
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0358AL381_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   16 , name T0358_D1.pdb
# PARAMETERS: T0358AL381_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:    14        40 - 53          4.86     6.77
  LCS_AVERAGE:     21.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        41 - 46          1.98    14.14
  LONGEST_CONTINUOUS_SEGMENT:     6        42 - 47          1.55    15.75
  LONGEST_CONTINUOUS_SEGMENT:     6        47 - 52          1.94     7.98
  LCS_AVERAGE:      8.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        42 - 46          0.54    16.62
  LCS_AVERAGE:      6.06

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     V      40     V      40      3    3   14     3    3    3    3    4    5    6    8   10   11   11   11   11   11   13   13   14   14   16   16 
LCS_GDT     V      41     V      41      3    6   14     3    3    3    3    4    6    6    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     R      42     R      42      5    6   14     4    5    5    5    5    6    6    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     D      43     D      43      5    6   14     4    5    5    5    5    7    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     T      44     T      44      5    6   14     4    5    5    5    5    6    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     E      45     E      45      5    6   14     4    5    5    5    5    6    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     G      46     G      46      5    6   14     3    5    5    6    6    7    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     R      47     R      47      3    6   14     3    3    4    4    5    6    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     M      48     M      48      4    6   14     3    3    4    6    6    7    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     V      49     V      49      4    6   14     3    4    4    6    6    7    7    8   10   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     W      50     W      50      4    6   14     3    4    4    6    6    7    7    8    9   11   11   12   13   13   14   15   15   15   16   16 
LCS_GDT     R      51     R      51      4    6   14     3    4    4    6    6    7    7    8    8   10   10   12   13   13   14   15   15   15   16   16 
LCS_GDT     A      52     A      52      4    6   14     0    4    4    6    6    7    7    8    8   10   10   12   13   13   14   15   15   15   16   16 
LCS_GDT     W      53     W      53      3    3   14     3    3    3    3    3    5    6    8    8   10   10   12   13   13   14   15   15   15   16   16 
LCS_GDT     N      54     N      54      3    3   13     3    3    3    3    4    5    5    5    7    8    9   12   13   13   14   15   15   15   16   16 
LCS_GDT     F      55     F      55      3    3   10     3    3    3    3    4    5    5    5    6    8    9   12   13   13   14   15   15   15   16   16 
LCS_AVERAGE  LCS_A:  11.73  (   6.06    8.08   21.06 )

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      4      5      5      6      6      7      7      8     10     11     11     12     13     13     14     15     15     15     16     16 
GDT PERCENT_CA   6.15   7.69   7.69   9.23   9.23  10.77  10.77  12.31  15.38  16.92  16.92  18.46  20.00  20.00  21.54  23.08  23.08  23.08  24.62  24.62
GDT RMS_LOCAL    0.38   0.54   0.54   1.53   1.53   2.11   2.11   2.64   3.32   3.57   3.57   4.11   4.32   4.32   4.93   5.29   5.29   5.29   5.81   5.81
GDT RMS_ALL_CA  16.95  16.62  16.62   6.75   6.75   6.43   6.43   6.55  11.82  10.61  10.61   7.04   6.49   6.49   5.86   5.85   5.85   5.85   5.81   5.81

#      Molecule1      Molecule2       DISTANCE
LGA    V      40      V      40         11.021
LGA    V      41      V      41          6.194
LGA    R      42      R      42          7.372
LGA    D      43      D      43          2.977
LGA    T      44      T      44          3.918
LGA    E      45      E      45          5.197
LGA    G      46      G      46          2.795
LGA    R      47      R      47          6.786
LGA    M      48      M      48          2.138
LGA    V      49      V      49          1.932
LGA    W      50      W      50          1.959
LGA    R      51      R      51          2.539
LGA    A      52      A      52          2.255
LGA    W      53      W      53          5.969
LGA    N      54      N      54         11.983
LGA    F      55      F      55         12.852

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   65    4.0      8    2.64    13.077    11.810     0.292

LGA_LOCAL      RMSD =  2.639  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.554  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  5.808  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.516882 * X  +   0.684723 * Y  +  -0.513797 * Z  +   1.181136
  Y_new =  -0.853865 * X  +   0.369449 * Y  +  -0.366637 * Z  +  29.515505
  Z_new =  -0.061223 * X  +   0.628221 * Y  +   0.775623 * Z  +  -9.347178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.680783   -2.460810  [ DEG:    39.0060   -140.9940 ]
  Theta =   0.061261    3.080332  [ DEG:     3.5100    176.4900 ]
  Phi   =  -1.026456    2.115136  [ DEG:   -58.8116    121.1884 ]
 
