
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    34       5_B - 38_B        4.83    13.16
  LCS_AVERAGE:     71.77

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       5_B - 24_B        1.87    11.86
  LCS_AVERAGE:     32.45

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       5_B - 19_B        1.00    12.85
  LCS_AVERAGE:     20.34

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     15   20   34     12   13   13   16   17   19   20   21   23   26   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     L     6_B     L     6_B     15   20   34     12   13   13   16   17   19   21   22   24   27   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     E     7_B     E     7_B     15   20   34     12   13   13   16   17   19   21   22   24   27   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     T     8_B     T     8_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     K     9_B     K     9_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     K    10_B     K    10_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     A    11_B     A    11_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     Y    12_B     Y    12_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     A    13_B     A    13_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     A    14_B     A    14_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     R    15_B     R    15_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     T    16_B     T    16_B     15   20   34     12   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     R    17_B     R    17_B     15   20   34      8   13   13   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     R    18_B     R    18_B     15   20   34      8    9   12   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     S    19_B     S    19_B     15   20   34      8    9   12   16   17   19   21   22   24   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     N    20_B     N    20_B     10   20   34      8    9   12   16   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     Y    21_B     Y    21_B     10   20   34      8    9   10   15   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     A    22_B     A    22_B     10   20   34      8    9   10   14   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     A    23_B     A    23_B     10   20   34      8    9   10   14   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     S    24_B     S    24_B     10   20   34      8    9   10   13   17   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     L    25_B     L    25_B     10   18   34      3    5   10   11   13   16   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     R    26_B     R    26_B      4   17   34      3    4    4    8   14   19   21   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     L    27_B     L    27_B      4    8   34      3    4    4    7   11   15   18   21   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     E    28_B     E    28_B      4    8   34      3    4    4   11   14   16   18   21   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     G    29_B     G    29_B      4    8   34      3    4    5   11   14   16   18   21   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     F    30_B     F    30_B      5    8   34      3    5    9   11   14   16   20   22   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     K    31_B     K    31_B      5    8   34      4    5    6   11   14   15   18   21   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     V    32_B     V    32_B      5    8   34      4    5    6   11   14   16   18   21   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     T    33_B     T    33_B      5    8   34      4    5    5    7   10   12   18   21   24   28   31   32   32   32   32   32   32   32   33   34 
LCS_GDT     F    34_B     F    34_B      5    8   34      4    5    5    7    8   10   14   14   24   28   31   32   32   32   32   32   32   32   33   33 
LCS_GDT     A    35_B     A    35_B      4    6   34      3    4    4    6    8   12   18   21   25   28   31   32   32   32   32   32   32   33   33   34 
LCS_GDT     D    36_B     D    36_B      4    6   34      3    4    4    5    6    8    9   12   14   27   30   32   32   32   32   32   32   33   33   34 
LCS_GDT     G    37_B     G    37_B      4    9   34      3    3    4    7    8    9    9   11   12   14   15   16   17   17   19   29   32   33   33   34 
LCS_GDT     E    38_B     E    38_B      4    9   34      3    3    4    7    8    9    9   12   13   14   15   16   17   17   19   26   31   33   33   34 
LCS_GDT     R    39_B     R    39_B      4    9   19      3    4    5    7    8    9    9   12   13   14   15   16   18   26   28   29   32   33   33   34 
LCS_GDT     K    40_B     K    40_B      4    9   19      2    4    5    7    8    9    9   12   13   14   15   16   17   17   18   19   22   22   23   25 
LCS_GDT     M    41_B     M    41_B      4    9   19      3    3    4    6    6    9    9   12   13   14   15   16   17   17   18   19   22   22   23   23 
LCS_GDT     P    42_B     P    42_B      4    9   19      3    3    4    7    8    9    9   12   13   14   15   16   17   17   18   19   22   22   23   26 
LCS_GDT     T    43_B     T    43_B      4    9   19      3    4    5    7    8    9    9   12   13   14   15   16   17   17   17   19   22   22   23   24 
LCS_GDT     R    44_B     R    44_B      4    9   19      3    4    5    7    8    9    9   12   13   14   15   16   17   17   17   19   22   22   23   24 
LCS_GDT     E    45_B     E    45_B      4    9   19      3    3    5    7    8    9    9   12   13   14   15   16   17   17   18   19   22   22   23   24 
LCS_GDT     E    46_B     E    46_B      3    5   19      3    3    3    3    4    5    6    8   11   11   14   16   17   18   19   19   22   22   24   27 
LCS_GDT     V    47_B     V    47_B      3    3   19      3    3    3    3    3    3    6    6    7    8   11   12   14   16   16   19   22   22   24   27 
LCS_AVERAGE  LCS_A:  41.52  (  20.34   32.45   71.77 )

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     12     13     13     16     17     19     21     22     25     28     31     32     32     32     32     32     32     33     33     34 
GDT PERCENT_AT  27.91  30.23  30.23  37.21  39.53  44.19  48.84  51.16  58.14  65.12  72.09  74.42  74.42  74.42  74.42  74.42  74.42  76.74  76.74  79.07
GDT RMS_LOCAL    0.23   0.44   0.44   1.14   1.36   1.68   2.23   2.45   3.29   3.51   3.87   3.96   3.96   3.96   3.96   3.96   3.96   4.95   4.34   5.10
GDT RMS_ALL_AT  14.01  13.67  13.67  12.66  12.28  12.02  11.67  11.74  13.66  14.07  13.69  13.56  13.56  13.56  13.56  13.56  13.56  12.51  13.39  12.72

