
#######################################################
#                                                     #
#                        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:    41       2_B - 42_B        3.70     3.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_B - 36_B        1.98     4.36
  LONGEST_CONTINUOUS_SEGMENT:    33       5_B - 37_B        1.89     4.47
  LCS_AVERAGE:     74.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       5_B - 24_B        0.95     4.66
  LONGEST_CONTINUOUS_SEGMENT:    20       6_B - 25_B        0.90     5.15
  LONGEST_CONTINUOUS_SEGMENT:    20       8_B - 27_B        0.98     5.96
  LONGEST_CONTINUOUS_SEGMENT:    20       9_B - 28_B        0.98     5.83
  LCS_AVERAGE:     39.08

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   23   41      3    3    4   11   16   21   25   25   31   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     S     3_B     S     3_B      4   23   41      3    4    4   12   19   23   30   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B      4   33   41      3    4    4   11   16   21   27   31   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     20   33   41      4   12   16   22   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     20   33   41      4   14   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     20   33   41      4   13   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     20   33   41      4   14   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     20   33   41     10   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     20   33   41     14   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     20   33   41      3    4   20   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     20   33   41     12   14   14   15   16   27   30   32   34   35   37   38   38   40   40   40   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     20   33   41     12   17   20   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     20   33   41     12   14   20   25   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     14   33   41     12   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     14   33   41     12   14   14   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     14   33   41     12   14   21   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     14   33   41     12   17   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     14   33   41     12   14   14   25   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     14   33   41     12   14   14   18   28   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     14   33   41     12   14   22   26   29   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     14   33   41     12   14   14   17   28   31   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     14   33   41     12   14   14   15   18   26   32   33   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     14   18   41      7   14   14   15   16   19   26   32   34   35   37   38   39   40   40   40   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     14   18   41      3    6   14   15   16   16   17   20   25   31   35   38   39   40   40   40   41   41   41   41 
LCS_GDT     E    40_B     E    40_B      5   18   41      3    4    7   14   16   16   16   16   17   18   19   23   27   31   36   38   41   41   41   41 
LCS_GDT     W    41_B     W    41_B      4   18   41     10   14   14   15   16   16   17   20   24   29   32   35   39   40   40   40   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   18   41      0    3    3    3    3    4    5   11   17   18   22   33   39   40   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  71.31  (  39.08   74.84  100.00 )

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     14     17     22     26     29     31     32     33     34     35     37     38     39     40     40     40     41     41     41     41 
GDT PERCENT_AT  34.15  41.46  53.66  63.41  70.73  75.61  78.05  80.49  82.93  85.37  90.24  92.68  95.12  97.56  97.56  97.56 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.26   0.46   0.92   1.14   1.36   1.53   1.74   1.96   2.12   2.24   2.59   2.85   3.29   3.36   3.36   3.36   3.70   3.70   3.70   3.70
GDT RMS_ALL_AT   4.59   5.34   4.71   4.79   4.74   4.58   4.43   4.18   4.10   4.13   3.96   3.84   3.72   3.72   3.72   3.72   3.70   3.70   3.70   3.70

