
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        4.73     6.98
  LCS_AVERAGE:     82.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.73    11.50
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.61    11.95
  LCS_AVERAGE:     37.87

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     L     8_D     L     8_F      3    3   19      0    3    3    3    3    3    4    7   14   15   16   17   18   19   21   22   24   25   25   25 
LCS_GDT     Q     9_D     Q     9_F      3    4   19      3    3    4    6    6    8   11   13   14   14   16   18   19   21   23   24   24   25   25   25 
LCS_GDT     K    10_D     K    10_F      3    4   19      3    4    4    6    6    6    7   11   11   14   15   16   17   20   22   24   24   25   25   25 
LCS_GDT     L    11_D     L    11_F      3   12   20      3    4    4    6    9   11   12   13   14   15   16   18   19   21   23   24   24   25   25   25 
LCS_GDT     N    12_D     N    12_F     10   12   22      7    8    9   11   11   11   12   13   14   16   17   20   20   21   23   24   24   25   25   25 
LCS_GDT     S    13_D     S    13_F     10   12   22      7    8    9   11   11   11   12   13   14   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     W    14_D     W    14_F     10   12   22      7    8    9   11   11   11   12   13   14   15   16   17   19   21   23   24   24   25   25   25 
LCS_GDT     D    15_D     D    15_F     10   12   22      7    8    9   11   11   11   12   13   14   16   17   20   20   21   23   24   24   25   25   25 
LCS_GDT     V    16_D     V    16_F     10   12   22      7    8    9   11   11   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     F    17_D     F    17_F     10   12   22      7    8    9   11   11   11   12   13   14   16   18   20   20   20   23   24   24   25   25   25 
LCS_GDT     G    18_D     G    18_F     10   12   22      7    8    9   11   11   11   12   13   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     N    19_D     N    19_F     10   12   22      7    8   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     W    20_D     W    20_F     10   12   22      3    6    9   11   11   11   12   14   15   15   16   17   18   19   20   21   22   22   25   25 
LCS_GDT     F    21_D     F    21_F     10   13   22      3    4    9   11   11   11   13   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      8   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     R    32_D     R    32_F     12   13   22      9   11   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   12   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   25 
LCS_AVERAGE  LCS_A:  55.08  (  37.87   44.38   82.99 )

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      9     11     12     12     13     14     14     15     16     16     18     20     20     21     23     24     24     25     25     25 
GDT PERCENT_AT  34.62  42.31  46.15  46.15  50.00  53.85  53.85  57.69  61.54  61.54  69.23  76.92  76.92  80.77  88.46  92.31  92.31  96.15  96.15  96.15
GDT RMS_LOCAL    0.26   0.38   0.61   0.61   0.97   1.77   1.77   2.19   2.64   2.64   3.59   4.15   4.15   4.72   5.02   5.25   5.25   5.60   5.60   5.60
GDT RMS_ALL_AT  11.74  11.96  11.95  11.95  11.06   9.63   9.63   9.82   9.12   9.12   8.09   6.97   6.97   6.11   6.09   6.00   6.00   5.93   5.93   5.93

# Checking swapping
#   possible swapping detected:  D    15_D      D    15_F
#   possible swapping detected:  F    17_D      F    17_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    24.574     0    0.276   0.345    26.765    0.000    0.000
LGA    Q     9_D      Q     9_F    18.639     0    0.587   0.591    21.003    0.000    0.000
LGA    K    10_D      K    10_F    19.516     0    0.092   0.369    24.491    0.000    0.000
LGA    L    11_D      L    11_F    16.526     0    0.592   0.723    17.910    0.000    0.000
LGA    N    12_D      N    12_F    13.137     0    0.580   0.945    14.570    0.357    0.179
LGA    S    13_D      S    13_F    12.574     0    0.052   0.150    14.917    0.000    0.000
LGA    W    14_D      W    14_F    14.776     0    0.034   1.212    23.157    0.000    0.000
LGA    D    15_D      D    15_F    10.276     0    0.063   0.959    14.170    6.786    3.393
LGA    V    16_D      V    16_F     4.262     0    0.019   0.044     6.377   29.405   32.177
LGA    F    17_D      F    17_F     9.381     0    0.083   1.276    18.129    4.524    1.645
LGA    G    18_D      G    18_F     6.866     0    0.214   0.214     7.635   26.905   26.905
LGA    N    19_D      N    19_F     1.791     0    0.270   1.006     7.364   54.643   40.536
LGA    W    20_D      W    20_F     6.433     0    0.078   1.107    15.543   19.643    5.952
LGA    F    21_D      F    21_F     4.710     0    0.593   1.171    11.690   40.833   18.442
LGA    D    22_D      D    22_F     2.567     0    0.565   0.855     7.374   64.881   41.012
LGA    L    23_D      L    23_F     2.257     0    0.100   0.677     4.089   66.786   61.369
LGA    A    24_D      A    24_F     1.966     0    0.025   0.024     2.270   72.976   71.333
LGA    S    25_D      S    25_F     1.595     0    0.153   0.727     2.186   79.405   77.302
LGA    W    26_D      W    26_F     1.266     0    0.026   0.431     2.653   85.952   74.320
LGA    I    27_D      I    27_F     0.575     0    0.041   0.116     1.424   95.238   91.786
LGA    K    28_D      K    28_F     0.609     0    0.135   0.311     3.773   88.214   74.021
LGA    Y    29_D      Y    29_F     0.323     0    0.050   0.252     1.055   97.619   94.484
LGA    I    30_D      I    30_F     0.859     0    0.052   0.686     2.803   88.333   80.774
LGA    Q    31_D      Q    31_F     1.590     0    0.044   1.234     6.412   72.976   55.503
LGA    R    32_D      R    32_F     1.312     0    0.407   0.659     2.517   79.286   79.264
LGA    R    33_D      R    33_F     1.616     0    0.565   0.385     9.090   72.976   39.351

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     5.911          5.735                  7.586           44.144   37.298

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.19    59.615    55.444     0.656

LGA_LOCAL      RMSD:   2.186  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.822  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.911  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.573891 * X  +   0.689913 * Y  +   0.441213 * Z  +  46.318829
  Y_new =   0.283275 * X  +  -0.338269 * Y  +   0.897402 * Z  + -64.523285
  Z_new =   0.768378 * X  +   0.639995 * Y  +  -0.001305 * Z  +  -2.529082 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.683075 -0.876302  1.572836   [DEG:  153.7289  -50.2084   90.1169 ]
ZXZ:  2.684643  1.572102  0.876303   [DEG:  153.8187   90.0748   50.2085 ]
 
# END of job
