
#######################################################
#                                                     #
#                        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        2.46     2.46
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       5_B - 45_B        1.89     2.53
  LCS_AVERAGE:     93.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.99     3.12
  LCS_AVERAGE:     56.14

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     29   41   43      4   15   21   30   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   41   43     13   24   29   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   41   43     13   24   29   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   41   43     15   22   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   41   43     15   23   28   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   41   43     15   23   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   41   43     15   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   41   43     13   24   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   41   43      8   14   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     25   41   43      8   14   28   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     17   41   43      8   14   28   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     17   41   43      8   21   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     17   41   43      8   21   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     17   41   43      8   19   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     17   41   43      8   20   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     17   41   43      7   19   30   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     15   41   43      5   14   25   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     15   41   43      7   14   24   34   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     15   41   43      4    9   21   32   36   38   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     12   41   43      4    9   15   27   33   37   39   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   41   43      4    7   11   20   30   33   38   40   41   41   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   37   43      3    3    3    6    8    8   10   12   28   40   42   42   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    5    8   34   37   40   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  83.07  (  56.14   93.08  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     15     24     30     34     36     38     39     40     41     41     42     42     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  34.88  55.81  69.77  79.07  83.72  88.37  90.70  93.02  95.35  95.35  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.62   0.96   1.10   1.20   1.36   1.50   1.67   1.89   1.89   2.16   2.16   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46
GDT RMS_ALL_AT   3.96   3.25   2.82   2.89   2.92   2.82   2.72   2.63   2.53   2.53   2.48   2.48   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  E    38_B      E    38_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     3.083     0    0.620   0.675     7.692   65.595   48.492
LGA    L     6_B      L     6_B     2.281     0    0.052   0.867     2.654   66.905   66.905
LGA    E     7_B      E     7_B     1.813     0    0.085   1.027     6.155   75.119   59.735
LGA    T     8_B      T     8_B     0.877     0    0.042   1.154     3.006   88.214   79.728
LGA    K     9_B      K     9_B     1.052     0    0.015   0.137     2.005   85.952   77.831
LGA    K    10_B      K    10_B     1.060     0    0.052   0.911     3.731   85.952   76.402
LGA    A    11_B      A    11_B     0.900     0    0.025   0.039     0.963   90.476   90.476
LGA    Y    12_B      Y    12_B     0.449     0    0.025   0.064     1.784   95.238   87.579
LGA    A    13_B      A    13_B     0.507     0    0.018   0.025     0.678   92.857   94.286
LGA    A    14_B      A    14_B     0.772     0    0.055   0.068     1.400   85.952   86.857
LGA    R    15_B      R    15_B     1.362     0    0.067   0.791     2.121   77.143   76.797
LGA    T    16_B      T    16_B     1.639     0    0.057   0.056     2.299   79.286   75.374
LGA    R    17_B      R    17_B     0.511     0    0.049   0.990     5.780   90.476   66.277
LGA    R    18_B      R    18_B     1.531     0    0.044   1.256     5.992   75.000   59.827
LGA    S    19_B      S    19_B     2.143     0    0.047   0.746     2.592   70.833   68.889
LGA    N    20_B      N    20_B     1.540     0    0.062   0.444     2.108   77.143   75.060
LGA    Y    21_B      Y    21_B     0.530     0    0.064   0.158     3.657   90.476   73.849
LGA    A    22_B      A    22_B     1.257     0    0.039   0.036     1.598   83.690   81.524
LGA    A    23_B      A    23_B     1.439     0    0.056   0.062     1.702   81.429   79.714
LGA    S    24_B      S    24_B     1.106     0    0.060   0.705     1.192   85.952   85.952
LGA    L    25_B      L    25_B     0.777     0    0.025   0.082     1.268   90.476   88.214
LGA    R    26_B      R    26_B     0.928     0    0.020   1.064     4.522   90.476   71.299
LGA    L    27_B      L    27_B     0.939     0    0.079   0.213     2.130   90.476   83.869
LGA    E    28_B      E    28_B     0.704     0    0.025   0.897     3.228   90.476   83.968
LGA    G    29_B      G    29_B     0.574     0    0.036   0.036     0.731   92.857   92.857
LGA    F    30_B      F    30_B     0.767     0    0.055   0.139     1.828   90.476   84.026
LGA    K    31_B      K    31_B     1.153     0    0.079   0.624     4.842   83.690   65.926
LGA    V    32_B      V    32_B     0.916     0    0.098   0.256     2.056   81.548   80.408
LGA    T    33_B      T    33_B     1.728     0    0.066   1.063     4.091   77.143   66.803
LGA    F    34_B      F    34_B     2.040     0    0.032   1.429     6.037   70.833   53.550
LGA    A    35_B      A    35_B     1.911     0    0.023   0.033     2.079   75.000   72.952
LGA    D    36_B      D    36_B     0.777     0    0.015   0.225     1.543   90.595   88.333
LGA    G    37_B      G    37_B     1.022     0    0.050   0.050     1.063   83.690   83.690
LGA    E    38_B      E    38_B     1.376     0    0.027   1.013     6.325   81.429   61.640
LGA    R    39_B      R    39_B     1.166     0    0.125   1.198     4.906   85.952   68.961
LGA    K    40_B      K    40_B     1.004     0    0.091   0.864     7.484   81.548   58.413
LGA    M    41_B      M    41_B     2.219     0    0.051   0.960     3.831   66.786   60.298
LGA    P    42_B      P    42_B     2.561     0    0.067   0.074     3.124   59.048   57.211
LGA    T    43_B      T    43_B     3.589     0    0.010   0.069     3.983   45.000   44.286
LGA    R    44_B      R    44_B     4.679     0    0.605   0.952     5.767   38.929   30.000
LGA    E    45_B      E    45_B     6.307     0    0.485   1.334    11.352   16.190   10.265
LGA    E    46_B      E    46_B     8.063     0    0.598   1.384    12.714    8.810    3.968
LGA    V    47_B      V    47_B     8.984     0    0.412   1.359    11.646    3.571    2.109

# 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):     2.461          2.327                  3.178           75.318   68.014

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     40    1.67    81.977    87.774     2.265

LGA_LOCAL      RMSD:   1.666  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.626  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   2.461  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.359119 * X  +  -0.002143 * Y  +   0.933289 * Z  +  25.463575
  Y_new =  -0.879393 * X  +  -0.335691 * Y  +   0.337609 * Z  + -32.257343
  Z_new =   0.312574 * X  +  -0.941970 * Y  +  -0.122438 * Z  +  18.581688 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.183094 -0.317901 -1.700052   [DEG:  -67.7863  -18.2144  -97.4058 ]
ZXZ:  1.917892  1.693542  2.821196   [DEG:  109.8871   97.0328  161.6426 ]
 
# END of job
