
#######################################################
#                                                     #
#                        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   58 (  435),  selected   58 , name one
# Molecule2: number of CA atoms   63 (  472),  selected   58 , 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:    23      24_A - 46_A        4.84    17.73
  LCS_AVERAGE:     31.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9      47_A - 55_A        1.91    14.59
  LONGEST_CONTINUOUS_SEGMENT:     9      48_A - 56_A        1.84    15.33
  LCS_AVERAGE:      9.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      49_A - 55_A        0.94    15.84
  LCS_AVERAGE:      6.73

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     G     1_A     G     1_A      4    4   17      0    3    4    4    4    7    7    8    9   11   15   16   17   18   20   22   23   25   27   33 
LCS_GDT     S     2_A     S     2_A      4    4   17      3    3    4    6    6    7    7   10   11   14   15   16   18   20   23   24   26   27   28   33 
LCS_GDT     S     3_A     S     3_A      4    4   17      3    3    4    6    6    7    7   10   11   15   16   19   20   21   23   25   26   27   28   33 
LCS_GDT     F     4_A     F     4_A      4    4   17      3    3    4    4    4    7    7    8   11   14   15   16   19   20   23   24   26   27   28   32 
LCS_GDT     C     5_A     C     5_A      3    4   18      3    3    4    4    4    5    7   10   11   14   16   17   19   21   23   24   26   27   28   33 
LCS_GDT     D     6_A     D     6_A      3    5   18      3    3    4    4    5    7    8    9   11   11   16   19   20   21   23   25   26   27   28   33 
LCS_GDT     S     7_A     S     7_A      4    5   18      3    4    4    4    5    7    9   10   12   15   16   19   20   21   23   25   26   27   28   33 
LCS_GDT     K     8_A     K     8_A      4    5   18      3    4    4    4    4    7    9    9   12   13   16   16   17   18   22   23   25   27   28   29 
LCS_GDT     C     9_A     C     9_A      4    5   18      3    4    4    4    4    7    9    9   12   13   16   16   16   17   19   23   24   26   27   28 
LCS_GDT     G    10_A     G    10_A      4    6   18      3    4    4    5    6    6    9   10   12   15   16   19   20   21   23   25   26   27   28   32 
LCS_GDT     V    11_A     V    11_A      4    6   18      3    4    4    5    6    6    8   10   12   15   16   19   20   21   23   25   26   27   28   33 
LCS_GDT     R    12_A     R    12_A      4    6   18      3    4    4    5    6    6    8   10   12   15   16   19   20   21   23   25   26   27   28   33 
LCS_GDT     C    13_A     C    13_A      4    6   18      3    4    4    5    6    7    9   10   12   13   16   17   20   21   23   26   27   29   29   33 
LCS_GDT     S    14_A     S    14_A      5    7   18      3    3    5    6    7    7    8   10   11   13   16   17   18   21   23   26   28   29   30   33 
LCS_GDT     K    15_A     K    15_A      5    7   18      4    4    5    6    7    8   10   12   12   13   16   16   18   21   23   26   28   29   30   32 
LCS_GDT     A    16_A     A    16_A      5    7   18      4    5    5    6    7    8   10   12   12   13   16   16   18   21   22   26   28   29   30   33 
LCS_GDT     G    17_A     G    17_A      5    7   18      4    4    5    6    7    8   10   12   12   13   16   16   18   21   23   26   28   29   30   33 
LCS_GDT     Y    18_A     Y    18_A      5    7   18      4    5    5    6    7    8   10   12   12   13   16   17   18   21   23   26   28   29   30   33 
LCS_GDT     Q    19_A     Q    19_A      4    7   18      4    4    5    6    6    7    9   10   12   15   16   19   20   21   23   26   28   29   30   33 
LCS_GDT     E    20_A     E    20_A      4    7   18      4    4    5    6    7    7    8   10   12   15   16   19   20   21   23   26   28   29   30   33 
LCS_GDT     R    21_A     R    21_A      4    5   18      4    4    5    6    6    7    8   10   12   14   16   19   20   21   23   26   28   29   30   33 
LCS_GDT     C    22_A     C    22_A      4    5   18      4    4    5    6    7    7    8   10   12   15   16   19   20   21   23   26   28   29   30   33 
