
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0349TS677_1
# Molecule2: number of CA atoms   75 ( 1131),  selected   64 , name T0349.pdb
# PARAMETERS: T0349TS677_1.T0349.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:    63         2 - 73          4.67     5.77
  LCS_AVERAGE:     82.98

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    55         2 - 65          2.00     6.36
  LCS_AVERAGE:     65.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        44 - 65          1.00     6.12
  LCS_AVERAGE:     21.31

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:   75
LCS_GDT     R       2     R       2      6   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     E       3     E       3      6   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L       4     L       4      6   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L       5     L       5      6   55   63    13   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     R       6     R       6      6   55   63     4   23   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     T       7     T       7     18   55   63     4   12   32   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     N       8     N       8     18   55   63     3    3    3   11   26   46   54   55   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D       9     D       9     20   55   63    15   25   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      10     A      10     20   55   63    15   25   40   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     V      11     V      11     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      12     L      12     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      13     L      13     20   55   63    15   25   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     S      14     S      14     20   55   63    15   25   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      15     A      15     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     V      16     V      16     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     G      17     G      17     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      18     A      18     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      19     L      19     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      20     L      20     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D      21     D      21     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     G      22     G      22     20   55   63    15   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      23     A      23     20   55   63     6   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D      24     D      24     20   55   63     6   17   39   47   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     I      25     I      25     20   55   63    10   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     G      26     G      26     20   55   63     6   26   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     H      27     H      27     20   55   63    10   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      28     L      28     20   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     V      29     V      29     19   55   63     4   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      30     L      30      3   55   63     3   12   37   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D      31     D      31      3   55   63     3    4   13   26   44   50   53   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     Q      32     Q      32      3   55   63     3    3    4   18   35   52   53   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     G      42     G      42      3   55   63     3    3    3    4    6    9   10   34   48   52   54   57   58   60   60   60   60   60   61   61 
LCS_GDT     V      43     V      43      4   55   63    15   17   25   42   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     I      44     I      44     22   55   63     9   21   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     P      45     P      45     22   55   63     9   22   40   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     R      46     R      46     22   55   63     4   22   40   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     R      47     R      47     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     V      48     V      48     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      49     L      49     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     V      50     V      50     22   55   63    13   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     H      51     H      51     22   55   63     6   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     E      52     E      52     22   55   63     3   22   40   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D      53     D      53     22   55   63     3   16   36   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D      54     D      54     22   55   63     3   25   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      55     L      55     22   55   63     9   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      56     A      56     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     G      57     G      57     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      58     A      58     22   55   63    13   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     R      59     R      59     22   55   63    12   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     R      60     R      60     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      61     L      61     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      62     L      62     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     T      63     T      63     22   55   63    14   27   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     D      64     D      64     22   55   63     7   25   41   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      65     A      65     22   55   63     4   18   37   49   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     G      66     G      66      4   27   63     3    4    6   15   38   53   54   55   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      67     L      67      3   27   63     3    3   17   45   51   53   54   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     A      68     A      68      3   27   63     3    5   12   16   42   48   52   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     H      69     H      69      3   27   63     3    4   13   28   43   49   53   56   58   58   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     E      70     E      70      5    6   63     3    4    5   11   12   15   21   34   43   56   59   59   59   60   60   60   60   60   61   61 
LCS_GDT     L      71     L      71      5    6   63     3    4    5    5    6    7    8   11   17   21   27   29   42   49   56   59   60   60   61   61 
LCS_GDT     R      72     R      72      5    6   63     3    4    5    5    6    7    8   10   11   15   16   18   21   30   33   41   43   44   52   55 
LCS_GDT     S      73     S      73      5    6   63     3    4    5    5    6    7    8   10   10   12   14   18   19   22   24   24   26   27   30   40 
LCS_GDT     D      74     D      74      5    6   14     3    3    5    5    6    7    8   10   10   12   12   12   13   17   17   18   18   27   28   30 
LCS_AVERAGE  LCS_A:  56.73  (  21.31   65.90   82.98 )

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     15     27     41     49     51     53     54     56     58     58     59     59     59     60     60     60     60     60     61     61 
GDT PERCENT_CA  20.00  36.00  54.67  65.33  68.00  70.67  72.00  74.67  77.33  77.33  78.67  78.67  78.67  80.00  80.00  80.00  80.00  80.00  81.33  81.33
GDT RMS_LOCAL    0.25   0.60   0.95   1.21   1.27   1.43   1.52   1.79   1.91   1.91   2.15   2.15   2.15   2.41   2.41   2.41   2.41   2.41   2.91   2.91
GDT RMS_ALL_CA   6.38   6.34   6.35   6.29   6.31   6.34   6.35   6.20   6.23   6.23   6.16   6.16   6.16   6.20   6.20   6.20   6.20   6.20   6.08   6.08

