
#######################################################
#                                                     #
#                        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   56 (   56),  selected   56 , name T0349TS677_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   56 , name T0349_D1.pdb
# PARAMETERS: T0349TS677_1-D1.T0349_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:    56         2 - 72          3.54     3.54
  LCS_AVERAGE:     98.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    54         2 - 70          1.98     3.66
  LCS_AVERAGE:     91.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35        15 - 64          0.98     3.66
  LCS_AVERAGE:     45.58

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:   57
LCS_GDT     R       2     R       2      6   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     E       3     E       3      6   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L       4     L       4      6   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L       5     L       5      6   54   56    13   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     R       6     R       6      6   54   56     4   17   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     T       7     T       7     18   54   56     4   12   17   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     N       8     N       8     18   54   56     3    3    3   11   24   32   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     D       9     D       9     20   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      10     A      10     20   54   56    14   25   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     V      11     V      11     20   54   56    14   26   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      12     L      12     20   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      13     L      13     20   54   56    14   26   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     S      14     S      14     20   54   56    14   25   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      15     A      15     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     V      16     V      16     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     G      17     G      17     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      18     A      18     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      19     L      19     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      20     L      20     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     D      21     D      21     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     G      22     G      22     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      23     A      23     35   54   56     6   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     D      24     D      24     35   54   56     6   16   39   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     I      25     I      25     35   54   56    11   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     G      26     G      26     35   54   56     6   26   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     H      27     H      27     35   54   56    10   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      28     L      28     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     V      29     V      29     35   54   56     4   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     P      45     P      45     35   54   56     5   20   39   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     R      46     R      46     35   54   56     4   20   38   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     R      47     R      47     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     V      48     V      48     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      49     L      49     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     V      50     V      50     35   54   56    13   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     H      51     H      51     35   54   56     5   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     E      52     E      52     35   54   56     3   26   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     D      53     D      53     35   54   56     3   12   36   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     D      54     D      54     35   54   56     3   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      55     L      55     35   54   56     9   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      56     A      56     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     G      57     G      57     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      58     A      58     35   54   56    13   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     R      59     R      59     35   54   56    11   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     R      60     R      60     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      61     L      61     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      62     L      62     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     T      63     T      63     35   54   56    14   27   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     D      64     D      64     35   54   56     7   26   40   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      65     A      65     22   54   56     4   18   37   47   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     G      66     G      66      4   54   56     3    4    6    7   15   20   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      67     L      67      3   54   56     3    3   17   45   49   49   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     A      68     A      68      3   54   56     3    5   12   16   36   48   50   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     H      69     H      69      3   54   56     3    3   12   28   39   48   49   51   53   53   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     E      70     E      70      3   54   56     3    3    3   11   12   15   20   32   41   52   54   54   54   54   54   54   55   55   55   55 
LCS_GDT     L      71     L      71      3    5   56     3    3    3    4    6    7    8    8    9   22   23   26   29   32   42   52   55   55   55   55 
LCS_GDT     R      72     R      72      3    4   56     3    3    3    4    6    7    8    8    9   10   11   11   16   17   23   24   25   40   41   48 
LCS_AVERAGE  LCS_A:  78.49  (  45.58   91.64   98.25 )

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     14     27     40     47     49     49     50     51     53     53     54     54     54     54     54     54     55     55     55     55 
GDT PERCENT_CA  24.56  47.37  70.18  82.46  85.96  85.96  87.72  89.47  92.98  92.98  94.74  94.74  94.74  94.74  94.74  94.74  96.49  96.49  96.49  96.49
GDT RMS_LOCAL    0.25   0.60   0.90   1.13   1.21   1.21   1.31   1.41   1.66   1.66   1.98   1.98   1.98   1.98   1.98   1.98   2.61   2.61   2.61   2.61
GDT RMS_ALL_CA   4.36   3.77   3.81   3.75   3.78   3.78   3.80   3.79   3.73   3.73   3.66   3.66   3.66   3.66   3.66   3.66   3.59   3.59   3.59   3.59

