
#######################################################
#                                                     #
#                        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   53 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_F - 34_F        4.72    14.04
  LONGEST_CONTINUOUS_SEGMENT:    28       8_F - 35_F        4.63    14.01
  LCS_AVERAGE:     52.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      11_F - 28_F        1.98    15.30
  LCS_AVERAGE:     23.12

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      11_F - 25_F        0.87    16.55
  LCS_AVERAGE:     15.58

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F      3    4   10      0    3    3    3    4    4    5    5    7    7    7    9   12   15   17   18   21   24   24   26 
LCS_GDT     G     2_F     G     2_F      3    4   13      0    3    3    4    4    5    6    9    9   10   12   12   13   15   17   20   21   24   24   26 
LCS_GDT     K     3_F     K     3_F      3    4   13      3    3    3    4    4    5    7    9    9   10   12   12   13   15   17   20   21   24   25   26 
LCS_GDT     I     4_F     I     4_F      3    4   13      3    3    3    4    4    5    7    9    9   10   12   12   13   15   17   20   21   24   25   26 
LCS_GDT     K     5_F     K     5_F      3    4   13      3    3    3    4    4    5    7    9    9   10   12   15   16   17   17   22   22   24   26   28 
LCS_GDT     R     6_F     R     6_F      3    3   13      1    3    3    3    3    4    6    6    7    9   10   12   13   15   17   22   22   25   26   29 
LCS_GDT     F     7_F     F     7_F      3    3   28      0    3    3    3    4    4    6    6    7    9   10   13   18   22   24   28   28   30   32   34 
LCS_GDT     F     8_F     F     8_F      3    3   28      1    3    3    7    8    8   10   12   18   22   23   24   26   27   31   33   34   35   37   37 
LCS_GDT     A     9_F     A     9_F      4    4   28      3    3    4    4    4    6   11   16   20   22   25   25   26   27   31   33   34   35   37   38 
LCS_GDT     K    10_F     K    10_F      4   17   28      3    5    6   10   13   16   19   21   22   22   25   25   26   27   31   33   34   35   37   38 
LCS_GDT     D    11_F     D    11_F     15   18   28      7   13   14   15   18   18   19   21   22   22   25   25   26   28   32   34   35   36   38   39 
LCS_GDT     M    12_F     M    12_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     R    13_F     R    13_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     A    14_F     A    14_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   28   32   34   35   36   38   39 
LCS_GDT     A    15_F     A    15_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     L    16_F     L    16_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     A    17_F     A    17_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     Q    18_F     Q    18_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   28   32   34   35   36   38   39 
LCS_GDT     V    19_F     V    19_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     K    20_F     K    20_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     D    21_F     D    21_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     T    22_F     T    22_F     15   18   28      8   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     L    23_F     L    23_F     15   18   28      7   13   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     G    24_F     G    24_F     15   18   28      3    4   14   15   18   18   19   21   22   22   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     S    25_F     S    25_F     15   18   28      3   10   12   15   15   16   19   21   22   24   25   25   26   27   30   30   34   36   38   39 
LCS_GDT     D    26_F     D    26_F      6   18   28      3    9   14   15   18   18   19   21   22   24   25   25   26   27   32   34   35   36   38   39 
LCS_GDT     A    27_F     A    27_F      6   18   28      3    5    7   15   18   18   19   21   22   24   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     V    28_F     V    28_F      6   18   28      3    5    7   11   12   16   18   20   22   24   25   25   26   28   32   34   35   36   38   39 
LCS_GDT     I    29_F     I    29_F      6   13   28      3    4    7   12   18   18   19   21   22   24   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     M    30_F     M    30_F      6   13   28      3    5    7   11   12   16   18   20   22   24   24   25   26   28   31   33   34   36   38   39 
LCS_GDT     S    31_F     S    31_F      6    9   28      3    5    7   15   18   18   19   21   22   24   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     N    32_F     N    32_F      5    9   28      3    4    5    8   10   16   19   21   22   24   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     K    33_F     K    33_F      5    9   28      3    4    7   11   12   16   18   20   22   24   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     K    34_F     K    34_F      5    9   28      3    4    5    8   12   16   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     V    35_F     V    35_F      4    7   28      3    4    4    6    6    7   13   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     N    36_F     N    36_F      3    8   27      3    3    4    6   11   16   18   20   22   24   24   24   25   29   31   34   35   36   38   39 
LCS_GDT     G    37_F     G    37_F      5    8   27      3    4    5    6    6    8   14   20   22   24   24   24   24   27   28   32   34   36   38   39 
LCS_GDT     G    38_F     G    38_F      5    8   27      3    4    5    8   12   16   18   20   22   24   24   24   24   27   28   29   29   35   37   39 
LCS_GDT     I    39_F     I    39_F      5    8   27      3    4    5    8   12   16   18   20   22   24   24   24   25   29   31   34   35   36   38   39 
LCS_GDT     E    40_F     E    40_F      5    8   27      3    4    6   11   12   16   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     I    41_F     I    41_F      5    8   27      3    4    7   11   12   16   18   20   22   24   25   25   26   29   32   34   35   36   38   39 
LCS_GDT     V    42_F     V    42_F      5    8   27      4    5    5    8   12   16   18   20   22   24   24   24   24   28   32   34   35   36   38   39 
LCS_GDT     A    43_F     A    43_F      5    8   27      4    5    5    8   10   14   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     A    44_F     A    44_F      5    8   27      4    5    7   11   12   16   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     V    45_F     V    45_F      5    8   27      4    5    7   11   12   16   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     L    46_F     L    46_F      5    8   27      4    5    5    7    8   11   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     E    47_F     E    47_F      3    8   27      3    3    5    7    9   16   18   20   22   24   24   24   26   29   32   34   35   36   38   39 
LCS_GDT     H    48_F     H    48_F      3    8   27      3    3    4    5    6   11   18   20   22   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     H    49_F     H    49_F      3    8   27      0    3    4    7    8    8   10   12   13   16   21   22   26   29   32   34   35   36   38   39 
LCS_AVERAGE  LCS_A:  30.46  (  15.58   23.12   52.69 )

