
#######################################################
#                                                     #
#                        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:    43       5_B - 47_B        4.24     4.24
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      10_B - 35_B        1.90     5.57
  LCS_AVERAGE:     48.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      15_B - 32_B        0.95     6.61
  LONGEST_CONTINUOUS_SEGMENT:    18      16_B - 33_B        0.93     6.77
  LCS_AVERAGE:     30.77

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     14   20   43     11   12   13   17   19   22   23   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     14   20   43     11   12   13   17   19   22   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     14   20   43     11   12   13   17   19   23   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     14   20   43     11   12   13   17   20   24   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     14   24   43     11   12   13   17   20   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     14   26   43     11   12   13   17   21   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     14   26   43     11   12   13   17   21   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     14   26   43     11   12   13   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     14   26   43     11   12   15   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     16   26   43     11   12   16   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     18   26   43     11   12   13   18   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     18   26   43     11   16   17   19   23   25   28   30   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     18   26   43     11   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     18   26   43     10   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     18   26   43      3   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     18   26   43      3   16   17   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     18   26   43      3    4   10   17   23   25   28   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B      6   26   43      3    4   11   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B      6   26   43      5    6   14   19   23   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B      6   25   43      5    6    6    8    9    9   13   22   26   29   34   35   40   41   42   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B      6   10   43      5    6    6    8    9    9   11   11   12   25   34   35   37   41   42   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B      6   10   43      5    6    6    8    9   11   17   25   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B      7   10   43      5    7    9   14   19   25   29   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B      7   10   43      4    7   11   16   19   22   27   32   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      7   10   43      5   12   13   17   19   22   23   28   35   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      7   10   43      5    7   13   16   19   20   23   25   30   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      7   10   43      5    7    8   15   19   20   22   25   30   34   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   10   43      5    7    8   14   17   20   21   24   28   33   36   37   40   41   42   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7    8   43      5    7    7   14   19   20   21   25   30   34   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    8   43      3    3    3    3    4    5    9   11   28   35   37   38   40   41   42   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    5   17   17   25   30   33   37   39   41   43   43   43   43 
LCS_AVERAGE  LCS_A:  59.89  (  30.77   48.89  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     11     16     17     19     23     25     29     32     35     35     37     38     40     41     42     42     43     43     43     43 
GDT PERCENT_AT  25.58  37.21  39.53  44.19  53.49  58.14  67.44  74.42  81.40  81.40  86.05  88.37  93.02  95.35  97.67  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.20   0.48   0.56   1.09   1.52   1.71   2.33   2.60   2.86   2.86   3.22   3.40   3.71   3.85   4.01   4.01   4.24   4.24   4.24   4.24
GDT RMS_ALL_AT   8.95   6.98   6.94   6.43   5.86   5.73   5.20   4.93   4.80   4.80   4.50   4.39   4.28   4.26   4.25   4.25   4.24   4.24   4.24   4.24

