
#######################################################
#                                                     #
#                        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        4.69     7.16
  LCS_AVERAGE:     83.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.72    12.17
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.64    12.71
  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   20      0    3    3    3    3    3    4    7   14   16   17   18   19   19   22   22   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      4    4   20      3    3    4    6    6    8   10   13   14   15   17   18   19   19   22   23   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      4    4   20      3    4    4    6    6    6    7   10   11   13   15   15   17   18   19   20   23   25   25   26 
LCS_GDT     L    11_D     L    11_F      4   12   20      3    4    4    6    9   11   12   13   14   16   17   18   19   21   22   23   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     11   12   22      8    8    9   11   11   12   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     11   12   22      8    8    9   11   11   11   12   13   14   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     11   12   22      8    8    9   11   11   11   12   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     11   12   22      8    8    9   13   13   13   14   15   16   16   17   19   20   21   22   23   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     11   12   22      3    8    9   11   11   11   12   13   15   16   17   19   20   21   22   22   24   25   25   26 
LCS_GDT     F    21_D     F    21_F     11   13   22      3    4    9   11   11   12   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22     10   11   11   13   13   13   14   15   16   16   17   18   19   21   22   23   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22     10   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22     10   11   11   13   13   13   14   15   16   16   17   17   19   21   22   23   23   24   25   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      7   11   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   11   13   13   13   14   15   16   16   18   19   20   21   22   23   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.87  (  39.79   44.38   83.43 )

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     13     13     13     14     15     16     16     18     19     20     21     22     23     24     25     25     26 
GDT PERCENT_AT  38.46  42.31  42.31  50.00  50.00  50.00  53.85  57.69  61.54  61.54  69.23  73.08  76.92  80.77  84.62  88.46  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.30   0.36   0.36   1.00   1.00   1.00   1.76   2.24   2.64   2.64   3.95   4.16   4.33   4.50   4.69   5.20   5.52   5.76   5.74   5.99
GDT RMS_ALL_AT  12.62  12.67  12.67  11.80  11.80  11.80  11.63  10.40   9.69   9.69   6.73   6.81   6.91   7.08   7.16   6.27   6.04   6.04   6.03   5.99

# 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    26.324     0    0.280   0.261    28.550    0.000    0.000
LGA    Q     9_D      Q     9_F    20.493     0    0.576   0.489    22.888    0.000    0.000
LGA    K    10_D      K    10_F    21.021     0    0.049   0.636    27.557    0.000    0.000
LGA    L    11_D      L    11_F    17.684     0    0.597   0.629    19.126    0.000    0.000
LGA    N    12_D      N    12_F    14.128     0    0.573   0.562    17.549    0.000    0.000
LGA    S    13_D      S    13_F    13.080     0    0.035   0.073    15.570    0.000    0.000
LGA    W    14_D      W    14_F    14.855     0    0.061   1.493    23.647    0.000    0.000
LGA    D    15_D      D    15_F    10.458     0    0.011   0.164    15.451    6.071    3.036
LGA    V    16_D      V    16_F     4.632     0    0.004   0.051     6.830   27.024   29.116
LGA    F    17_D      F    17_F     9.199     0    0.031   1.174    18.035    6.429    2.338
LGA    G    18_D      G    18_F     6.592     0    0.212   0.212     7.448   30.952   30.952
LGA    N    19_D      N    19_F     1.618     0    0.232   0.989     6.779   56.548   43.036
LGA    W    20_D      W    20_F     6.454     0    0.152   1.301    12.289   20.595    6.327
LGA    F    21_D      F    21_F     4.485     0    0.599   1.258    11.630   45.833   20.216
LGA    D    22_D      D    22_F     2.816     0    0.570   1.355     8.121   62.976   38.690
LGA    L    23_D      L    23_F     2.122     0    0.115   0.909     2.870   68.810   66.905
LGA    A    24_D      A    24_F     1.818     0    0.026   0.029     1.984   75.000   74.571
LGA    S    25_D      S    25_F     1.794     0    0.155   0.721     2.552   79.405   76.032
LGA    W    26_D      W    26_F     1.387     0    0.032   0.216     3.220   83.810   68.197
LGA    I    27_D      I    27_F     0.465     0    0.040   0.091     0.769   97.619   96.429
LGA    K    28_D      K    28_F     0.474     0    0.079   0.620     5.312   97.619   72.540
LGA    Y    29_D      Y    29_F     0.353     0    0.056   0.458     2.937   95.238   80.556
LGA    I    30_D      I    30_F     1.062     0    0.077   0.114     1.957   83.690   79.345
LGA    Q    31_D      Q    31_F     1.765     0    0.034   1.233     6.860   75.000   56.825
LGA    R    32_D      R    32_F     1.398     0    0.480   1.250     2.906   79.286   70.173
LGA    R    33_D      R    33_F     1.776     0    0.585   1.265     5.743   75.000   53.117

# 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):     5.986          5.811                  7.788           44.881   37.246

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.24    59.615    54.904     0.642

LGA_LOCAL      RMSD:   2.236  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.401  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.986  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.019372 * X  +   0.295135 * Y  +   0.955259 * Z  +  26.377205
  Y_new =   0.437201 * X  +   0.861749 * Y  +  -0.257378 * Z  + -83.647163
  Z_new =  -0.899155 * X  +   0.412654 * Y  +  -0.145727 * Z  +   5.912784 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.615077  1.117835  1.910271   [DEG:   92.5371   64.0472  109.4505 ]
ZXZ:  1.307613  1.717045 -1.140536   [DEG:   74.9207   98.3794  -65.3479 ]
 
# END of job
