
#######################################################
#                                                     #
#                        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        4.70     7.17
  LCS_AVERAGE:     82.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.71    11.96
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.63    12.48
  LCS_AVERAGE:     39.79

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   16   16   17   19   19   21   23   24   24   25   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   19      3    3    4    6    6    9   10   13   14   14   16   17   19   20   23   23   24   24   25   26 
LCS_GDT     K    10_D     K    10_F      4    4   19      3    4    4    6    6    6    7   10   12   13   15   15   17   18   19   20   24   24   25   26 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    4    6    9   10   12   13   14   16   16   17   19   20   23   23   24   24   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    8    9   11   11   11   12   13   14   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    8   10   11   11   11   12   13   14   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    8   10   11   11   11   12   13   14   16   17   18   19   21   23   23   24   24   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    8   10   11   11   11   12   13   14   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    8   10   11   11   11   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    8   10   11   11   11   12   13   14   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    8   10   11   11   11   12   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    8   10   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    7   10   11   11   11   12   13   15   16   16   18   19   20   21   23   24   24   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4   10   11   11   11   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22     10   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      9   11   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   11   12   13   13   14   15   16   16   17   18   20   21   23   23   24   24   25   26 
LCS_AVERAGE  LCS_A:  55.72  (  39.79   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     10     11     11     12     13     13     14     15     16     16     17     18     20     21     23     23     24     24     25     26 
GDT PERCENT_AT  38.46  42.31  42.31  46.15  50.00  50.00  53.85  57.69  61.54  61.54  65.38  69.23  76.92  80.77  88.46  88.46  92.31  92.31  96.15 100.00
GDT RMS_LOCAL    0.30   0.35   0.35   0.63   0.97   0.97   1.83   2.21   2.62   2.62   3.11   3.35   4.21   4.47   5.16   5.16   5.44   5.43   5.78   6.02
GDT RMS_ALL_AT  12.42  12.44  12.44  12.48  11.62  11.62  10.13  10.27   9.55   9.55   9.16   9.61   7.24   6.99   6.25   6.25   6.19   6.29   6.06   6.02

# Checking swapping
#   possible swapping detected:  F    21_D      F    21_F
#   possible swapping detected:  D    22_D      D    22_F
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    25.940     0    0.280   0.261    28.172    0.000    0.000
LGA    Q     9_D      Q     9_F    20.148     0    0.576   0.488    22.529    0.000    0.000
LGA    K    10_D      K    10_F    20.723     0    0.049   0.635    27.192    0.000    0.000
LGA    L    11_D      L    11_F    17.428     0    0.597   0.629    18.879    0.000    0.000
LGA    N    12_D      N    12_F    13.937     0    0.573   0.562    17.403    0.000    0.000
LGA    S    13_D      S    13_F    12.967     0    0.033   0.072    15.466    0.000    0.000
LGA    W    14_D      W    14_F    14.773     0    0.065   1.492    23.683    0.000    0.000
LGA    D    15_D      D    15_F    10.339     0    0.011   0.168    15.341    6.786    3.393
LGA    V    16_D      V    16_F     4.497     0    0.000   0.052     6.694   28.452   30.680
LGA    F    17_D      F    17_F     9.056     0    0.007   1.151    17.889    6.429    2.338
LGA    G    18_D      G    18_F     6.666     0    0.227   0.227     7.357   25.952   25.952
LGA    N    19_D      N    19_F     1.751     0    0.291   1.002     6.799   53.333   42.679
LGA    W    20_D      W    20_F     6.414     0    0.160   1.299    12.441   20.595    6.429
LGA    F    21_D      F    21_F     4.510     0    0.578   1.272    11.643   44.405   19.697
LGA    D    22_D      D    22_F     2.734     0    0.574   1.355     8.105   64.881   39.643
LGA    L    23_D      L    23_F     2.097     0    0.115   0.909     2.883   68.810   66.905
LGA    A    24_D      A    24_F     1.835     0    0.025   0.027     2.008   75.000   72.952
LGA    S    25_D      S    25_F     1.756     0    0.157   0.722     2.501   79.405   76.032
LGA    W    26_D      W    26_F     1.344     0    0.032   0.217     3.131   85.952   71.054
LGA    I    27_D      I    27_F     0.467     0    0.040   0.093     0.821   97.619   96.429
LGA    K    28_D      K    28_F     0.478     0    0.080   0.619     5.340   97.619   72.540
LGA    Y    29_D      Y    29_F     0.326     0    0.057   0.447     2.750   95.238   80.556
LGA    I    30_D      I    30_F     1.023     0    0.079   0.114     1.868   83.690   79.345
LGA    Q    31_D      Q    31_F     1.688     0    0.029   1.238     6.809   75.000   57.725
LGA    R    32_D      R    32_F     1.325     0    0.485   1.249     2.912   77.262   70.173
LGA    R    33_D      R    33_F     1.743     0    0.583   1.265     5.959   75.000   52.468

# 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):     6.018          5.854                  7.804           44.670   37.192

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.21    58.654    54.398     0.650

LGA_LOCAL      RMSD:   2.206  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.266  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   6.018  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.037842 * X  +   0.299345 * Y  +   0.953394 * Z  +  26.073849
  Y_new =   0.453432 * X  +   0.855347 * Y  +  -0.250562 * Z  + -83.045547
  Z_new =  -0.890487 * X  +   0.422817 * Y  +  -0.168101 * Z  +   5.559255 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.654061  1.098415  1.949209   [DEG:   94.7707   62.9345  111.6814 ]
ZXZ:  1.313797  1.739699 -1.127499   [DEG:   75.2750   99.6774  -64.6009 ]
 
# END of job
