
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36       2_B - 37_B        4.83     8.75
  LCS_AVERAGE:     83.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       6_B - 29_B        1.93    10.02
  LCS_AVERAGE:     49.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       9_B - 27_B        0.96    11.51
  LCS_AVERAGE:     36.47

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      3    5   36      3    3    4    4    5    6    6   11   12   14   26   28   31   31   33   33   34   34   35   35 
LCS_GDT     S     3_B     S     3_B      4   13   36      3    4    6   13   18   19   21   25   26   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     Q     4_B     Q     4_B      4   21   36      3    4    4    6   11   17   21   23   25   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     R     5_B     R     5_B     11   21   36      5    9   11   15   18   20   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     L     6_B     L     6_B     11   24   36      5    9   11   15   19   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     F     7_B     F     7_B     11   24   36      4    9   11   15   19   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     V     8_B     V     8_B     18   24   36      4    9   12   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     L     9_B     L     9_B     19   24   36      5   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     D    10_B     D    10_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     N    11_B     N    11_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     E    12_B     E    12_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     R    13_B     R    13_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     Y    14_B     Y    14_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     D    15_B     D    15_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     S    16_B     S    16_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     F    17_B     F    17_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     I    18_B     I    18_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     T    19_B     T    19_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     Q    20_B     Q    20_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     L    21_B     L    21_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     E    22_B     E    22_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     A    23_B     A    23_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     P    24_B     P    24_B     19   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     V    25_B     V    25_B     19   24   36      6   16   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     Q    26_B     Q    26_B     19   24   36      3    5   12   17   19   20   21   23   25   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     N    27_B     N    27_B     19   24   36      7   12   17   19   19   20   22   24   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     A    28_B     A    28_B     14   24   36     16   17   17   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     E    29_B     E    29_B     14   24   36      7   12   13   19   20   22   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     G    30_B     G    30_B     14   23   36      5   12   13   14   14   15   15   16   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     R    31_B     R    31_B     14   16   36      7   12   13   14   14   15   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     E    32_B     E    32_B     14   16   36      7   12   13   14   14   15   24   25   27   28   29   30   31   32   33   33   34   34   35   35 
LCS_GDT     R    33_B     R    33_B     14   16   36      7   12   13   14   14   15   15   16   16   20   28   30   31   32   33   33   34   34   35   35 
LCS_GDT     L    34_B     L    34_B     14   16   36      6   12   13   14   14   15   15   16   16   17   18   21   29   32   33   33   34   34   35   35 
LCS_GDT     M    35_B     M    35_B     14   16   36      6   12   13   14   14   15   15   16   16   22   28   30   31   32   33   33   34   34   35   35 
LCS_GDT     A    36_B     A    36_B     14   16   36      6   12   13   14   14   15   15   16   16   17   18   20   23   32   32   33   34   34   35   35 
LCS_GDT     V    37_B     V    37_B     14   16   36      7   12   13   14   14   15   15   16   16   17   17   18   19   22   23   26   33   33   35   35 
LCS_GDT     K    38_B     K    38_B     14   16   23      6   12   13   14   14   15   15   16   16   17   17   18   18   20   20   23   24   27   34   34 
LCS_GDT     P    39_B     P    39_B     14   16   21      3    3   11   14   14   15   15   16   16   17   17   18   18   18   19   20   21   22   24   25 
LCS_GDT     E    40_B     E    40_B     14   16   21      3    3   13   14   14   15   15   16   16   17   17   18   18   18   19   19   21   22   23   25 
LCS_GDT     W    41_B     W    41_B      4   16   21      3    3    4    4    4    4    9   13   16   17   17   18   18   18   19   19   20   22   23   23 
LCS_GDT     K    42_B     K    42_B      4    4   21      3    3    4    4    4    4    5    6    9   13   16   17   17   18   18   19   19   19   20   20 
LCS_AVERAGE  LCS_A:  56.61  (  36.47   49.91   83.46 )

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     16     17     17     19     20     22     24     25     27     28     29     30     31     32     33     33     34     34     35     35 
GDT PERCENT_AT  39.02  41.46  41.46  46.34  48.78  53.66  58.54  60.98  65.85  68.29  70.73  73.17  75.61  78.05  80.49  80.49  82.93  82.93  85.37  85.37
GDT RMS_LOCAL    0.29   0.42   0.42   0.82   1.11   1.52   1.92   2.12   2.44   2.58   2.84   3.00   3.23   3.54   3.73   3.73   3.98   3.98   4.35   4.35
GDT RMS_ALL_AT  10.43  10.35  10.35  10.85  10.03   9.70   9.51   9.40   9.49   9.58   9.39   9.36   9.41   9.11   9.16   9.16   9.07   9.07   8.91   8.91

