
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0363AL243_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   25 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_3-D1.T0363_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:    25        29 - 56          4.22     4.22
  LCS_AVERAGE:     54.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        36 - 54          1.99     5.24
  LONGEST_CONTINUOUS_SEGMENT:    17        37 - 55          1.98     5.34
  LCS_AVERAGE:     30.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        36 - 44          0.35     5.32
  LONGEST_CONTINUOUS_SEGMENT:     9        47 - 55          0.99     7.58
  LCS_AVERAGE:     16.26

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:   46
LCS_GDT     S      29     S      29      4    6   25     4    4    5   11   13   13   13   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     F      30     F      30      4    6   25     4    4    6   11   13   13   13   15   17   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     Q      31     Q      31      4    6   25     4    4    8   11   13   13   13   15   17   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     V      32     V      32      4    6   25     4    4    6   10   13   13   13   15   16   18   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     E      34     E      34      3    6   25     0    3    4    6    7    9   11   15   15   15   15   17   18   19   24   25   25   25   25   25 
LCS_GDT     G      35     G      35      3   10   25     3    3    4    6    7    9   11   15   15   17   20   21   22   24   24   25   25   25   25   25 
LCS_GDT     I      36     I      36      9   17   25     8    9    9   12   14   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     T      37     T      37      9   17   25     8    9    9   12   14   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     V      38     V      38      9   17   25     8    9    9   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     Q      39     Q      39      9   17   25     8    9    9   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     T      40     T      40      9   17   25     8    9    9   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     A      41     A      41      9   17   25     8    9    9   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     I      42     I      42      9   17   25     8    9   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     T      43     T      43      9   17   25     8    9   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     Q      44     Q      44      9   17   25     8    9    9   11   13   16   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     I      47     I      47      9   17   25     7    8   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     L      48     L      48      9   17   25     5    8   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     S      49     S      49      9   17   25     7    8   10   11   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     Q      50     Q      50      9   17   25     7    8   10   11   15   17   18   18   19   19   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     F      51     F      51      9   17   25     7    8   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     P      52     P      52      9   17   25     7    8   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     E      53     E      53      9   17   25     7    8   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     I      54     I      54      9   17   25     7    8   10   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     D      55     D      55      9   17   25     3    3    7   12   15   17   18   18   19   20   21   22   23   24   24   25   25   25   25   25 
LCS_GDT     L      56     L      56      3   10   25     3    4    5    6    7   11   12   13   16   17   20   21   23   24   24   25   25   25   25   25 
LCS_AVERAGE  LCS_A:  33.86  (  16.26   30.96   54.35 )

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      9     10     12     15     17     18     18     19     20     21     22     23     24     24     25     25     25     25     25 
GDT PERCENT_CA  17.39  19.57  21.74  26.09  32.61  36.96  39.13  39.13  41.30  43.48  45.65  47.83  50.00  52.17  52.17  54.35  54.35  54.35  54.35  54.35
GDT RMS_LOCAL    0.23   0.35   0.92   1.39   1.70   1.88   2.04   2.04   2.59   3.08   3.17   3.43   3.63   3.88   3.88   4.22   4.22   4.22   4.22   4.22
GDT RMS_ALL_CA   5.19   5.32   6.96   5.21   5.65   5.32   5.19   5.19   4.76   4.39   4.46   4.37   4.34   4.26   4.26   4.22   4.22   4.22   4.22   4.22

#      Molecule1      Molecule2       DISTANCE
LGA    S      29      S      29          8.669
LGA    F      30      F      30          9.102
LGA    Q      31      Q      31          9.094
LGA    V      32      V      32          9.211
LGA    E      34      E      34         11.711
LGA    G      35      G      35          9.413
LGA    I      36      I      36          2.576
LGA    T      37      T      37          1.854
LGA    V      38      V      38          0.696
LGA    Q      39      Q      39          0.875
LGA    T      40      T      40          1.085
LGA    A      41      A      41          1.800
LGA    I      42      I      42          2.150
LGA    T      43      T      43          1.715
LGA    Q      44      Q      44          3.697
LGA    I      47      I      47          2.721
LGA    L      48      L      48          1.379
LGA    S      49      S      49          2.681
LGA    Q      50      Q      50          2.920
LGA    F      51      F      51          1.500
LGA    P      52      P      52          1.027
LGA    E      53      E      53          1.492
LGA    I      54      I      54          1.062
LGA    D      55      D      55          2.490
LGA    L      56      L      56          6.960

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25   46    4.0     18    2.04    34.783    35.256     0.841