#      Molecule1      Molecule2       DISTANCE
LGA    R       2      R       2          1.034
LGA    E       3      E       3          0.932
LGA    L       4      L       4          0.717
LGA    L       5      L       5          0.300
LGA    R       6      R       6          1.345
LGA    T       7      T       7          2.658
LGA    N       8      N       8          4.614
LGA    D       9      D       9          1.250
LGA    A      10      A      10          1.619
LGA    V      11      V      11          0.999
LGA    L      12      L      12          0.524
LGA    L      13      L      13          1.365
LGA    S      14      S      14          1.282
LGA    A      15      A      15          0.745
LGA    V      16      V      16          0.634
LGA    G      17      G      17          1.086
LGA    A      18      A      18          1.008
LGA    L      19      L      19          0.807
LGA    L      20      L      20          0.888
LGA    D      21      D      21          1.071
LGA    G      22      G      22          0.606
LGA    A      23      A      23          1.064
LGA    D      24      D      24          1.887
LGA    I      25      I      25          0.604
LGA    G      26      G      26          1.453
LGA    H      27      H      27          1.118
LGA    L      28      L      28          1.112
LGA    V      29      V      29          1.025
LGA    P      45      P      45          2.190
LGA    R      46      R      46          2.074
LGA    R      47      R      47          0.772
LGA    V      48      V      48          0.698
LGA    L      49      L      49          0.624
LGA    V      50      V      50          0.545
LGA    H      51      H      51          0.979
LGA    E      52      E      52          1.663
LGA    D      53      D      53          2.161
LGA    D      54      D      54          1.333
LGA    L      55      L      55          0.743
LGA    A      56      A      56          0.503
LGA    G      57      G      57          0.580
LGA    A      58      A      58          0.199
LGA    R      59      R      59          0.713
LGA    R      60      R      60          0.962
LGA    L      61      L      61          0.744
LGA    L      62      L      62          0.533
LGA    T      63      T      63          0.900
LGA    D      64      D      64          1.564
LGA    A      65      A      65          1.852
LGA    G      66      G      66          3.626
LGA    L      67      L      67          2.099
LGA    A      68      A      68          3.846
LGA    H      69      H      69          5.165
LGA    E      70      E      70          8.571
LGA    L      71      L      71         13.595
LGA    R      72      R      72         19.888

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   56   57    4.0     51    1.41    78.509    85.620     3.388

LGA_LOCAL      RMSD =  1.405  Number of atoms =   51  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.786  Number of atoms =   56 
Std_ALL_ATOMS  RMSD =  3.544  (standard rmsd on all 56 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.694864 * X  +  -0.632281 * Y  +   0.342614 * Z  +   7.386635
  Y_new =   0.673643 * X  +   0.739053 * Y  +  -0.002336 * Z  + -66.426483
  Z_new =  -0.251733 * X  +   0.232423 * Y  +   0.939473 * Z  + -40.086731 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.242527   -2.899065  [ DEG:    13.8958   -166.1042 ]
  Theta =   0.254471    2.887122  [ DEG:    14.5801    165.4199 ]
  Phi   =   0.769893   -2.371700  [ DEG:    44.1116   -135.8884 ]
 
