
#######################################################
#                                                     #
#                        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        3.06     3.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       8_B - 42_B        1.94     3.64
  LONGEST_CONTINUOUS_SEGMENT:    35       9_B - 43_B        1.91     3.53
  LONGEST_CONTINUOUS_SEGMENT:    35      10_B - 44_B        1.98     3.49
  LCS_AVERAGE:     75.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      13_B - 31_B        1.00     4.35
  LONGEST_CONTINUOUS_SEGMENT:    19      14_B - 32_B        0.90     4.46
  LONGEST_CONTINUOUS_SEGMENT:    19      16_B - 34_B        0.99     4.80
  LCS_AVERAGE:     37.97

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   22   43      4   12   13   16   18   20   25   30   38   40   40   42   42   42   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     15   23   43     11   12   14   16   18   27   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     15   26   43     11   12   14   16   19   31   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     15   35   43     11   12   14   17   29   32   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     15   35   43     11   12   14   23   29   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     15   35   43     11   12   14   24   29   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     15   35   43     11   12   14   23   29   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     15   35   43     11   12   20   27   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     19   35   43     11   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     19   35   43     11   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     19   35   43     11   12   14   20   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     19   35   43     16   17   19   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     19   35   43     16   17   20   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     19   35   43     16   17   18   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     19   35   43     16   17   19   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     19   35   43     16   17   19   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     19   35   43     16   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     19   35   43     16   17   20   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     19   35   43     11   17   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     19   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     19   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     17   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     17   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     17   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     17   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     17   35   43      9   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     17   35   43      6   12   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     17   35   43      3   10   21   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     15   35   43      4    7   18   28   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     10   35   43      4    6   11   21   31   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   35   43      4    6    8   13   15   33   36   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   15   43      4    6    7    9   15   21   35   40   40   40   41   42   42   42   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   12   43      3    3    3    5    6    7    9   14   20   36   38   39   40   41   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3   29   37   38   39   41   42   42   42   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  71.16  (  37.97   75.50  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     16     17     21     28     31     33     36     40     40     40     41     42     42     42     43     43     43     43     43     43 
GDT PERCENT_AT  37.21  39.53  48.84  65.12  72.09  76.74  83.72  93.02  93.02  93.02  95.35  97.67  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.35   1.06   1.34   1.49   1.73   2.13   2.55   2.55   2.48   2.71   2.83   2.83   2.83   3.06   3.06   3.06   3.06   3.06   3.06
GDT RMS_ALL_AT   4.90   4.87   4.02   4.20   4.01   3.75   3.58   3.15   3.15   3.32   3.10   3.09   3.09   3.09   3.06   3.06   3.06   3.06   3.06   3.06

