
#######################################################
#                                                     #
#                        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   67 (   67),  selected   64 , name T0379TS168_3-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS168_3-D2.T0379_D2.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:    64        17 - 83          3.66     3.66
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        17 - 38          1.74     6.28
  LONGEST_CONTINUOUS_SEGMENT:    22        18 - 39          1.99     6.47
  LCS_AVERAGE:     32.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        17 - 30          0.88     6.66
  LONGEST_CONTINUOUS_SEGMENT:    14        55 - 68          0.65     4.71
  LCS_AVERAGE:     17.58

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:   64
LCS_GDT     N      17     N      17     14   22   64     3   14   18   21   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     R      18     R      18     14   22   64    11   14   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      19     E      19     14   22   64    10   10   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      20     E      20     14   22   64    11   14   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     S      21     S      21     14   22   64    10   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     I      22     I      22     14   22   64    10   11   22   26   33   39   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     R      23     R      23     14   22   64    10   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     R      24     R      24     14   22   64    10   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     F      25     F      25     14   22   64    10   11   22   26   28   39   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     K      26     K      26     14   22   64    10   11   22   26   29   36   45   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     A      27     A      27     14   22   64    10   11   22   26   29   39   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     I      28     I      28     14   22   64     3    9   22   26   29   36   45   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     G      29     G      29     14   22   64     3   11   22   26   29   36   45   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     V      30     V      30     14   22   64     4   11   16   26   28   33   40   48   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     A      31     A      31      4   22   64     3    4   14   26   32   39   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     D      32     D      32      7   22   64     7    7   17   22   31   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     I      33     I      33      7   22   64     7    7   14   21   30   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      34     E      34      7   22   64     7    7   10   22   30   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      35     E      35      7   22   64     7    7   12   17   28   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     M      36     M      36      7   22   64     7    7   12   18   28   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      37     L      37      7   22   64     7    7   12   20   30   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     D      38     D      38      7   22   64     7    7   14   20   29   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     P      39     P      39      3   22   64     3    3    4    5   10   15   19   24   38   44   54   59   63   63   64   64   64   64   64   64 
LCS_GDT     K      43     K      43      0   10   64     0    0    4   21   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     G      44     G      44      9   13   64     7    8   11   15   27   38   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      45     L      45      9   13   64     7    8   13   23   32   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     F      46     F      46      9   17   64     7    8    9   13   19   22   23   25   42   53   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      47     L      47      9   20   64     7    8    9   15   19   22   24   31   49   55   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     D      48     D      48      9   20   64     7    8   10   15   19   34   47   52   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      49     L      49      9   20   64     7    8    9   13   19   22   23   27   42   53   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      50     E      50      9   20   64     7    8    9   11   17   22   23   25   26   32   41   51   58   63   64   64   64   64   64   64 
LCS_GDT     S      51     S      51      9   20   64     3    8    9   14   19   22   23   25   28   43   55   60   63   63   64   64   64   64   64   64 
LCS_GDT     G      52     G      52      9   20   64     0    5    9   13   19   22   23   32   47   53   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     R      53     R      53      6   20   64     4    5    6   13   17   22   40   48   54   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     K      54     K      54      6   20   64     4    4    9   15   27   34   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     S      55     S      55     14   20   64     4    4   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      56     E      56     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      57     E      57     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      58     E      58     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     F      59     F      59     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     R      60     R      60     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     T      61     T      61     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      62     E      62     14   20   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      63     L      63     14   21   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     S      64     S      64     14   21   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     R      65     R      65     14   21   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     Y      66     Y      66     14   21   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     I      67     I      67     14   21   64    12   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     G      68     G      68     14   21   64    10   14   18   23   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     K      69     K      69      5   21   64     4    4   11   19   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     E      70     E      70      5   21   64     4    4   12   22   29   39   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      71     L      71     13   21   64     3    8   14   26   29   36   42   51   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     T      72     T      72     13   21   64     6   11   22   26   29   36   45   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     Y      73     Y      73     13   21   64     6   11   22   26   29   36   45   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     Q      74     Q      74     13   21   64     6   11   22   26   29   39   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     Q      75     Q      75     13   21   64     7   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     V      76     V      76     13   21   64     7   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     Y      77     Y      77     13   21   64     7   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     D      78     D      78     13   21   64     7   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     A      79     A      79     13   21   64     7   14   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      80     L      80     13   21   64     7   11   17   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     L      81     L      81     13   21   64     7   11   19   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     G      82     G      82     13   21   64     3   11   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_GDT     F      83     F      83     13   21   64     3    8   22   26   33   40   47   53   56   57   58   61   63   63   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  49.93  (  17.58   32.23  100.00 )

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     12     14     22     26     33     40     47     53     56     57     58     61     63     63     64     64     64     64     64     64 
GDT PERCENT_CA  18.75  21.88  34.38  40.62  51.56  62.50  73.44  82.81  87.50  89.06  90.62  95.31  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.46   1.05   1.22   1.79   2.05   2.33   2.62   2.78   2.83   2.96   3.26   3.50   3.50   3.66   3.66   3.66   3.66   3.66   3.66
GDT RMS_ALL_CA   4.86   4.52   5.56   5.56   3.99   3.97   3.86   3.82   3.80   3.80   3.76   3.70   3.67   3.67   3.66   3.66   3.66   3.66   3.66   3.66

