
#######################################################
#                                                     #
#                        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        4.18     4.18
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      10_B - 34_B        1.94     5.69
  LONGEST_CONTINUOUS_SEGMENT:    25      11_B - 35_B        1.92     5.83
  LCS_AVERAGE:     46.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      15_B - 33_B        0.98     6.92
  LCS_AVERAGE:     31.69

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   14   17   19   21   26   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     14   20   43     11   12   14   17   19   22   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     14   20   43     11   12   14   17   19   24   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     14   20   43     11   12   14   17   19   24   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     14   22   43     11   12   14   17   21   24   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     14   25   43     11   12   14   17   21   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     14   25   43     11   12   14   17   21   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     14   25   43     11   12   14   17   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     14   25   43     11   12   14   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     14   25   43     11   12   16   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     19   25   43     11   12   14   18   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     19   25   43     12   18   18   20   22   25   29   31   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     19   25   43     10   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     19   25   43     10   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     19   25   43     10   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     19   25   43     12   18   18   20   22   25   29   33   34   35   36   39   41   42   42   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     19   25   43     12   18   18   20   22   25   29   33   34   35   36   39   41   42   42   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     19   25   43     12   18   18   20   22   25   29   33   34   35   36   39   41   42   42   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     19   25   43     12   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     19   25   43      4   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     19   25   43      4   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     19   25   43     10   18   18   20   22   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B      6   25   43      4    5    6   13   21   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B      6   25   43      4    5    6   13   19   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B      6   10   43      4    5    6    7    9   12   18   26   32   34   36   39   41   42   42   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B      6   10   43      4    5    6    7    8    9   12   13   22   27   35   37   41   42   42   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B      7   10   43      4    6   10   16   21   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B      7   10   43      3    6   10   16   21   25   29   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B      7   10   43      3    6    8   15   17   21   28   33   34   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      7   10   43      3   11   14   17   19   21   23   27   31   35   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      7   10   43      4   11   14   17   19   20   22   26   29   34   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      7   10   43      4    6   13   15   19   20   22   26   28   34   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   10   43      4    5   12   14   16   20   22   25   28   34   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      6   10   43      4    5    6   15   19   20   22   26   31   34   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    5    5    5   19   20   31   34   37   39   41   42   42   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    5    5   17   24   30   32   38   39   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  59.47  (  31.69   46.73  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     12     18     18     20     22     25     29     33     34     35     37     39     41     42     42     43     43     43     43     43 
GDT PERCENT_AT  27.91  41.86  41.86  46.51  51.16  58.14  67.44  76.74  79.07  81.40  86.05  90.70  95.35  97.67  97.67 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.57   0.57   1.14   1.46   1.90   2.22   2.64   2.72   2.87   3.49   3.59   3.82   3.95   3.95   4.18   4.18   4.18   4.18   4.18
GDT RMS_ALL_AT   7.18   7.28   7.28   6.68   6.21   5.95   5.32   4.88   4.89   4.76   4.23   4.23   4.19   4.19   4.19   4.18   4.18   4.18   4.18   4.18