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  D    36_B      D    36_B
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     5.990     0    0.616   0.925     9.900   26.310   17.857
LGA    L     6_B      L     6_B     4.506     0    0.054   1.227     5.891   36.190   36.726
LGA    E     7_B      E     7_B     4.181     0    0.031   0.842     7.403   41.905   29.735
LGA    T     8_B      T     8_B     3.259     0    0.034   1.225     5.931   53.810   46.259
LGA    K     9_B      K     9_B     2.218     0    0.006   0.142     4.558   69.048   55.026
LGA    K    10_B      K    10_B     1.548     0    0.015   0.837     3.992   77.143   67.937
LGA    A    11_B      A    11_B     2.299     0    0.008   0.009     2.969   68.810   66.476
LGA    Y    12_B      Y    12_B     0.760     0    0.006   0.047     2.895   83.810   80.476
LGA    A    13_B      A    13_B     1.184     0    0.000   0.000     2.374   77.381   78.190
LGA    A    14_B      A    14_B     2.360     0    0.078   0.083     3.931   57.738   59.143
LGA    R    15_B      R    15_B     3.351     0    0.070   0.810     4.402   46.905   57.576
LGA    T    16_B      T    16_B     3.675     0    0.170   1.056     5.904   45.000   43.129
LGA    R    17_B      R    17_B     2.896     0    0.054   0.734     6.469   55.357   38.182
LGA    R    18_B      R    18_B     2.729     0    0.016   1.107     6.790   57.143   43.896
LGA    S    19_B      S    19_B     3.353     0    0.043   0.053     3.946   51.786   48.968
LGA    N    20_B      N    20_B     3.061     0    0.029   0.346     3.856   55.476   52.798
LGA    Y    21_B      Y    21_B     1.834     0    0.045   0.124     2.383   70.833   73.651
LGA    A    22_B      A    22_B     1.949     0    0.007   0.008     2.325   72.857   71.238
LGA    A    23_B      A    23_B     2.180     0    0.016   0.015     2.594   68.810   66.476
LGA    S    24_B      S    24_B     2.023     0    0.025   0.575     2.204   68.810   70.238
LGA    L    25_B      L    25_B     1.495     0    0.033   0.049     1.682   77.143   78.214
LGA    R    26_B      R    26_B     1.413     0    0.037   1.024     4.724   81.429   67.749
LGA    L    27_B      L    27_B     1.539     0    0.008   0.235     2.477   75.000   71.905
LGA    E    28_B      E    28_B     1.703     0    0.044   0.586     2.681   72.857   69.365
LGA    G    29_B      G    29_B     1.868     0    0.065   0.065     1.911   72.857   72.857
LGA    F    30_B      F    30_B     1.952     0    0.015   0.152     2.877   72.857   67.836
LGA    K    31_B      K    31_B     2.437     0    0.119   0.624     6.763   66.786   47.037
LGA    V    32_B      V    32_B     1.727     0    0.021   0.276     2.692   68.810   68.367
LGA    T    33_B      T    33_B     1.801     0    0.044   1.080     3.901   77.143   71.156
LGA    F    34_B      F    34_B     1.867     0    0.015   0.093     2.535   72.857   66.320
LGA    A    35_B      A    35_B     1.711     0    0.023   0.024     1.800   77.143   76.286
LGA    D    36_B      D    36_B     0.782     0    0.008   0.071     1.104   88.214   89.345
LGA    G    37_B      G    37_B     0.778     0    0.045   0.045     1.238   85.952   85.952
LGA    E    38_B      E    38_B     1.643     0    0.029   0.852     3.372   75.000   66.931
LGA    R    39_B      R    39_B     1.928     0    0.080   1.283     4.465   72.857   68.485
LGA    K    40_B      K    40_B     2.127     0    0.031   1.232     8.744   64.762   45.397
LGA    M    41_B      M    41_B     2.142     0    0.011   0.964     4.264   70.833   64.405
LGA    P    42_B      P    42_B     1.752     0    0.022   0.038     2.356   68.810   68.231
LGA    T    43_B      T    43_B     2.490     0    0.040   0.055     3.070   57.381   58.367
LGA    R    44_B      R    44_B     3.921     0    0.592   0.890     9.746   48.452   27.359
LGA    E    45_B      E    45_B     6.102     0    0.446   1.590    10.906   16.310   11.111
LGA    E    46_B      E    46_B     9.254     0    0.602   1.436    13.092    4.524    2.011
LGA    V    47_B      V    47_B     6.811     0    0.438   1.375     8.490    9.405   11.973

# 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):     3.061          2.974                  3.756           61.919   57.224

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     40    2.55    74.419    77.239     1.510

LGA_LOCAL      RMSD:   2.548  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.154  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.061  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.992948 * X  +  -0.034530 * Y  +  -0.113409 * Z  +  22.939777
  Y_new =  -0.116388 * X  +   0.102130 * Y  +   0.987939 * Z  + -31.424978
  Z_new =  -0.022531 * X  +   0.994172 * Y  +  -0.105429 * Z  +  19.897696 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.024910  0.022533  1.676448   [DEG: -173.3146    1.2910   96.0534 ]
ZXZ: -3.027300  1.676421 -0.022659   [DEG: -173.4515   96.0519   -1.2983 ]
 
# END of job