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      8     13     14     15     18     18     19     21     22     24     25     25     26     29     32     34     35     36     38     39 
GDT PERCENT_AT  16.33  26.53  28.57  30.61  36.73  36.73  38.78  42.86  44.90  48.98  51.02  51.02  53.06  59.18  65.31  69.39  71.43  73.47  77.55  79.59
GDT RMS_LOCAL    0.32   0.52   0.68   0.87   1.64   1.64   1.90   2.34   2.63   3.28   3.47   3.32   3.64   5.63   5.58   5.84   6.01   6.10   6.41   6.60
GDT RMS_ALL_AT  16.15  16.31  16.24  16.55  14.74  14.74  14.82  14.70  14.63  14.80  14.23  14.38  14.23  13.12  13.10  13.07  13.07  13.06  13.18  13.24

# Checking swapping
#   possible swapping detected:  E    40_F      E    40_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F    42.588     0    0.360   0.531    48.589    0.000    0.000
LGA    G     2_F      G     2_F    38.748     0    0.638   0.638    40.557    0.000    0.000
LGA    K     3_F      K     3_F    32.944     0    0.553   1.197    35.862    0.000    0.000
LGA    I     4_F      I     4_F    27.844     0    0.592   1.167    30.254    0.000    0.000
LGA    K     5_F      K     5_F    24.101     0    0.615   1.273    28.228    0.000    0.000
LGA    R     6_F      R     6_F    20.767     0    0.588   1.268    22.760    0.000    0.000
LGA    F     7_F      F     7_F    14.941     0    0.597   0.748    21.899    0.000    0.000
LGA    F     8_F      F     8_F     9.931     0    0.592   1.115    12.081    1.190    1.212
LGA    A     9_F      A     9_F     8.522     0    0.606   0.583     9.661   11.071    8.952
LGA    K    10_F      K    10_F     4.832     0    0.091   1.449     6.000   36.786   45.397
LGA    D    11_F      D    11_F     2.257     0    0.615   0.941     8.309   73.214   46.548
LGA    M    12_F      M    12_F     2.233     0    0.066   1.356     7.789   68.810   52.083
LGA    R    13_F      R    13_F     1.736     0    0.048   1.240     7.281   77.143   57.273
LGA    A    14_F      A    14_F     0.749     0    0.037   0.039     1.134   88.214   88.667
LGA    A    15_F      A    15_F     1.312     0    0.064   0.062     1.783   81.429   79.714
LGA    L    16_F      L    16_F     1.536     0    0.037   1.191     5.447   79.286   68.333
LGA    A    17_F      A    17_F     1.210     0    0.050   0.051     1.639   85.952   83.333
LGA    Q    18_F      Q    18_F     1.461     0    0.036   0.820     4.763   81.548   64.444
LGA    V    19_F      V    19_F     1.434     0    0.030   0.085     2.509   83.690   75.646
LGA    K    20_F      K    20_F     0.959     0    0.076   0.202     3.244   88.214   74.656
LGA    D    21_F      D    21_F     1.583     0    0.048   0.818     4.891   79.405   61.071
LGA    T    22_F      T    22_F     1.544     0    0.038   1.107     3.452   75.000   70.816
LGA    L    23_F      L    23_F     1.851     0    0.031   0.193     2.285   68.810   69.821
LGA    G    24_F      G    24_F     1.926     0    0.616   0.616     4.507   58.571   58.571
LGA    S    25_F      S    25_F     3.670     0    0.634   0.798     7.011   57.500   42.857
