
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   25 (  216),  selected   25 , name one
# Molecule2: number of CA atoms  431 ( 3484),  selected   25 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      74_A - 87_A        4.95    14.61
  LCS_AVERAGE:      2.91

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      70_A - 77_A        1.47    13.61
  LCS_AVERAGE:      1.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      70_A - 76_A        0.98    14.10
  LCS_AVERAGE:      1.19

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   25
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     D    70_A     D    70_A      7    8   11      3    5    7    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     V    71_A     V    71_A      7    8   11      4    6    7    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     I    72_A     I    72_A      7    8   11      4    6    7    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     S    73_A     S    73_A      7    8   13      4    6    7    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     F    74_A     F    74_A      7    8   14      4    6    7    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     T    75_A     T    75_A      7    8   14      3    6    7    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     C    76_A     C    76_A      7    8   14      3    6    6    8    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     L    77_A     L    77_A      5    8   14      4    5    5    7    8    9    9    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     K    78_A     K    78_A      5    6   14      4    5    5    5    6    6    7    9    9   10   12   14   14   14   15   16   18   19   19   20 
LCS_GDT     N    79_A     N    79_A      5    6   14      4    5    5    5    6    6    7    9    9   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     K    80_A     K    80_A      5    6   14      4    5    5    5    6    6    7    7    8    9   10   11   12   14   15   16   18   19   19   20 
LCS_GDT     T    81_A     T    81_A      5    6   14      4    5    5    5    6    6    7    9    9    9   10   11   13   14   15   16   18   19   19   20 
LCS_GDT     V    82_A     V    82_A      4    6   14      3    3    4    4    6    6    7    9    9    9   10   11   13   14   15   16   18   19   19   20 
LCS_GDT     W    83_A     W    83_A      3    4   14      3    3    3    4    4    5    7    9    9    9   10   11   12   14   15   16   18   19   19   20 
LCS_GDT     N    84_A     N    84_A      3    4   14      3    3    3    4    4    5    6    9    9   10   11   13   13   14   15   16   18   19   19   20 
LCS_GDT     R    85_A     R    85_A      3    4   14      3    3    3    5    6    6    7    8    8   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     R    86_A     R    86_A      3    5   14      3    4    4    6    6    7    8    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     A    87_A     A    87_A      5    7   14      4    4    5    6    7    7    8    9   11   11   13   14   14   14   15   16   18   19   19   20 
LCS_GDT     Y    88_A     Y    88_A      5    7   12      4    6    7    8    8    9    9    9   11   11   13   14   14   14   15   16   17   19   19   20 
LCS_GDT     I    89_A     I    89_A      5    7   10      4    4    5    6    7    7    7    8   10   10   10   11   12   13   14   16   16   17   19   20 
LCS_GDT     K    90_A     K    90_A      5    7   10      4    4    5    6    7    7    7    8    9   10   10   10   11   11   11   12   13   15   16   16 
LCS_GDT     F    91_A     F    91_A      5    7   10      3    4    5    6    7    7    7    8    9   10   10   10   11   11   11   12   13   13   14   15 
LCS_GDT     K    92_A     K    92_A      5    7   10      3    4    5    6    7    7    7    8    9   10   10   10   11   11   11   12   13   13   14   15 
LCS_GDT     D    93_A     D    93_A      5    7   10      3    3    5    6    7    7    7    8    9   10   10   10   11   11   11   12   13   13   14   15 
LCS_GDT     K    94_A     K    94_A      3    3   10      3    3    3    3    3    5    6    7    8    8    8    8   11   11   11   12   12   13   14   15 
LCS_AVERAGE  LCS_A:   1.87  (   1.19    1.51    2.91 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT      4      6      7      8      8      9      9      9     11     11     13     14     14     14     15     16     18     19     19     20 
GDT PERCENT_AT   0.93   1.39   1.62   1.86   1.86   2.09   2.09   2.09   2.55   2.55   3.02   3.25   3.25   3.25   3.48   3.71   4.18   4.41   4.41   4.64
GDT RMS_LOCAL    0.13   0.66   0.86   1.17   1.17   1.45   1.45   1.45   2.87   2.87   3.75   3.98   3.98   3.98   4.47   4.93   5.77   5.95   5.95   6.30
GDT RMS_ALL_AT  13.24  13.49  13.30  13.33  13.33  13.37  13.37  13.37  13.33  13.33  13.41  13.67  13.67  13.67  13.69  13.33  14.55  14.19  14.19  13.73