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  D    36_B      D    36_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     4.520     0    0.627   0.936     8.430   40.357   29.365
LGA    L     6_B      L     6_B     3.494     0    0.058   1.219     5.070   53.810   51.190
LGA    E     7_B      E     7_B     2.920     0    0.039   0.839     6.321   61.190   44.021
LGA    T     8_B      T     8_B     2.046     0    0.038   1.211     4.833   73.452   62.857
LGA    K     9_B      K     9_B     1.563     0    0.015   0.141     4.243   79.405   63.333
LGA    K    10_B      K    10_B     0.553     0    0.014   0.945     4.954   90.595   76.508
LGA    A    11_B      A    11_B     1.498     0    0.010   0.012     2.055   79.524   76.571
LGA    Y    12_B      Y    12_B     1.338     0    0.016   1.223     8.344   75.476   51.706
LGA    A    13_B      A    13_B     2.041     0    0.010   0.012     2.921   64.881   66.476
LGA    A    14_B      A    14_B     2.469     0    0.075   0.081     4.061   56.190   57.905
LGA    R    15_B      R    15_B     3.710     0    0.050   1.200     4.898   40.476   52.900
LGA    T    16_B      T    16_B     4.525     0    0.201   1.067     6.940   37.262   33.878
LGA    R    17_B      R    17_B     3.167     0    0.045   0.792     7.254   51.905   32.944
LGA    R    18_B      R    18_B     2.830     0    0.010   1.466     4.810   55.357   44.978
LGA    S    19_B      S    19_B     3.732     0    0.045   0.718     4.569   48.452   44.762
LGA    N    20_B      N    20_B     3.214     0    0.022   0.322     4.506   57.381   48.869
LGA    Y    21_B      Y    21_B     1.255     0    0.054   0.174     2.630   81.786   80.437
LGA    A    22_B      A    22_B     1.427     0    0.008   0.014     2.190   83.690   79.905
LGA    A    23_B      A    23_B     1.711     0    0.024   0.024     2.481   77.143   74.667
LGA    S    24_B      S    24_B     1.750     0    0.062   0.721     2.069   75.000   77.460
LGA    L    25_B      L    25_B     0.929     0    0.065   0.066     1.528   85.952   84.881
LGA    R    26_B      R    26_B     0.791     0    0.052   1.221     5.095   83.810   67.662
LGA    L    27_B      L    27_B     1.764     0    0.029   0.223     2.538   69.048   68.929
LGA    E    28_B      E    28_B     2.355     0    0.016   1.103     5.015   62.976   55.132
LGA    G    29_B      G    29_B     2.605     0    0.092   0.092     2.762   60.952   60.952
LGA    F    30_B      F    30_B     2.039     0    0.121   1.392     7.489   62.857   45.844
LGA    K    31_B      K    31_B     2.711     0    0.202   0.860     8.910   59.048   35.820
LGA    V    32_B      V    32_B     2.609     0    0.591   0.540     6.002   43.690   50.544
LGA    T    33_B      T    33_B     3.608     0    0.236   0.986     6.431   55.595   43.265
LGA    F    34_B      F    34_B     2.020     0    0.092   0.242     4.153   66.905   55.714
LGA    A    35_B      A    35_B     3.247     0    0.619   0.576     3.946   53.810   51.714
LGA    D    36_B      D    36_B     6.810     0    0.008   1.380    12.165   17.262    8.810
LGA    G    37_B      G    37_B     7.677     0    0.040   0.040     7.677   11.905   11.905
LGA    E    38_B      E    38_B     4.247     0    0.143   1.266    10.495   42.143   22.910
LGA    R    39_B      R    39_B     2.580     0    0.401   1.135    10.137   67.857   30.130
LGA    K    40_B      K    40_B     4.300     0    0.324   1.162     4.994   37.262   41.746
LGA    M    41_B      M    41_B     5.840     0    0.014   0.273     6.606   18.571   20.655
LGA    P    42_B      P    42_B     8.112     0    0.015   0.076     8.746    6.071    5.986
LGA    T    43_B      T    43_B     9.652     0    0.058   0.048    10.820    0.476    0.340
LGA    R    44_B      R    44_B    11.163     0    0.596   1.380    16.973    0.000    0.000
LGA    E    45_B      E    45_B    11.495     0    0.451   1.387    13.185    0.000    0.000
LGA    E    46_B      E    46_B     7.813     0    0.609   1.425    11.439    2.500    6.455
LGA    V    47_B      V    47_B    13.191     0    0.424   1.359    15.780    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):     4.240          4.218                  5.159           50.977   44.654

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     32    2.60    63.372    61.907     1.186

LGA_LOCAL      RMSD:   2.599  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.929  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.240  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.984354 * X  +  -0.135159 * Y  +   0.113048 * Z  +  29.499111
  Y_new =   0.169457 * X  +  -0.901981 * Y  +   0.397134 * Z  + -57.939316
  Z_new =   0.048291 * X  +   0.410077 * Y  +   0.910772 * Z  +  21.051634 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.971113 -0.048310  0.423064   [DEG:  170.2322   -2.7679   24.2398 ]
ZXZ:  2.864268  0.425647  0.117221   [DEG:  164.1105   24.3878    6.7163 ]
 
# END of job