#      Molecule1      Molecule2       DISTANCE
LGA    R       2      R       2          2.898
LGA    E       3      E       3          2.597
LGA    L       4      L       4          2.016
LGA    L       5      L       5          1.767
LGA    R       6      R       6          2.214
LGA    T       7      T       7          2.862
LGA    N       8      N       8          4.709
LGA    D       9      D       9          1.844
LGA    A      10      A      10          1.870
LGA    V      11      V      11          1.171
LGA    L      12      L      12          1.069
LGA    L      13      L      13          1.854
LGA    S      14      S      14          1.396
LGA    A      15      A      15          0.715
LGA    V      16      V      16          1.180
LGA    G      17      G      17          1.544
LGA    A      18      A      18          0.812
LGA    L      19      L      19          1.045
LGA    L      20      L      20          1.702
LGA    D      21      D      21          1.973
LGA    G      22      G      22          1.668
LGA    A      23      A      23          2.292
LGA    D      24      D      24          3.109
LGA    I      25      I      25          1.548
LGA    G      26      G      26          2.437
LGA    H      27      H      27          1.938
LGA    L      28      L      28          2.473
LGA    V      29      V      29          1.694
LGA    L      30      L      30          1.204
LGA    D      31      D      31          4.000
LGA    Q      32      Q      32          3.893
LGA    G      42      G      42          9.175
LGA    V      43      V      43          3.755
LGA    I      44      I      44          1.338
LGA    P      45      P      45          1.502
LGA    R      46      R      46          1.782
LGA    R      47      R      47          1.480
LGA    V      48      V      48          1.673
LGA    L      49      L      49          1.931
LGA    V      50      V      50          1.699
LGA    H      51      H      51          1.782
LGA    E      52      E      52          1.912
LGA    D      53      D      53          1.221
LGA    D      54      D      54          1.343
LGA    L      55      L      55          0.532
LGA    A      56      A      56          1.269
LGA    G      57      G      57          1.050
LGA    A      58      A      58          0.843
LGA    R      59      R      59          1.094
LGA    R      60      R      60          1.049
LGA    L      61      L      61          0.801
LGA    L      62      L      62          1.114
LGA    T      63      T      63          1.429
LGA    D      64      D      64          0.493
LGA    A      65      A      65          2.229
LGA    G      66      G      66          4.642
LGA    L      67      L      67          3.161
LGA    A      68      A      68          3.738
LGA    H      69      H      69          3.315
LGA    E      70      E      70          6.847
LGA    L      71      L      71         11.935
LGA    R      72      R      72         17.820
LGA    S      73      S      73         23.660
LGA    D      74      D      74         28.861

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   75    4.0     56    1.79    64.000    67.603     2.967

LGA_LOCAL      RMSD =  1.787  Number of atoms =   56  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.936  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  5.716  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.647078 * X  +  -0.587437 * Y  +   0.486012 * Z  +   0.282698
  Y_new =   0.692545 * X  +   0.719466 * Y  +  -0.052446 * Z  + -63.114235
  Z_new =  -0.318861 * X  +   0.370522 * Y  +   0.872377 * Z  + -44.768719 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.401639   -2.739954  [ DEG:    23.0122   -156.9878 ]
  Theta =   0.324527    2.817065  [ DEG:    18.5940    161.4059 ]
  Phi   =   0.819325   -2.322267  [ DEG:    46.9439   -133.0561 ]
 