LCS_GDT     L    23_A     L    23_A      3    5   17      3    4    4    5    5    6    7    9   12   15   16   19   20   21   23   26   28   29   30   33 
LCS_GDT     K    24_A     K    24_A      4    4   23      3    4    4    7    8   10   10   13   15   16   19   20   22   24   26   27   28   29   31   33 
LCS_GDT     Y    25_A     Y    25_A      4    5   23      3    3    4    6    6    7    8   13   13   15   16   19   20   21   23   26   28   29   30   32 
LCS_GDT     C    26_A     C    26_A      4    5   23      3    4    4    6    6   10   11   13   15   16   19   20   21   24   25   27   28   29   31   32 
LCS_GDT     G    27_A     G    27_A      4    5   23      3    4    4    6    7   10   12   14   16   17   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     I    28_A     I    28_A      4    5   23      3    4    4    4    5    6    8   10   12   13   15   20   22   24   26   27   28   29   31   32 
LCS_GDT     C    29_A     C    29_A      4    5   23      3    4    4    4    6   10   12   14   16   17   19   20   22   24   26   27   28   29   31   33 
LCS_GDT     C    30_A     C    30_A      4    5   23      1    4    5    5    8   10   12   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     E    31_A     E    31_A      4    7   23      3    4    4    5    6    8   11   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     K    32_A     K    32_A      4    7   23      3    4    4    5    7   10   12   14   15   17   19   20   22   24   26   27   28   29   31   32 
LCS_GDT     C    33_A     C    33_A      4    7   23      3    4    5    6    8   11   12   14   16   17   19   20   21   21   26   27   28   29   31   32 
LCS_GDT     H    34_A     H    34_A      4    7   23      3    3    4    5    6    9   12   14   17   18   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     C    35_A     C    35_A      4    7   23      4    4    5    6    9   11   12   14   17   18   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     V    36_A     V    36_A      4    7   23      4    4    4    7    9   11   12   14   17   18   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     P    37_A     P    37_A      4    7   23      4    4    4    5    8   11   12   14   17   18   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     S    38_A     S    38_A      4    6   23      4    4    4    6    9   11   12   14   16   17   19   20   21   21   25   27   28   29   31   32 
LCS_GDT     G    39_A     G    39_A      3    6   23      3    3    4    7    9   11   12   14   16   17   19   20   21   21   23   24   28   29   31   32 
LCS_GDT     T    40_A     T    40_A      3    6   23      3    3    5    7    9   11   12   14   16   17   19   20   21   21   22   24   24   29   30   32 
LCS_GDT     Y    41_A     Y    41_A      3    6   23      3    3    5    6    8   11   12   14   16   17   19   20   21   21   22   24   24   29   31   32 
LCS_GDT     G    42_A     G    42_A      3    5   23      3    3    4    7    9   11   12   14   16   17   19   20   21   21   23   26   28   29   30   32 
LCS_GDT     N    43_A     N    43_A      3    5   23      3    3    4    5    7    8   11   13   15   16   18   20   21   21   23   26   28   29   30   33 
LCS_GDT     K    44_A     K    44_A      3    5   23      3    5    5    7    9   11   12   14   16   17   19   20   21   21   25   26   28   29   31   33 
LCS_GDT     D    45_A     D    45_A      3    5   23      3    5    5    7    9   11   12   14   16   17   19   20   21   23   26   27   28   29   31   33 
LCS_GDT     E    46_A     E    46_A      3    5   23      3    5    5    7    9   11   12   14   16   17   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     C    47_A     C    47_A      4    9   22      3    3    5    6    8   10   10   11   15   18   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     P    48_A     P    48_A      4    9   20      3    3    4    6    8   10   11   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     C    49_A     C    49_A      7    9   18      3    5    7    8    8   10   11   11   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     Y    50_A     Y    50_A      7    9   18      3    5    7    8    8   10   11   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     R    51_A     R    51_A      7    9   18      3    5    7    8    8   10   11   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     D    52_A     D    52_A      7    9   18      3    5    7    8    8   10   11   11   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     L    53_A     L    53_A      7    9   18      3    4    7    8    8   10   11   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     K    54_A     K    54_A      7    9   18      3    4    7    8    8   10   11   14   17   18   20   20   22   24   26   27   28   29   31   33 