LGA_LOCAL      RMSD =  2.039  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.195  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  4.224  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.553718 * X  +   0.816266 * Y  +   0.164636 * Z  +  14.813102
  Y_new =  -0.742756 * X  +   0.394775 * Y  +   0.540801 * Z  +   4.457094
  Z_new =   0.376444 * X  +  -0.421736 * Y  +   0.824881 * Z  +  19.040026 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.472622    2.668970  [ DEG:   -27.0793    152.9207 ]
  Theta =  -0.385955   -2.755638  [ DEG:   -22.1136   -157.8864 ]
  Phi   =  -0.930187    2.211406  [ DEG:   -53.2958    126.7042 ]
 
# 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: T0363AL243_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_3-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25   46   4.0   18   2.04  35.256     4.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_3-D1
REMARK Aligment from pdb entry: 1v8cA
ATOM      1  N   SER    29      24.694  21.014  -0.907  1.00  0.00              
ATOM      2  CA  SER    29      24.191  19.803  -0.268  1.00  0.00              
ATOM      3  C   SER    29      24.794  18.550  -0.874  1.00  0.00              
ATOM      4  O   SER    29      25.057  18.484  -2.076  1.00  0.00              
ATOM      5  N   PHE    30      25.019  17.556  -0.021  1.00  0.00              
ATOM      6  CA  PHE    30      25.597  16.292  -0.440  1.00  0.00              
ATOM      7  C   PHE    30      24.888  15.160   0.284  1.00  0.00              
ATOM      8  O   PHE    30      24.345  15.356   1.365  1.00  0.00              
ATOM      9  N   GLN    31      24.875  13.989  -0.338  1.00  0.00              
ATOM     10  CA  GLN    31      24.286  12.799   0.260  1.00  0.00              
ATOM     11  C   GLN    31      25.488  11.898   0.536  1.00  0.00              
ATOM     12  O   GLN    31      26.222  11.536  -0.389  1.00  0.00              
ATOM     13  N   VAL    32      25.698  11.547   1.803  1.00  0.00              
ATOM     14  CA  VAL    32      26.833  10.709   2.189  1.00  0.00              
ATOM     15  C   VAL    32      26.392   9.613   3.136  1.00  0.00              
ATOM     16  O   VAL    32      25.518   9.827   3.970  1.00  0.00              
ATOM     17  N   GLU    34      26.996   8.420   3.026  1.00  0.00              
ATOM     18  CA  GLU    34      26.620   7.312   3.909  1.00  0.00              
ATOM     19  C   GLU    34      27.168   7.465   5.328  1.00  0.00              
ATOM     20  O   GLU    34      28.108   8.227   5.570  1.00  0.00              
ATOM     21  N   GLY    35      26.556   6.750   6.266  1.00  0.00              
ATOM     22  CA  GLY    35      27.010   6.805   7.646  1.00  0.00              
ATOM     23  C   GLY    35      25.864   6.639   8.618  1.00  0.00              
ATOM     24  O   GLY    35      24.797   7.218   8.413  1.00  0.00              
ATOM     25  N   ILE    36      26.096   5.854   9.673  1.00  0.00              
ATOM     26  CA  ILE    36      25.089   5.580  10.694  1.00  0.00              
ATOM     27  C   ILE    36      25.244   6.446  11.947  1.00  0.00              
ATOM     28  O   ILE    36      24.432   6.356  12.871  1.00  0.00              
ATOM     29  N   THR    37      26.298   7.260  11.980  1.00  0.00              
ATOM     30  CA  THR    37      26.530   8.193  13.087  1.00  0.00              
ATOM     31  C   THR    37      27.044   9.481  12.471  1.00  0.00              
ATOM     32  O   THR    37      27.517   9.492  11.324  1.00  0.00              
ATOM     33  N   VAL    38      26.949  10.566  13.225  1.00  0.00              
ATOM     34  CA  VAL    38      27.419  11.853  12.734  1.00  0.00              
ATOM     35  C   VAL    38      28.892  11.742  12.330  1.00  0.00              
ATOM     36  O   VAL    38      29.298  12.242  11.278  1.00  0.00              
ATOM     37  N   GLN    39      29.684  11.066  13.157  1.00  0.00              
ATOM     38  CA  GLN    39      31.098  10.895  12.866  1.00  0.00              
ATOM     39  C   GLN    39      31.353  10.178  11.551  1.00  0.00              
ATOM     40  O   GLN    39      32.206  10.605  10.777  1.00  0.00              
ATOM     41  N   THR    40      30.627   9.089  11.305  1.00  0.00              
ATOM     42  CA  THR    40      30.808   8.331  10.068  1.00  0.00              
ATOM     43  C   THR    40      30.505   9.221   8.868  1.00  0.00              
ATOM     44  O   THR    40      31.240   9.212   7.875  1.00  0.00              