# 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: T0349TS677_1                                  
REMARK     2: T0349.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS677_1.T0349.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   64   75   4.0   56   1.79  67.603     5.72
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS677_1
PFRMAT TS
TARGET T0349
MODEL  1
PARENT 1YJ7_A
ATOM     22  CA  ARG     2       2.547   9.375  -5.783  1.00 54.00
ATOM     23  CA  GLU     3       2.594   5.773  -4.579  1.00 54.00
ATOM     24  CA  LEU     4       3.980   5.266  -1.089  1.00 54.00
ATOM     25  CA  LEU     5       3.845   1.491  -0.622  1.00 57.00
ATOM     26  CA  ARG     6       2.431  -1.608  -2.338  1.00 68.00
ATOM     27  CA  THR     7       2.117  -5.202  -1.129  1.00 79.00
ATOM     28  CA  ASN     8       0.549  -4.259   2.212  1.00 91.00
ATOM     29  CA  ASP     9      -1.850  -6.399   4.250  1.00 99.00
ATOM     30  CA  ALA    10      -5.285  -4.935   4.787  1.00 99.00
ATOM     31  CA  VAL    11      -4.575  -4.487   8.530  1.00 94.00
ATOM     32  CA  LEU    12      -1.280  -2.630   8.072  1.00 92.00
ATOM     33  CA  LEU    13      -2.543  -0.453   5.194  1.00 92.00
ATOM     34  CA  SER    14      -5.423   0.490   7.502  1.00 56.00
ATOM     35  CA  ALA    15      -3.059   1.393  10.329  1.00 27.00
ATOM     36  CA  VAL    16      -0.932   3.512   7.972  1.00 46.00
ATOM     37  CA  GLY    17      -3.963   5.175   6.327  1.00 59.00
ATOM     38  CA  ALA    18      -5.521   6.055   9.678  1.00 41.00
ATOM     39  CA  LEU    19      -2.180   7.374  10.970  1.00 50.00
ATOM     40  CA  LEU    20      -1.771   9.673   7.949  1.00 50.00
ATOM     41  CA  ASP    21      -5.350  10.922   7.990  1.00 43.00
ATOM     42  CA  GLY    22      -5.169  11.647  11.720  1.00 32.00
ATOM     43  CA  ALA    23      -1.948  13.604  11.119  1.00 37.00
ATOM     44  CA  ASP    24      -3.620  15.739   8.434  1.00 25.00
ATOM     45  CA  ILE    25      -2.303  14.021   5.346  1.00 37.00
ATOM     46  CA  GLY    26      -4.777  12.874   2.698  1.00 60.00
ATOM     47  CA  HIS    27      -4.336   9.339   1.410  1.00 79.00
ATOM     48  CA  LEU    28      -5.852   7.088  -1.232  1.00 99.00
ATOM     49  CA  VAL    29      -5.935   3.301  -1.227  1.00 99.00
ATOM     50  CA  LEU    30      -6.386   0.586  -3.833  1.00 99.00
ATOM     51  CA  ASP    31      -6.200  -3.209  -3.969  1.00 99.00
ATOM     52  CA  GLN    32      -3.945  -4.700  -6.672  1.00 99.00
ATOM     53  CA  GLY    42      -4.572  -7.871  -8.702  1.00 99.00
ATOM     54  CA  VAL    43      -2.902 -10.088  -6.055  1.00 99.00
ATOM     55  CA  ILE    44      -5.185  -8.837  -3.267  1.00 86.00
ATOM     56  CA  PRO    45      -2.575  -6.599  -1.601  1.00 94.00
ATOM     57  CA  ARG    46      -3.052  -2.926  -0.705  1.00 58.00
ATOM     58  CA  ARG    47      -1.391   0.158  -2.171  1.00 45.00
ATOM     59  CA  VAL    48      -1.353   3.557  -0.444  1.00 45.00
ATOM     60  CA  LEU    49      -0.724   6.805  -2.343  1.00 55.00
ATOM     61  CA  VAL    50      -0.690  10.517  -1.522  1.00 64.00
ATOM     62  CA  HIS    51      -0.875  13.770  -3.453  1.00 79.00
ATOM     63  CA  GLU    52       2.668  14.357  -4.698  1.00 62.00
ATOM     64  CA  ASP    53       3.092  17.579  -2.715  1.00 70.00
ATOM     65  CA  ASP    54       2.442  15.632   0.487  1.00 71.00
ATOM     66  CA  LEU    55       5.072  12.952  -0.120  1.00 55.00
ATOM     67  CA  ALA    56       7.749  14.254   2.287  1.00 49.00
ATOM     68  CA  GLY    57       5.238  14.915   5.111  1.00 55.00
ATOM     69  CA  ALA    58       3.769  11.438   4.604  1.00 69.00
ATOM     70  CA  ARG    59       7.072   9.558   4.638  1.00 85.00
ATOM     71  CA  ARG    60       8.098  11.595   7.715  1.00 86.00
ATOM     72  CA  LEU    61       4.976  10.536   9.620  1.00 94.00
ATOM     73  CA  LEU    62       5.334   6.906   8.537  1.00 89.00
ATOM     74  CA  THR    63       9.082   6.815   9.394  1.00 71.00
ATOM     75  CA  ASP    64       8.343   8.373  12.810  1.00 35.00
ATOM     76  CA  ALA    65       5.888   5.564  13.551  1.00 35.00
ATOM     77  CA  GLY    66       8.015   2.704  12.222  1.00 34.00
ATOM     78  CA  LEU    67       5.916   1.945   9.118  1.00 40.00
ATOM     79  CA  ALA    68       6.029  -0.190   7.178  1.00 49.00
ATOM     80  CA  HIS    69       6.605  -2.494  10.144  1.00 94.00
ATOM     81  CA  GLU    70       9.703  -4.590  10.426  1.00 99.00
ATOM     82  CA  LEU    71       9.286  -8.349  10.488  1.00 99.00
ATOM     83  CA  ARG    72      10.848 -10.719  13.011  1.00 99.00
ATOM     84  CA  SER    73      12.136 -14.268  12.780  1.00 99.00
ATOM     85  CA  ASP    74       9.582 -17.051  12.469  1.00 99.00
TER
END
