0.401  11.237   9.075  1.00 25.00           C
ATOM     65  CA  ARG    65      -0.196  14.999   9.473  1.00 25.00           C
ATOM     66  CA  TYR    66      -2.783  14.913   6.650  1.00 25.00           C
ATOM     67  CA  ILE    67      -4.546  11.951   8.323  1.00 25.00           C
ATOM     68  CA  ARG    68      -4.605  13.838  11.655  1.00 25.00           C
ATOM     69  CA  THR    69      -6.080  16.914   9.915  1.00 25.00           C
ATOM     70  CA  SER    70      -5.126  19.518   7.290  1.00 25.00           C
ATOM     71  CA  GLY    71      -4.079  22.630   9.182  1.00 25.00           C
ATOM     72  CA  ILE    72      -5.040  21.091  12.544  1.00 25.00           C
ATOM     73  CA  ARG    73      -5.263  24.684  13.912  1.00 25.00           C
ATOM     74  CA  THR    74      -7.611  25.025  16.931  1.00 25.00           C
TER
END