ATOM     45  N   ALA    41      29.436  10.002   8.962  1.00  0.00              
ATOM     46  CA  ALA    41      29.071  10.891   7.866  1.00  0.00              
ATOM     47  C   ALA    41      30.149  11.944   7.626  1.00  0.00              
ATOM     48  O   ALA    41      30.528  12.199   6.479  1.00  0.00              
ATOM     49  N   ILE    42      30.649  12.553   8.698  1.00  0.00              
ATOM     50  CA  ILE    42      31.677  13.574   8.565  1.00  0.00              
ATOM     51  C   ILE    42      33.000  13.008   8.057  1.00  0.00              
ATOM     52  O   ILE    42      33.709  13.683   7.321  1.00  0.00              
ATOM     53  N   THR    43      33.333  11.773   8.437  1.00  0.00              
ATOM     54  CA  THR    43      34.566  11.167   7.950  1.00  0.00              
ATOM     55  C   THR    43      34.406  10.976   6.446  1.00  0.00              
ATOM     56  O   THR    43      35.347  11.196   5.678  1.00  0.00              
ATOM     57  N   GLN    44      33.213  10.579   6.009  1.00  0.00              
ATOM     58  CA  GLN    44      33.007  10.410   4.576  1.00  0.00              
ATOM     59  C   GLN    44      33.028  11.747   3.851  1.00  0.00              
ATOM     60  O   GLN    44      33.489  11.835   2.710  1.00  0.00              
ATOM     61  N   ILE    47      32.558  12.796   4.515  1.00  0.00              
ATOM     62  CA  ILE    47      32.554  14.121   3.907  1.00  0.00              
ATOM     63  C   ILE    47      33.975  14.549   3.536  1.00  0.00              
ATOM     64  O   ILE    47      34.207  15.069   2.438  1.00  0.00              
ATOM     65  N   LEU    48      34.931  14.320   4.438  1.00  0.00              
ATOM     66  CA  LEU    48      36.306  14.717   4.161  1.00  0.00              
ATOM     67  C   LEU    48      37.013  13.754   3.208  1.00  0.00              
ATOM     68  O   LEU    48      38.033  14.099   2.616  1.00  0.00              
ATOM     69  N   SER    49      36.476  12.547   3.061  1.00  0.00              
ATOM     70  CA  SER    49      37.044  11.594   2.113  1.00  0.00              
ATOM     71  C   SER    49      36.594  12.061   0.728  1.00  0.00              
ATOM     72  O   SER    49      37.289  11.846  -0.270  1.00  0.00              
ATOM     73  N   GLN    50      35.435  12.716   0.680  1.00  0.00              
ATOM     74  CA  GLN    50      34.883  13.224  -0.582  1.00  0.00              
ATOM     75  C   GLN    50      35.435  14.607  -0.938  1.00  0.00              
ATOM     76  O   GLN    50      35.700  14.897  -2.109  1.00  0.00              
ATOM     77  N   PHE    51      35.597  15.453   0.075  1.00  0.00              
ATOM     78  CA  PHE    51      36.102  16.812  -0.099  1.00  0.00              
ATOM     79  C   PHE    51      37.143  17.092   0.972  1.00  0.00              
ATOM     80  O   PHE    51      36.871  17.767   1.964  1.00  0.00              
ATOM     81  N   PRO    52      38.367  16.586   0.767  1.00  0.00              
ATOM     82  CA  PRO    52      39.459  16.776   1.724  1.00  0.00              
ATOM     83  C   PRO    52      39.814  18.222   2.062  1.00  0.00              
ATOM     84  O   PRO    52      40.459  18.477   3.078  1.00  0.00              
ATOM     85  N   GLU    53      39.387  19.166   1.225  1.00  0.00              
ATOM     86  CA  GLU    53      39.650  20.578   1.467  1.00  0.00              
ATOM     87  C   GLU    53      38.994  21.023   2.773  1.00  0.00              
ATOM     88  O   GLU    53      39.401  22.009   3.380  1.00  0.00              
ATOM     89  N   ILE    54      37.982  20.279   3.210  1.00  0.00              
ATOM     90  CA  ILE    54      37.269  20.596   4.445  1.00  0.00              
ATOM     91  C   ILE    54      37.893  19.994   5.701  1.00  0.00              
ATOM     92  O   ILE    54      37.515  20.351   6.815  1.00  0.00              
ATOM     93  N   ASP    55      38.848  19.087   5.529  1.00  0.00              
ATOM     94  CA  ASP    55      39.462  18.428   6.678  1.00  0.00              
ATOM     95  C   ASP    55      40.067  19.387   7.699  1.00  0.00              
ATOM     96  O   ASP    55      39.829  19.257   8.904  1.00  0.00              
ATOM     97  N   LEU    56      40.846  20.343   7.203  1.00  0.00              
ATOM     98  CA  LEU    56      41.523  21.332   8.033  1.00  0.00              
ATOM     99  C   LEU    56      40.573  22.175   8.875  1.00  0.00              
ATOM    100  O   LEU    56      40.911  22.570   9.988  1.00  0.00              
END