# 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: T0358AL381_2-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_2-D1.T0358_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   65   4.0    8   2.64  11.810     5.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_2-D1
REMARK Aligment from pdb entry: 2eql
ATOM      1  N   VAL    40      -2.381 -10.150   3.434  1.00  0.00              
ATOM      2  CA  VAL    40      -3.290  -9.124   3.946  1.00  0.00              
ATOM      3  C   VAL    40      -4.340  -8.792   2.894  1.00  0.00              
ATOM      4  O   VAL    40      -5.520  -8.925   3.219  1.00  0.00              
ATOM      5  N   VAL    41      -3.988  -8.393   1.647  1.00  0.00              
ATOM      6  CA  VAL    41      -4.971  -7.978   0.599  1.00  0.00              
ATOM      7  C   VAL    41      -6.098  -8.971   0.324  1.00  0.00              
ATOM      8  O   VAL    41      -7.065  -8.635  -0.352  1.00  0.00              
ATOM      9  N   ARG    42      -5.837 -10.203   0.747  1.00  0.00              
ATOM     10  CA  ARG    42      -6.696 -11.334   0.610  1.00  0.00              
ATOM     11  C   ARG    42      -7.740 -11.452   1.703  1.00  0.00              
ATOM     12  O   ARG    42      -8.397 -12.477   1.859  1.00  0.00              
ATOM     13  N   ASP    43      -7.834 -10.474   2.554  1.00  0.00              
ATOM     14  CA  ASP    43      -8.919 -10.479   3.476  1.00  0.00              
ATOM     15  C   ASP    43     -10.019  -9.626   2.809  1.00  0.00              
ATOM     16  O   ASP    43      -9.783  -8.925   1.810  1.00  0.00              
ATOM     17  N   THR    44     -11.265  -9.691   3.284  1.00  0.00              
ATOM     18  CA  THR    44     -12.359  -8.805   2.858  1.00  0.00              
ATOM     19  C   THR    44     -12.087  -7.305   2.838  1.00  0.00              
ATOM     20  O   THR    44     -12.685  -6.626   2.010  1.00  0.00              
ATOM     21  N   GLU    45     -11.260  -6.687   3.689  1.00  0.00              
ATOM     22  CA  GLU    45     -10.987  -5.259   3.548  1.00  0.00              
ATOM     23  C   GLU    45     -10.155  -5.005   2.296  1.00  0.00              
ATOM     24  O   GLU    45     -10.169  -3.848   1.835  1.00  0.00              
ATOM     25  N   GLY    46      -9.410  -5.954   1.720  1.00  0.00              
ATOM     26  CA  GLY    46      -8.598  -5.631   0.557  1.00  0.00              
ATOM     27  C   GLY    46      -7.607  -4.517   0.905  1.00  0.00              
ATOM     28  O   GLY    46      -7.202  -4.419   2.087  1.00  0.00              
ATOM     29  N   ARG    47      -7.285  -3.574  -0.026  1.00  0.00              
ATOM     30  CA  ARG    47      -6.302  -2.547   0.335  1.00  0.00              
ATOM     31  C   ARG    47      -6.750  -1.471   1.279  1.00  0.00              
ATOM     32  O   ARG    47      -5.987  -0.603   1.702  1.00  0.00              
ATOM     33  N   MET    48      -7.971  -1.674   1.732  1.00  0.00              
ATOM     34  CA  MET    48      -8.567  -0.756   2.654  1.00  0.00              
ATOM     35  C   MET    48      -8.081  -1.051   4.066  1.00  0.00              
ATOM     36  O   MET    48      -8.269  -0.257   5.011  1.00  0.00              
ATOM     37  N   VAL    49      -7.334  -2.166   4.186  1.00  0.00              
ATOM     38  CA  VAL    49      -6.630  -2.421   5.437  1.00  0.00              
ATOM     39  C   VAL    49      -5.606  -1.301   5.675  1.00  0.00              
ATOM     40  O   VAL    49      -5.183  -1.111   6.812  1.00  0.00              
ATOM     41  N   TRP    50      -5.225  -0.514   4.638  1.00  0.00              
ATOM     42  CA  TRP    50      -4.250   0.554   4.734  1.00  0.00              
ATOM     43  C   TRP    50      -4.846   1.928   4.635  1.00  0.00              
ATOM     44  O   TRP    50      -5.012   2.471   3.559  1.00  0.00              
ATOM     45  N   ARG    51      -5.083   2.565   5.767  1.00  0.00              
ATOM     46  CA  ARG    51      -5.615   3.936   5.911  1.00  0.00              
ATOM     47  C   ARG    51      -5.022   5.021   5.027  1.00  0.00              
ATOM     48  O   ARG    51      -5.754   5.906   4.562  1.00  0.00              
ATOM     49  N   ALA    52      -3.716   4.951   4.764  1.00  0.00              
ATOM     50  CA  ALA    52      -3.087   5.941   3.909  1.00  0.00              
ATOM     51  C   ALA    52      -3.428   5.714   2.445  1.00  0.00              
ATOM     52  O   ALA    52      -3.501   6.669   1.652  1.00  0.00              
ATOM     53  N   TRP    53      -3.693   4.453   2.073  1.00  0.00              
ATOM     54  CA  TRP    53      -4.037   4.132   0.713  1.00  0.00              
ATOM     55  C   TRP    53      -5.451   4.629   0.560  1.00  0.00              
ATOM     56  O   TRP    53      -5.758   5.285  -0.424  1.00  0.00              
ATOM     57  N   ASN    54      -6.345   4.286   1.479  1.00  0.00              
ATOM     58  CA  ASN    54      -7.734   4.746   1.456  1.00  0.00              
ATOM     59  C   ASN    54      -7.790   6.259   1.286  1.00  0.00              
ATOM     60  O   ASN    54      -8.454   6.727   0.373  1.00  0.00              
ATOM     61  N   PHE    55      -7.030   6.996   2.112  1.00  0.00              
ATOM     62  CA  PHE    55      -6.968   8.441   2.101  1.00  0.00              
ATOM     63  C   PHE    55      -6.156   9.026   0.961  1.00  0.00              
ATOM     64  O   PHE    55      -6.260  10.208   0.633  1.00  0.00              
END