LCS_GDT     N    55_A     N    55_A      7    9   18      3    5    7    8    8   10   11   14   17   18   20   20   22   24   26   27   28   29   31   32 
LCS_GDT     S    56_A     S    56_A      4    9   18      3    4    5    8    8    9   11   14   17   18   20   20   22   24   26   27   28   29   31   31 
LCS_GDT     K    57_A     K    57_A      4    6   18      3    4    5    6    7    9   11   14   17   18   20   20   22   23   26   27   28   29   31   31 
LCS_GDT     G    58_A     G    58_A      3    6   18      0    3    3    6    7    9   11   14   17   18   20   20   22   24   26   27   28   29   31   31 
LCS_AVERAGE  LCS_A:  16.13  (   6.73    9.91   31.75 )

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      5      7      8      9     11     12     14     17     18     20     20     22     24     26     27     28     29     31     33 
GDT PERCENT_AT   6.35   7.94  11.11  12.70  14.29  17.46  19.05  22.22  26.98  28.57  31.75  31.75  34.92  38.10  41.27  42.86  44.44  46.03  49.21  52.38
GDT RMS_LOCAL    0.18   0.65   0.94   1.36   1.92   2.23   2.40   2.67   3.48   3.60   3.90   3.90   4.39   4.76   5.09   5.20   5.42   5.65   6.21   8.03
GDT RMS_ALL_AT  22.34  19.54  15.84  15.79  17.64  17.63  17.24  17.04  15.05  15.26  16.04  16.04  16.26  15.89  16.07  16.00  15.96  15.92  15.82  11.34

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  D     6_A      D     6_A
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  Y    50_A      Y    50_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A    21.617     0    0.724   0.724    21.617    0.000    0.000
LGA    S     2_A      S     2_A    22.481     0    0.680   0.842    24.026    0.000    0.000
LGA    S     3_A      S     3_A    22.793     0    0.310   0.395    23.124    0.000    0.000
LGA    F     4_A      F     4_A    24.483     0    0.101   0.257    28.813    0.000    0.000
LGA    C     5_A      C     5_A    20.565     0    0.667   0.999    22.657    0.000    0.000
LGA    D     6_A      D     6_A    21.906     0    0.116   1.180    25.802    0.000    0.000
LGA    S     7_A      S     7_A    27.295     0    0.638   0.786    28.771    0.000    0.000
LGA    K     8_A      K     8_A    28.881     0    0.233   0.354    31.947    0.000    0.000
LGA    C     9_A      C     9_A    26.825     0    0.191   0.219    27.651    0.000    0.000
LGA    G    10_A      G    10_A    25.854     0    0.331   0.331    26.405    0.000    0.000
LGA    V    11_A      V    11_A    26.406     0    0.618   0.666    29.207    0.000    0.000
LGA    R    12_A      R    12_A    21.179     0    0.208   0.828    22.708    0.000    0.000
LGA    C    13_A      C    13_A    20.985     0    0.641   0.669    21.172    0.000    0.000
LGA    S    14_A      S    14_A    21.044     0    0.603   0.743    22.995    0.000    0.000
LGA    K    15_A      K    15_A    20.498     0    0.280   0.700    21.691    0.000    0.000
LGA    A    16_A      A    16_A    21.086     0    0.050   0.056    24.241    0.000    0.000
LGA    G    17_A      G    17_A    25.249     0    0.317   0.317    26.894    0.000    0.000
LGA    Y    18_A      Y    18_A    25.044     0    0.512   1.343    25.300    0.000    0.000
LGA    Q    19_A      Q    19_A    23.303     0    0.655   1.140    28.971    0.000    0.000
LGA    E    20_A      E    20_A    21.177     0    0.070   0.868    25.550    0.000    0.000
LGA    R    21_A      R    21_A    17.492     0    0.104   1.306    19.614    0.000    0.000
LGA    C    22_A      C    22_A    16.487     0    0.537   0.839    18.407    0.000    0.000
LGA    L    23_A      L    23_A    14.615     0    0.007   1.380    18.249    0.000    0.000