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    45_B      E    45_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     4.634     0    0.615   0.690     8.652   38.810   27.540
LGA    L     6_B      L     6_B     2.698     0    0.074   1.202     6.733   61.190   50.298
LGA    E     7_B      E     7_B     2.323     0    0.047   0.942     5.485   64.762   52.275
LGA    T     8_B      T     8_B     2.759     0    0.015   0.993     5.662   62.976   51.497
LGA    K     9_B      K     9_B     1.882     0    0.014   0.670     5.215   77.381   58.995
LGA    K    10_B      K    10_B     0.241     0    0.017   0.847     2.825   90.595   87.143
LGA    A    11_B      A    11_B     1.747     0    0.020   0.018     2.480   77.143   74.667
LGA    Y    12_B      Y    12_B     0.538     0    0.013   0.389     5.412   90.476   62.659
LGA    A    13_B      A    13_B     2.026     0    0.040   0.043     3.111   65.238   63.619
LGA    A    14_B      A    14_B     2.909     0    0.056   0.061     3.984   53.810   54.476
LGA    R    15_B      R    15_B     2.627     0    0.028   1.261     6.133   57.262   48.831
LGA    T    16_B      T    16_B     2.759     0    0.162   0.836     3.844   59.048   58.503
LGA    R    17_B      R    17_B     3.082     0    0.028   1.160     9.622   53.571   28.139
LGA    R    18_B      R    18_B     2.511     0    0.027   0.891     7.816   62.976   39.437
LGA    S    19_B      S    19_B     1.789     0    0.012   0.678     2.694   77.381   71.905
LGA    N    20_B      N    20_B     1.746     0    0.018   1.003     4.067   77.143   69.583
LGA    Y    21_B      Y    21_B     1.060     0    0.031   0.301     1.502   86.190   83.016
LGA    A    22_B      A    22_B     1.158     0    0.079   0.093     1.943   81.548   79.810
LGA    A    23_B      A    23_B     1.224     0    0.043   0.042     2.164   77.381   80.000
LGA    S    24_B      S    24_B     1.955     0    0.100   0.120     2.858   65.000   63.651
LGA    L    25_B      L    25_B     3.972     0    0.224   0.961     9.234   45.119   27.857
LGA    R    26_B      R    26_B     3.192     0    0.363   0.932    11.801   41.548   18.658
LGA    L    27_B      L    27_B     9.079     0    0.101   1.139    12.794    4.405    2.560
LGA    E    28_B      E    28_B     6.281     0    0.281   1.184     7.420   23.452   18.889
LGA    G    29_B      G    29_B     6.407     0    0.163   0.163     7.040   17.500   17.500
LGA    F    30_B      F    30_B     4.689     0    0.147   1.610    10.041   22.500   18.528
LGA    K    31_B      K    31_B     9.148     0    0.053   0.737    12.830    3.333    1.481
LGA    V    32_B      V    32_B     8.662     0    0.117   0.317    10.224    1.548    7.959
LGA    T    33_B      T    33_B    12.519     0    0.256   1.267    16.365    0.000    0.000
LGA    F    34_B      F    34_B    12.962     0    0.176   1.369    13.048    0.000    0.087
LGA    A    35_B      A    35_B    10.314     0    0.346   0.346    11.408    1.548    1.333
LGA    D    36_B      D    36_B     9.106     0    0.392   1.150    13.425    0.476    0.238
LGA    G    37_B      G    37_B    11.904     0    0.564   0.564    13.887    0.000    0.000
LGA    E    38_B      E    38_B    12.769     0    0.381   1.075    16.005    0.000    0.000
LGA    R    39_B      R    39_B    10.631     0    0.213   1.520    13.800    0.000    1.558
LGA    K    40_B      K    40_B    14.988     0    0.300   1.302    15.942    0.000    0.000
LGA    M    41_B      M    41_B    18.104     0    0.257   0.973    23.679    0.000    0.000
LGA    P    42_B      P    42_B    18.370     0    0.225   0.226    20.906    0.000    0.000
LGA    T    43_B      T    43_B    24.688     0    0.069   0.824    28.875    0.000    0.000
LGA    R    44_B      R    44_B    25.333     0    0.572   1.153    30.668    0.000    0.000
LGA    E    45_B      E    45_B    29.853     0    0.471   1.233    31.466    0.000    0.000
LGA    E    46_B      E    46_B    27.657     0    0.593   1.334    30.100    0.000    0.000
LGA    V    47_B      V    47_B    26.843     0    0.455   1.105    29.790    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):    10.818         10.839                 11.415           35.844   30.760

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     22    2.45    48.256    46.444     0.863

LGA_LOCAL      RMSD:   2.450  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.738  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:  10.818  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.731907 * X  +   0.009247 * Y  +   0.681342 * Z  +  29.206678
  Y_new =  -0.494551 * X  +   0.680653 * Y  +  -0.540491 * Z  + -34.087322
  Z_new =  -0.468756 * X  +  -0.732547 * Y  +  -0.493602 * Z  +  27.258715 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.547361  0.487881 -2.163732   [DEG: -145.9530   27.9535 -123.9727 ]
ZXZ:  0.900169  2.087023 -2.572352   [DEG:   51.5759  119.5776 -147.3849 ]
 
# END of job