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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     4.358     0    0.635   0.942     8.295   45.119   32.540
LGA    L     6_B      L     6_B     3.478     0    0.052   1.222     5.275   53.810   51.190
LGA    E     7_B      E     7_B     2.902     0    0.036   0.839     6.465   61.190   44.021
LGA    T     8_B      T     8_B     1.868     0    0.052   1.212     4.551   77.381   67.279
LGA    K     9_B      K     9_B     1.614     0    0.021   0.776     3.062   77.143   68.677
LGA    K    10_B      K    10_B     0.565     0    0.014   0.944     5.083   90.595   75.926
LGA    A    11_B      A    11_B     1.466     0    0.012   0.014     2.117   79.524   78.190
LGA    Y    12_B      Y    12_B     1.461     0    0.016   1.229     8.426   75.476   50.754
LGA    A    13_B      A    13_B     2.218     0    0.005   0.010     3.102   63.095   63.429
LGA    A    14_B      A    14_B     2.578     0    0.063   0.070     4.099   52.262   54.762
LGA    R    15_B      R    15_B     3.795     0    0.051   1.204     5.010   39.167   52.424
LGA    T    16_B      T    16_B     4.659     0    0.207   1.068     7.028   35.714   32.517
LGA    R    17_B      R    17_B     3.378     0    0.041   1.160     7.175   50.119   38.874
LGA    R    18_B      R    18_B     3.026     0    0.012   0.792     4.486   51.786   46.494
LGA    S    19_B      S    19_B     3.806     0    0.041   0.716     4.636   46.667   43.571
LGA    N    20_B      N    20_B     3.303     0    0.019   0.324     4.560   55.476   47.917
LGA    Y    21_B      Y    21_B     1.288     0    0.070   0.106     2.894   79.524   78.254
LGA    A    22_B      A    22_B     1.519     0    0.007   0.014     2.286   79.405   76.476
LGA    A    23_B      A    23_B     1.908     0    0.022   0.022     2.700   75.000   71.429
LGA    S    24_B      S    24_B     1.897     0    0.064   0.717     2.249   75.000   75.873
LGA    L    25_B      L    25_B     0.835     0    0.022   0.121     1.494   85.952   90.595
LGA    R    26_B      R    26_B     0.818     0    0.060   1.223     4.966   83.810   67.619
LGA    L    27_B      L    27_B     2.032     0    0.028   0.215     2.935   67.024   64.940
LGA    E    28_B      E    28_B     2.733     0    0.030   1.101     5.498   57.262   49.524
LGA    G    29_B      G    29_B     2.961     0    0.088   0.088     3.173   55.357   55.357
LGA    F    30_B      F    30_B     2.615     0    0.019   0.056     3.468   59.048   57.273
LGA    K    31_B      K    31_B     3.372     0    0.085   0.884    10.516   50.000   28.677
LGA    V    32_B      V    32_B     2.917     0    0.557   1.138     4.958   47.143   53.741
LGA    T    33_B      T    33_B     2.172     0    0.172   0.287     2.785   64.881   68.367
LGA    F    34_B      F    34_B     2.984     0    0.173   1.588     6.094   53.690   40.000
LGA    A    35_B      A    35_B     3.346     0    0.031   0.035     6.184   42.857   42.952
LGA    D    36_B      D    36_B     5.901     0    0.256   0.329     7.176   20.476   20.476
LGA    G    37_B      G    37_B     7.136     0    0.719   0.719     7.136   19.048   19.048
LGA    E    38_B      E    38_B     1.294     0    0.081   1.269     4.466   61.905   57.937
LGA    R    39_B      R    39_B     1.348     0    0.284   1.468     5.445   79.286   68.268
LGA    K    40_B      K    40_B     4.430     0    0.586   0.915     8.186   34.524   21.746
LGA    M    41_B      M    41_B     6.394     0    0.099   0.314     7.648   13.929   16.607
LGA    P    42_B      P    42_B     8.550     0    0.037   0.052     9.003    3.571    4.150
LGA    T    43_B      T    43_B     9.906     0    0.043   0.049    10.624    0.238    0.204
LGA    R    44_B      R    44_B    11.087     0    0.595   1.426    16.714    0.000    0.000
LGA    E    45_B      E    45_B    10.990     0    0.473   1.145    11.679    0.000    0.000
LGA    E    46_B      E    46_B     7.695     0    0.610   1.413    11.309    2.976    5.450
LGA    V    47_B      V    47_B    13.088     0    0.419   1.397    15.790    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):     4.176          4.216                  4.802           50.382   46.129

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     33    2.64    66.279    62.182     1.205

LGA_LOCAL      RMSD:   2.638  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.879  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.176  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.573929 * X  +  -0.505260 * Y  +   0.644452 * Z  +  29.819414
  Y_new =   0.565836 * X  +  -0.813567 * Y  +  -0.133933 * Z  + -59.167404
  Z_new =   0.591976 * X  +   0.287786 * Y  +   0.752824 * Z  +  19.956450 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.363295 -0.633508  0.365134   [DEG:  135.4068  -36.2973   20.9206 ]
ZXZ:  1.365889  0.718454  1.118294   [DEG:   78.2597   41.1644   64.0735 ]
 
# END of job