LGA    D    26_F      D    26_F     1.169     0    0.607   0.808     5.113   63.810   63.631
LGA    A    27_F      A    27_F     3.152     0    0.089   0.142     4.135   59.286   54.857
LGA    V    28_F      V    28_F     5.022     0    0.104   0.134     8.690   27.976   18.095
LGA    I    29_F      I    29_F     2.973     0    0.162   0.492     4.669   43.929   58.631
LGA    M    30_F      M    30_F     6.203     0    0.645   0.852    13.579   22.976   12.262
LGA    S    31_F      S    31_F     2.278     0    0.069   0.735     5.192   57.500   51.032
LGA    N    32_F      N    32_F     4.048     0    0.487   1.134     7.266   36.786   30.119
LGA    K    33_F      K    33_F     6.095     0    0.037   0.835    10.077   15.119   10.899
LGA    K    34_F      K    34_F    11.205     0    0.289   1.109    13.442    0.357    0.159
LGA    V    35_F      V    35_F    14.778     0    0.608   0.897    18.837    0.000    0.000
LGA    N    36_F      N    36_F    19.836     0    0.634   0.857    24.704    0.000    0.000
LGA    G    37_F      G    37_F    21.620     0    0.206   0.206    22.439    0.000    0.000
LGA    G    38_F      G    38_F    20.232     0    0.186   0.186    20.434    0.000    0.000
LGA    I    39_F      I    39_F    14.092     0    0.032   0.724    16.820    0.000    0.000
LGA    E    40_F      E    40_F    12.411     0    0.194   0.941    16.946    1.190    0.529
LGA    I    41_F      I    41_F     9.103     0    0.157   1.029    12.334    0.357    1.548
LGA    V    42_F      V    42_F    11.354     0    0.621   0.651    11.844    0.357    0.204
LGA    A    43_F      A    43_F    11.109     0    0.041   0.067    11.417    0.000    0.000
LGA    A    44_F      A    44_F    12.210     0    0.037   0.044    12.845    0.000    0.000
LGA    V    45_F      V    45_F    12.838     0    0.046   0.952    13.787    0.000    0.000
LGA    L    46_F      L    46_F    14.466     0    0.569   1.073    19.328    0.000    0.000
LGA    E    47_F      E    47_F    14.760     0    0.568   0.911    18.177    0.000    0.000
LGA    H    48_F      H    48_F    20.148     0    0.604   0.803    25.800    0.000    0.000
LGA    H    49_F      H    49_F    18.365     0    0.623   1.424    21.916    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):    12.108         12.002                 12.834           31.132   27.579

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     21    2.34    42.347    37.170     0.861

LGA_LOCAL      RMSD:   2.339  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.697  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:  12.108  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.711770 * X  +   0.616291 * Y  +  -0.337000 * Z  +  57.324265
  Y_new =  -0.109748 * X  +  -0.571458 * Y  +  -0.813260 * Z  + -23.212940
  Z_new =  -0.693786 * X  +  -0.541869 * Y  +   0.474383 * Z  +  15.872339 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.988607  0.766733 -0.851707   [DEG: -171.2346   43.9305  -48.7992 ]
ZXZ: -0.392843  1.076533 -2.233864   [DEG:  -22.5082   61.6808 -127.9910 ]
 
# END of job