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    11.204     0    0.290   0.401    13.406    3.214    2.571
LGA    S     3_B      S     3_B     7.093     0    0.341   0.640     8.916   18.333   21.825
LGA    Q     4_B      Q     4_B     7.436     0    0.245   1.246    13.314   10.357    4.603
LGA    R     5_B      R     5_B     3.783     0    0.664   1.215     8.512   46.667   34.589
LGA    L     6_B      L     6_B     2.941     0    0.141   1.383     5.799   57.262   51.964
LGA    F     7_B      F     7_B     2.683     0    0.150   0.183     3.477   57.262   53.290
LGA    V     8_B      V     8_B     1.602     0    0.063   1.183     3.907   77.143   71.156
LGA    L     9_B      L     9_B     0.988     0    0.096   1.412     2.537   85.952   79.821
LGA    D    10_B      D    10_B     1.142     0    0.088   0.898     3.005   81.429   78.631
LGA    N    11_B      N    11_B     1.505     0    0.020   0.943     4.127   77.143   71.726
LGA    E    12_B      E    12_B     1.159     0    0.027   0.992     3.820   81.429   72.646
LGA    R    13_B      R    13_B     1.203     0    0.027   1.129     3.658   81.429   78.052
LGA    Y    14_B      Y    14_B     1.355     0    0.044   0.173     2.163   81.429   76.508
LGA    D    15_B      D    15_B     1.038     0    0.016   0.461     1.329   85.952   85.952
LGA    S    16_B      S    16_B     0.728     0    0.026   0.168     1.010   88.214   88.968
LGA    F    17_B      F    17_B     1.412     0    0.025   0.248     2.225   81.429   73.766
LGA    I    18_B      I    18_B     1.246     0    0.018   0.107     1.584   81.429   79.286
LGA    T    19_B      T    19_B     0.799     0    0.029   0.242     1.088   90.476   89.184
LGA    Q    20_B      Q    20_B     1.202     0    0.014   1.141     4.728   81.429   69.683
LGA    L    21_B      L    21_B     1.446     0    0.065   0.274     1.985   79.286   77.143
LGA    E    22_B      E    22_B     1.203     0    0.089   0.751     2.838   81.429   70.635
LGA    A    23_B      A    23_B     1.143     0    0.067   0.097     1.327   81.429   81.429
LGA    P    24_B      P    24_B     1.269     0    0.045   0.349     2.655   71.190   74.354
LGA    V    25_B      V    25_B     3.010     0    0.061   1.260     4.977   52.024   51.633
LGA    Q    26_B      Q    26_B     5.614     0    0.691   1.182    10.221   18.690   12.751
LGA    N    27_B      N    27_B     4.862     0    0.346   0.403     7.757   37.381   27.679
LGA    A    28_B      A    28_B     1.742     0    0.010   0.012     2.970   75.476   73.333
LGA    E    29_B      E    29_B     1.852     0    0.110   0.794     4.424   65.000   56.243
LGA    G    30_B      G    30_B     5.550     0    0.120   0.120     6.522   24.881   24.881
LGA    R    31_B      R    31_B     4.331     0    0.044   0.690     4.991   34.286   47.619
LGA    E    32_B      E    32_B     4.745     0    0.044   0.843     7.441   25.476   29.577
LGA    R    33_B      R    33_B     8.126     0    0.043   1.192    10.374    4.881   10.563
LGA    L    34_B      L    34_B     9.557     0    0.026   1.387    12.794    0.952    0.655
LGA    M    35_B      M    35_B     8.427     0    0.092   1.063     9.980    2.619   14.226
LGA    A    36_B      A    36_B    11.631     0    0.035   0.032    14.344    0.000    0.000
LGA    V    37_B      V    37_B    14.555     0    0.018   0.045    16.257    0.000    0.000
LGA    K    38_B      K    38_B    17.156     4    0.194   0.227    20.661    0.000    0.000
LGA    P    39_B      P    39_B    19.645     0    0.662   0.624    23.094    0.000    0.000
LGA    E    40_B      E    40_B    23.094     0    0.331   0.307    24.726    0.000    0.000
LGA    W    41_B      W    41_B    23.103     0    0.078   1.243    27.234    0.000    0.000
LGA    K    42_B      K    42_B    29.504     0    0.483   1.206    36.508    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     8.174          8.302                  8.847           46.902   44.803

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     25    2.12    57.317    56.423     1.126

LGA_LOCAL      RMSD:   2.120  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.400  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   8.174  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.281580 * X  +   0.810993 * Y  +   0.512838 * Z  +   3.842376
  Y_new =   0.523883 * X  +   0.317839 * Y  +  -0.790269 * Z  + -26.222631
  Z_new =  -0.803903 * X  +   0.491191 * Y  +  -0.335368 * Z  +  44.879490 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.077611  0.933828  2.169862   [DEG:   61.7426   53.5044  124.3239 ]
ZXZ:  0.575630  1.912793 -1.022322   [DEG:   32.9812  109.5949  -58.5748 ]
 
# END of job