LGA    K    24_A      K    24_A    11.217     0    0.231   1.030    12.277    0.000    2.169
LGA    Y    25_A      Y    25_A    15.853     0    0.200   1.016    27.562    0.000    0.000
LGA    C    26_A      C    26_A    11.477     0    0.590   0.882    12.994    2.143    1.429
LGA    G    27_A      G    27_A     7.702     0    0.207   0.207     9.121    5.119    5.119
LGA    I    28_A      I    28_A    10.184     0    0.282   1.461    15.142    1.786    0.893
LGA    C    29_A      C    29_A     6.660     0    0.637   0.567    10.899   17.262   12.698
LGA    C    30_A      C    30_A     2.118     0    0.658   0.731     6.205   59.405   51.984
LGA    E    31_A      E    31_A     5.489     0    0.611   0.746    12.722   25.714   12.857
LGA    K    32_A      K    32_A     3.005     0    0.256   1.251     5.140   59.405   50.106
LGA    C    33_A      C    33_A     1.572     0    0.564   0.603     6.189   77.381   61.667
LGA    H    34_A      H    34_A     3.614     0    0.606   1.228    12.245   59.524   25.857
LGA    C    35_A      C    35_A     1.591     0    0.614   0.657     5.593   54.286   56.508
LGA    V    36_A      V    36_A     3.503     0    0.049   0.973     6.797   70.238   49.524
LGA    P    37_A      P    37_A     3.456     0    0.482   0.466     7.489   50.357   35.102
LGA    S    38_A      S    38_A     2.584     0    0.570   0.761     6.691   71.310   54.127
LGA    G    39_A      G    39_A     3.354     0    0.374   0.374     3.354   57.262   57.262
LGA    T    40_A      T    40_A     1.936     0    0.575   0.501     3.812   61.429   68.776
LGA    Y    41_A      Y    41_A     1.230     0    0.078   1.234     8.528   62.857   36.627
LGA    G    42_A      G    42_A     5.450     0    0.658   0.658     7.648   25.119   25.119
LGA    N    43_A      N    43_A     7.146     0    0.237   1.057     9.367   21.190   12.381
LGA    K    44_A      K    44_A     3.546     0    0.138   0.861    10.752   57.262   31.587
LGA    D    45_A      D    45_A     1.812     0    0.568   1.121     7.996   61.905   43.214
LGA    E    46_A      E    46_A     2.199     0    0.527   1.162     6.510   46.429   42.751
LGA    C    47_A      C    47_A     8.956     0    0.230   0.785    11.122    5.833    3.889
LGA    P    48_A      P    48_A    13.111     0    0.442   0.462    16.244    0.000    0.000
LGA    C    49_A      C    49_A    15.491     0    0.215   0.687    17.256    0.000    0.000
LGA    Y    50_A      Y    50_A    14.249     0    0.619   0.712    17.182    0.000    0.000
LGA    R    51_A      R    51_A    17.511     0    0.067   1.226    24.110    0.000    0.000
LGA    D    52_A      D    52_A    20.050     0    0.150   0.796    24.029    0.000    0.000
LGA    L    53_A      L    53_A    17.240     0    0.172   0.489    17.708    0.000    0.000
LGA    K    54_A      K    54_A    20.412     0    0.636   0.634    31.310    0.000    0.000
LGA    N    55_A      N    55_A    20.391     0    0.069   0.909    21.001    0.000    0.000
LGA    S    56_A      S    56_A    22.468     0    0.067   0.750    23.372    0.000    0.000
LGA    K    57_A      K    57_A    22.752     0    0.488   0.775    26.933    0.000    0.000
LGA    G    58_A      G    58_A    21.358     0    0.702   0.702    21.987    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     435    435  100.00                63
SUMMARY(RMSD_GDC):    10.767         10.817                 11.522           15.130   11.772

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   63    4.0     14    2.67    21.429    18.948     0.506

LGA_LOCAL      RMSD:   2.668  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.040  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  10.767  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.269048 * X  +  -0.842287 * Y  +   0.467082 * Z  + -23.577536
  Y_new =  -0.932124 * X  +   0.349773 * Y  +   0.093824 * Z  +   4.369952
  Z_new =  -0.242400 * X  +  -0.410136 * Y  +  -0.879222 * Z  +  22.299034 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.851798  0.244839 -2.705122   [DEG: -106.1002   14.0282 -154.9921 ]
ZXZ:  1.769031  2.645023 -2.607800   [DEG:  101.3580  151.5486 -149.4159 ]
 
# END of job