# Checking swapping
#   possible swapping detected:  F    91_A      F    91_A
#   possible swapping detected:  D    93_A      D    93_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    70_A      D    70_A     1.664     0    0.689   0.583     4.171   61.905   65.357
LGA    V    71_A      V    71_A     0.802     0    0.386   0.339     2.184   81.786   82.925
LGA    I    72_A      I    72_A     0.757     0    0.102   0.683     2.918   92.857   88.690
LGA    S    73_A      S    73_A     0.935     0    0.065   0.628     2.296   90.476   84.683
LGA    F    74_A      F    74_A     1.045     0    0.028   1.322     4.511   88.333   71.558
LGA    T    75_A      T    75_A     0.838     0    0.063   0.182     3.679   88.452   74.150
LGA    C    76_A      C    76_A     2.371     0    0.665   0.620     6.785   72.976   57.063
LGA    L    77_A      L    77_A     2.532     0    0.691   0.638     4.451   51.071   59.048
LGA    K    78_A      K    78_A     8.746     0    0.038   0.890    20.441    5.952    2.646
LGA    N    79_A      N    79_A     8.660     0    0.044   0.327    12.905    1.429    4.821
LGA    K    80_A      K    80_A    15.236     0    0.122   1.046    22.318    0.000    0.000
LGA    T    81_A      T    81_A    15.484     0    0.589   1.448    15.638    0.000    0.000
LGA    V    82_A      V    82_A    15.843     0    0.267   1.218    18.056    0.000    0.000
LGA    W    83_A      W    83_A    16.246     0    0.573   1.277    26.136    0.000    0.000
LGA    N    84_A      N    84_A    13.827     0    0.623   0.569    15.503    0.000    0.000
LGA    R    85_A      R    85_A    11.878     0    0.644   0.844    18.358    0.000    0.000
LGA    R    86_A      R    86_A     8.584     0    0.593   1.290     9.730    1.905   10.130
LGA    A    87_A      A    87_A     7.111     0    0.590   0.606     9.072   18.690   15.238
LGA    Y    88_A      Y    88_A     0.392     0    0.029   0.595     4.378   71.786   68.611
LGA    I    89_A      I    89_A     5.185     0    0.051   0.569     9.166   19.524   25.000
LGA    K    90_A      K    90_A    12.011     0    0.084   0.219    13.768    0.357    0.159
LGA    F    91_A      F    91_A    18.295     0    0.088   0.257    20.710    0.000    0.000
LGA    K    92_A      K    92_A    23.065     0    0.604   0.903    26.564    0.000    0.000
LGA    D    93_A      D    93_A    29.632     0    0.082   0.946    35.531    0.000    0.000
LGA    K    94_A      K    94_A    30.613     0    0.630   0.991    33.757    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       25     100    100  100.00     216    216  100.00               431
SUMMARY(RMSD_GDC):    10.824         10.667                 11.693            1.734    1.648

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   25  431    4.0      9    1.45     2.262     2.126     0.582

LGA_LOCAL      RMSD:   1.447  Number of atoms:    9  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.367  Number of assigned atoms:   25 
Std_ASGN_ATOMS RMSD:  10.824  Standard rmsd on all 25 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.272972 * X  +   0.450388 * Y  +  -0.850081 * Z  + -38.089886
  Y_new =   0.842089 * X  +  -0.315394 * Y  +  -0.437507 * Z  +  17.268967
  Z_new =  -0.465158 * X  +  -0.835271 * Y  +  -0.293173 * Z  +  53.940212 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.884268  0.483814 -1.908354   [DEG:  107.9606   27.7205 -109.3406 ]
ZXZ: -1.095486  1.868340 -2.633471   [DEG:  -62.7667  107.0480 -150.8868 ]
 
# END of job