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          2.462
LGA    R      18      R      18          1.558
LGA    E      19      E      19          2.732
LGA    E      20      E      20          2.051
LGA    S      21      S      21          1.413
LGA    I      22      I      22          2.373
LGA    R      23      R      23          2.382
LGA    R      24      R      24          1.587
LGA    F      25      F      25          2.784
LGA    K      26      K      26          3.639
LGA    A      27      A      27          2.702
LGA    I      28      I      28          3.309
LGA    G      29      G      29          3.910
LGA    V      30      V      30          4.365
LGA    A      31      A      31          2.310
LGA    D      32      D      32          2.658
LGA    I      33      I      33          2.857
LGA    E      34      E      34          2.657
LGA    E      35      E      35          3.346
LGA    M      36      M      36          2.873
LGA    L      37      L      37          2.363
LGA    D      38      D      38          2.923
LGA    P      39      P      39          7.440
LGA    K      43      K      43          1.656
LGA    G      44      G      44          3.270
LGA    L      45      L      45          3.669
LGA    F      46      F      46          7.411
LGA    L      47      L      47          7.317
LGA    D      48      D      48          4.953
LGA    L      49      L      49          7.874
LGA    E      50      E      50         10.793
LGA    S      51      S      51          9.186
LGA    G      52      G      52          7.760
LGA    R      53      R      53          5.245
LGA    K      54      K      54          3.956
LGA    S      55      S      55          3.712
LGA    E      56      E      56          3.793
LGA    E      57      E      57          3.915
LGA    E      58      E      58          3.513
LGA    F      59      F      59          2.852
LGA    R      60      R      60          3.006
LGA    T      61      T      61          3.262
LGA    E      62      E      62          2.741
LGA    L      63      L      63          1.909
LGA    S      64      S      64          2.642
LGA    R      65      R      65          2.582
LGA    Y      66      Y      66          1.450
LGA    I      67      I      67          2.491
LGA    G      68      G      68          2.111
LGA    K      69      K      69          1.420
LGA    E      70      E      70          2.509
LGA    L      71      L      71          4.189
LGA    T      72      T      72          3.548
LGA    Y      73      Y      73          3.684
LGA    Q      74      Q      74          2.759
LGA    Q      75      Q      75          1.299
LGA    V      76      V      76          1.312
LGA    Y      77      Y      77          1.910
LGA    D      78      D      78          1.485
LGA    A      79      A      79          1.312
LGA    L      80      L      80          2.031
LGA    L      81      L      81          2.496
LGA    G      82      G      82          2.484
LGA    F      83      F      83          2.372

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67   64    4.0     53    2.62    61.328    58.214     1.948

LGA_LOCAL      RMSD =  2.621  Number of atoms =   53  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.886  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  3.662  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.832872 * X  +  -0.536759 * Y  +   0.134959 * Z  +  60.919453
  Y_new =  -0.466053 * X  +  -0.811685 * Y  +  -0.352082 * Z  +   8.687979
  Z_new =   0.298527 * X  +   0.230341 * Y  +  -0.926188 * Z  +   7.358439 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.897840   -0.243753  [ DEG:   166.0340    -13.9660 ]
  Theta =  -0.303149   -2.838444  [ DEG:   -17.3692   -162.6308 ]
  Phi   =  -0.510163    2.631429  [ DEG:   -29.2302    150.7698 ]
 