# 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
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     7.421     0    0.553   0.564     8.686   22.143   18.286
LGA    S     3_B      S     3_B     4.967     0    0.504   0.429     6.327   35.714   36.190
LGA    Q     4_B      Q     4_B     5.430     0    0.048   0.270    11.738   28.095   14.127
LGA    R     5_B      R     5_B     2.687     0    0.659   1.223     7.335   64.881   35.844
LGA    L     6_B      L     6_B     1.752     0    0.158   1.386     4.090   70.833   63.631
LGA    F     7_B      F     7_B     1.737     0    0.142   0.202     2.362   72.857   70.649
LGA    V     8_B      V     8_B     1.843     0    0.040   1.180     4.159   72.857   69.116
LGA    L     9_B      L     9_B     1.502     0    0.646   0.577     4.098   66.071   72.679
LGA    D    10_B      D    10_B     0.987     0    0.046   0.839     3.299   85.952   74.881
LGA    N    11_B      N    11_B     0.891     0    0.056   0.964     3.550   88.214   80.119
LGA    E    12_B      E    12_B     0.801     0    0.007   0.930     3.571   90.476   77.884
LGA    R    13_B      R    13_B     0.897     0    0.023   1.198     5.259   90.476   72.684
LGA    Y    14_B      Y    14_B     0.852     0    0.037   0.167     1.330   90.476   88.214
LGA    D    15_B      D    15_B     0.684     0    0.011   0.457     1.038   90.476   90.536
LGA    S    16_B      S    16_B     0.577     0    0.018   0.171     0.901   90.476   90.476
LGA    F    17_B      F    17_B     0.823     0    0.031   0.243     0.846   90.476   90.476
LGA    I    18_B      I    18_B     0.789     0    0.013   0.119     1.212   90.476   89.345
LGA    T    19_B      T    19_B     0.791     0    0.024   0.244     1.106   90.476   89.184
LGA    Q    20_B      Q    20_B     0.957     0    0.007   1.151     3.758   85.952   76.402
LGA    L    21_B      L    21_B     1.264     0    0.018   1.321     2.604   81.429   77.440
LGA    E    22_B      E    22_B     1.132     0    0.094   0.745     2.321   81.429   75.820
LGA    A    23_B      A    23_B     0.770     0    0.065   0.094     0.921   90.476   90.476
LGA    P    24_B      P    24_B     0.687     0    0.028   0.358     1.548   83.810   86.667
LGA    V    25_B      V    25_B     2.304     0    0.102   1.263     4.871   67.024   59.184
LGA    Q    26_B      Q    26_B     4.777     0    0.689   0.694     9.424   29.881   17.513
LGA    N    27_B      N    27_B     2.792     0    0.145   0.128     3.057   57.262   57.262
LGA    A    28_B      A    28_B     2.765     0    0.039   0.039     3.533   65.000   60.667
LGA    E    29_B      E    29_B     1.150     0    0.051   0.853     2.705   81.548   72.381
LGA    G    30_B      G    30_B     1.857     0    0.144   0.144     1.864   77.262   77.262
LGA    R    31_B      R    31_B     1.815     0    0.074   1.207    10.528   79.405   43.939
LGA    E    32_B      E    32_B     0.936     0    0.047   0.849     5.646   83.810   61.958
LGA    R    33_B      R    33_B     2.104     0    0.080   1.171     3.480   65.238   62.900
LGA    L    34_B      L    34_B     2.632     0    0.032   1.396     6.742   60.952   51.071
LGA    M    35_B      M    35_B     1.351     0    0.059   1.144     6.686   75.000   62.857
LGA    A    36_B      A    36_B     2.833     0    0.046   0.045     4.324   50.595   50.476
LGA    V    37_B      V    37_B     4.605     0    0.038   0.084     5.814   34.405   31.701
LGA    K    38_B      K    38_B     5.962     4    0.149   0.171     9.259   13.571    7.143
LGA    P    39_B      P    39_B     8.676     0    0.067   0.105     9.522    4.881   10.000
LGA    E    40_B      E    40_B    12.489     0    0.418   1.205    16.790    0.000    0.000
LGA    W    41_B      W    41_B    10.497     0    0.572   0.453    11.491    0.000    0.000
LGA    K    42_B      K    42_B    10.298     0    0.174   1.109    17.063    3.333    1.481

# 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):     3.705          3.692                  4.721           63.505   57.535

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     33    1.96    70.732    74.946     1.599

LGA_LOCAL      RMSD:   1.964  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.184  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   3.705  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.955132 * X  +   0.065930 * Y  +   0.288749 * Z  +   6.728002
  Y_new =  -0.146957 * X  +  -0.740946 * Y  +   0.655289 * Z  + -23.468365
  Z_new =   0.257151 * X  +  -0.668321 * Y  +  -0.698012 * Z  +  43.771324 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.152663 -0.260072 -2.377922   [DEG:   -8.7469  -14.9011 -136.2449 ]
ZXZ:  2.726547  2.343414  2.774283   [DEG:  156.2196  134.2677  158.9547 ]
 
# END of job