# 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-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS677_1-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   56   57   4.0   51   1.41  85.620     3.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS677_1-D1
PFRMAT TS
TARGET T0349
MODEL  1
PARENT 1YJ7_A
ATOM     22  CA  ARG     2       4.109   8.168  -5.380  1.00 54.00
ATOM     23  CA  GLU     3       3.936   4.641  -3.982  1.00 54.00
ATOM     24  CA  LEU     4       4.754   4.334  -0.295  1.00 54.00
ATOM     25  CA  LEU     5       4.515   0.592   0.358  1.00 57.00
ATOM     26  CA  ARG     6       3.362  -2.601  -1.382  1.00 68.00
ATOM     27  CA  THR     7       2.833  -6.120  -0.037  1.00 79.00
ATOM     28  CA  ASN     8       0.768  -4.989   2.958  1.00 91.00
ATOM     29  CA  ASP     9      -1.940  -7.011   4.711  1.00 99.00
ATOM     30  CA  ALA    10      -5.403  -5.520   4.617  1.00 99.00
ATOM     31  CA  VAL    11      -5.286  -4.860   8.394  1.00 94.00
ATOM     32  CA  LEU    12      -1.945  -3.030   8.356  1.00 92.00
ATOM     33  CA  LEU    13      -2.722  -1.021   5.197  1.00 92.00
ATOM     34  CA  SER    14      -5.920   0.050   6.967  1.00 56.00
ATOM     35  CA  ALA    15      -4.023   1.114  10.075  1.00 27.00
ATOM     36  CA  VAL    16      -1.534   3.097   7.965  1.00 46.00
ATOM     37  CA  GLY    17      -4.256   4.661   5.774  1.00 59.00
ATOM     38  CA  ALA    18      -6.312   5.731   8.783  1.00 41.00
ATOM     39  CA  LEU    19      -3.205   7.123  10.507  1.00 50.00
ATOM     40  CA  LEU    20      -2.307   9.246   7.463  1.00 50.00
ATOM     41  CA  ASP    21      -5.838  10.493   6.871  1.00 43.00
ATOM     42  CA  GLY    22      -6.239  11.430  10.536  1.00 32.00
ATOM     43  CA  ALA    23      -2.947  13.351  10.340  1.00 37.00
ATOM     44  CA  ASP    24      -4.159  15.329   7.310  1.00 25.00
ATOM     45  CA  ILE    25      -2.388  13.439   4.569  1.00 37.00
ATOM     46  CA  GLY    26      -4.426  12.141   1.633  1.00 60.00
ATOM     47  CA  HIS    27      -3.817   8.538   0.633  1.00 79.00
ATOM     48  CA  LEU    28      -4.918   6.140  -2.084  1.00 99.00
ATOM     49  CA  VAL    29      -5.033   2.358  -1.878  1.00 99.00
ATOM     56  CA  PRO    45      -1.738  -7.544  -1.161  1.00 94.00
ATOM     57  CA  ARG    46      -2.320  -3.827  -0.559  1.00 58.00
ATOM     58  CA  ARG    47      -0.424  -0.830  -1.918  1.00 45.00
ATOM     59  CA  VAL    48      -0.629   2.662  -0.401  1.00 45.00
ATOM     60  CA  LEU    49       0.317   5.797  -2.357  1.00 55.00
ATOM     61  CA  VAL    50       0.254   9.549  -1.752  1.00 64.00
ATOM     62  CA  HIS    51       0.400  12.687  -3.868  1.00 79.00
ATOM     63  CA  GLU    52       4.100  13.205  -4.572  1.00 62.00
ATOM     64  CA  ASP    53       4.234  16.534  -2.732  1.00 70.00
ATOM     65  CA  ASP    54       3.073  14.772   0.432  1.00 71.00
ATOM     66  CA  LEU    55       5.744  12.064   0.399  1.00 55.00
ATOM     67  CA  ALA    56       8.021  13.503   3.119  1.00 49.00
ATOM     68  CA  GLY    57       5.104  14.322   5.472  1.00 55.00
ATOM     69  CA  ALA    58       3.704  10.821   4.937  1.00 69.00
ATOM     70  CA  ARG    59       6.944   8.948   5.596  1.00 85.00
ATOM     71  CA  ARG    60       7.492  11.158   8.676  1.00 86.00
ATOM     72  CA  LEU    61       4.101  10.207  10.123  1.00 94.00
ATOM     73  CA  LEU    62       4.594   6.522   9.317  1.00 89.00
ATOM     74  CA  THR    63       8.159   6.481  10.755  1.00 71.00
ATOM     75  CA  ASP    64       6.906   8.231  13.919  1.00 35.00
ATOM     76  CA  ALA    65       4.343   5.467  14.422  1.00 35.00
ATOM     77  CA  GLY    66       6.627   2.538  13.607  1.00 34.00
ATOM     78  CA  LEU    67       5.035   1.602  10.260  1.00 40.00
ATOM     79  CA  ALA    68       5.434  -0.640   8.486  1.00 49.00
ATOM     80  CA  HIS    69       5.518  -2.770  11.630  1.00 94.00
ATOM     81  CA  GLU    70       8.516  -4.846  12.514  1.00 99.00
ATOM     82  CA  LEU    71       8.063  -8.595  12.721  1.00 99.00
ATOM     83  CA  ARG    72       9.190 -10.816  15.588  1.00 99.00
TER
END