# 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: T0379TS168_3-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0379TS168_3-D2.T0379_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   67   64   4.0   53   2.62  58.214     3.66
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS168_3-D2
PFRMAT TS
TARGET T0379
MODEL 3
PARENT N/A
ATOM     17  CA  ASN    17      68.251   6.871  11.176  1.00 25.00           C
ATOM     18  CA  ARG    18      66.455   5.276  14.177  1.00 25.00           C
ATOM     19  CA  GLU    19      70.012   4.415  15.303  1.00 25.00           C
ATOM     20  CA  GLU    20      70.080   7.521  17.543  1.00 25.00           C
ATOM     21  CA  SER    21      66.710   6.527  19.066  1.00 25.00           C
ATOM     22  CA  ILE    22      68.023   2.991  19.726  1.00 25.00           C
ATOM     23  CA  ARG    23      71.148   4.437  21.401  1.00 25.00           C
ATOM     24  CA  ARG    24      68.960   6.695  23.588  1.00 25.00           C
ATOM     25  CA  PHE    25      66.807   3.688  24.581  1.00 25.00           C
ATOM     26  CA  LYS    26      69.954   1.698  25.477  1.00 25.00           C
ATOM     27  CA  ALA    27      71.226   4.620  27.601  1.00 25.00           C
ATOM     28  CA  ILE    28      69.503   5.318  30.954  1.00 25.00           C
ATOM     29  CA  GLY    29      68.476   1.785  31.833  1.00 25.00           C
ATOM     30  CA  VAL    30      66.112   0.204  29.299  1.00 25.00           C
ATOM     31  CA  ALA    31      64.352  -2.667  27.479  1.00 25.00           C
ATOM     32  CA  ASP    32      61.273  -0.736  28.685  1.00 25.00           C
ATOM     33  CA  ILE    33      62.270   2.257  26.514  1.00 25.00           C
ATOM     34  CA  GLU    34      62.695  -0.048  23.486  1.00 25.00           C
ATOM     35  CA  GLU    35      59.243  -1.576  24.133  1.00 25.00           C
ATOM     36  CA  MET    36      57.709   1.925  24.361  1.00 25.00           C
ATOM     37  CA  LEU    37      59.387   2.902  21.059  1.00 25.00           C
ATOM     38  CA  ASP    38      57.606  -0.021  19.411  1.00 25.00           C
ATOM     39  CA  PRO    39      54.737  -1.533  21.468  1.00 25.00           C
ATOM     40  CA  TYR    40      51.871  -1.533  24.009  1.00 25.00           C
ATOM     41  CA  LEU    41      52.438   2.194  24.683  1.00 25.00           C
ATOM     42  CA  GLN    42      52.389   2.907  20.921  1.00 25.00           C
ATOM     43  CA  LYS    43      49.122   0.941  20.565  1.00 25.00           C
ATOM     44  CA  GLY    44      47.587   2.919  23.463  1.00 25.00           C
ATOM     45  CA  LEU    45      48.668   6.207  21.824  1.00 25.00           C
ATOM     46  CA  PHE    46      47.110   5.096  18.506  1.00 25.00           C
ATOM     47  CA  LEU    47      43.852   4.202  20.310  1.00 25.00           C
ATOM     48  CA  ASP    48      43.823   7.632  22.013  1.00 25.00           C
ATOM     49  CA  LEU    49      44.374   9.342  18.630  1.00 25.00           C
ATOM     50  CA  GLU    50      41.493   7.326  17.114  1.00 25.00           C
ATOM     51  CA  SER    51      38.983   9.553  18.935  1.00 25.00           C
ATOM     52  CA  GLY    52      39.625  13.297  19.052  1.00 25.00           C
ATOM     53  CA  ARG    53      41.413  14.867  21.959  1.00 25.00           C
ATOM     54  CA  LYS    54      44.454  14.265  24.099  1.00 25.00           C
ATOM     55  CA  SER    55      47.242  16.202  22.380  1.00 25.00           C
ATOM     56  CA  GLU    56      50.715  14.772  22.993  1.00 25.00           C
ATOM     57  CA  GLU    57      49.840  15.375  26.673  1.00 25.00           C
ATOM     58  CA  GLU    58      47.887  12.082  26.774  1.00 25.00           C
ATOM     59  CA  PHE    59      50.865  10.240  25.224  1.00 25.00           C
ATOM     60  CA  ARG    60      53.210  11.789  27.826  1.00 25.00           C
ATOM     61  CA  THR    61      50.843  10.711  30.637  1.00 25.00           C
ATOM     62  CA  GLU    62      50.746   7.152  29.223  1.00 25.00           C
ATOM     63  CA  LEU    63      54.572   7.083  29.067  1.00 25.00           C
ATOM     64  CA  SER    64      54.766   8.282  32.699  1.00 25.00           C
ATOM     65  CA  ARG    65      52.298   5.551  33.758  1.00 25.00           C
ATOM     66  CA  TYR    66      54.386   2.917  31.923  1.00 25.00           C
ATOM     67  CA  ILE    67      57.554   4.179  33.667  1.00 25.00           C
ATOM     68  CA  GLY    68      56.585   4.104  37.294  1.00 25.00           C
ATOM     69  CA  LYS    69      59.949   5.303  38.721  1.00 25.00           C
ATOM     70  CA  GLU    70      61.162   8.934  38.846  1.00 25.00           C
ATOM     71  CA  LEU    71      63.384   8.634  35.718  1.00 25.00           C
ATOM     72  CA  THR    72      61.389  11.440  34.170  1.00 25.00           C
ATOM     73  CA  TYR    73      59.154  13.595  31.875  1.00 25.00           C
ATOM     74  CA  GLN    74      62.353  15.570  31.149  1.00 25.00           C
ATOM     75  CA  GLN    75      64.126  12.351  30.069  1.00 25.00           C
ATOM     76  CA  VAL    76      61.195  11.482  27.762  1.00 25.00           C
ATOM     77  CA  TYR    77      61.324  14.992  26.235  1.00 25.00           C
ATOM     78  CA  ASP    78      65.093  14.631  25.663  1.00 25.00           C
ATOM     79  CA  ALA    79      64.539  11.236  23.981  1.00 25.00           C
ATOM     80  CA  LEU    80      61.845  12.766  21.728  1.00 25.00           C
ATOM     81  CA  LEU    81      64.219  15.619  20.785  1.00 25.00           C
ATOM     82  CA  GLY    82      66.972  13.088  19.957  1.00 25.00           C
ATOM     83  CA  PHE    83      64.525  11.102  17.779  1.00 25.00           C
TER
END
