
#######################################################
#                                                     #
#                        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   56 (  447),  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        3.03     3.03
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38       5_B - 42_B        1.87     3.73
  LCS_AVERAGE:     81.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_B - 34_B        0.96     3.52
  LCS_AVERAGE:     57.92

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     30   38   43      4   21   28   30   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     30   38   43     26   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     30   38   43     12   27   28   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     30   38   43      5   16   27   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     30   38   43      6   13   25   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     29   38   43      6   13   27   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     17   38   43      6   13   26   31   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     16   38   43      6   13   15   19   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     16   38   43      6   13   15   18   31   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     16   38   43      6   13   15   19   32   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     16   38   43      4   13   15   19   31   36   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     15   38   43      4   10   14   17   21   27   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     14   38   43      4    7   11   15   18   24   38   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     11   24   43      4    6   11   13   16   21   33   39   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   20   43      4    6   10   12   13   15   20   27   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   15   43      4    6    7    9   12   13   15   18   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    3    6    8    9   11   13   15   34   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      2    3    3    3    3   29   34   38   42   42   42   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  79.95  (  57.92   81.94  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     26     27     28     31     32     36     38     39     42     42     42     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  60.47  62.79  65.12  72.09  74.42  83.72  88.37  90.70  97.67  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.41   0.48   1.08   1.12   1.53   1.87   2.09   2.74   2.74   2.74   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03
GDT RMS_ALL_AT   3.65   3.57   3.59   3.81   3.74   4.01   3.73   3.51   3.07   3.07   3.07   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03   3.03

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_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     1.883     0    0.611   0.911     4.180   77.143   65.952
LGA    L     6_B      L     6_B     0.730     0    0.044   1.225     3.270   92.976   84.464
LGA    E     7_B      E     7_B     0.799     0    0.057   1.115     3.951   88.333   79.312
LGA    T     8_B      T     8_B     1.634     0    0.039   1.170     3.320   77.143   69.728
LGA    K     9_B      K     9_B     0.990     0    0.015   0.114     1.888   88.214   83.545
LGA    K    10_B      K    10_B     0.778     0    0.045   0.930     4.196   85.952   78.571
LGA    A    11_B      A    11_B     1.598     0    0.025   0.038     1.835   75.000   74.571
LGA    Y    12_B      Y    12_B     1.636     0    0.041   0.056     2.659   75.000   68.929
LGA    A    13_B      A    13_B     0.896     0    0.015   0.023     1.120   85.952   86.857
LGA    A    14_B      A    14_B     1.506     0    0.074   0.087     1.903   75.000   74.571
LGA    R    15_B      R    15_B     2.163     0    0.047   0.809     3.794   66.786   60.130
LGA    T    16_B      T    16_B     1.941     0    0.014   0.095     2.478   72.857   70.544
LGA    R    17_B      R    17_B     0.850     0    0.037   1.220     4.891   83.690   74.156
LGA    R    18_B      R    18_B     1.778     0    0.024   0.724     2.681   72.857   67.143
LGA    S    19_B      S    19_B     2.250     0    0.037   0.639     3.371   68.810   63.730
LGA    N    20_B      N    20_B     1.570     0    0.070   0.496     1.774   77.143   78.214
LGA    Y    21_B      Y    21_B     0.803     0    0.062   0.195     2.604   85.952   78.214
LGA    A    22_B      A    22_B     1.462     0    0.035   0.033     1.733   81.429   79.714
LGA    A    23_B      A    23_B     1.632     0    0.039   0.044     1.781   77.143   76.286
LGA    S    24_B      S    24_B     1.084     0    0.091   0.725     1.896   85.952   84.524
LGA    L    25_B      L    25_B     0.775     0    0.021   0.066     0.910   90.476   90.476
LGA    R    26_B      R    26_B     1.093     0    0.023   1.030     4.786   85.952   68.831
LGA    L    27_B      L    27_B     1.048     0    0.039   0.191     2.170   85.952   81.607
LGA    E    28_B      E    28_B     0.434     0    0.027   1.039     4.412   97.619   82.063
LGA    G    29_B      G    29_B     0.696     0    0.032   0.032     0.762   90.476   90.476
LGA    F    30_B      F    30_B     0.836     0    0.061   0.117     1.029   85.952   89.740
LGA    K    31_B      K    31_B     1.352     0    0.020   0.624     5.528   81.429   61.481
LGA    V    32_B      V    32_B     0.675     0    0.053   1.234     3.383   88.214   79.728
LGA    T    33_B      T    33_B     1.177     0    0.059   1.072     3.687   83.690   77.279
LGA    F    34_B      F    34_B     2.055     0    0.015   1.365     4.068   68.810   61.818
LGA    A    35_B      A    35_B     1.696     0    0.025   0.025     1.969   72.857   74.571
LGA    D    36_B      D    36_B     1.489     0    0.015   0.142     2.142   75.119   81.726
LGA    G    37_B      G    37_B     2.662     0    0.046   0.046     3.176   57.262   57.262
LGA    E    38_B      E    38_B     3.290     0    0.017   0.808     4.850   50.119   45.820
LGA    R    39_B      R    39_B     3.076     0    0.146   1.140     4.646   50.119   50.736
LGA    K    40_B      K    40_B     3.111     0    0.081   1.229     6.645   48.452   48.148
LGA    M    41_B      M    41_B     4.010     0    0.028   0.953     7.848   40.238   33.750
LGA    P    42_B      P    42_B     4.657     0    0.039   0.044     5.434   30.238   31.565
LGA    T    43_B      T    43_B     5.868     0    0.021   0.147     6.524   18.571   19.864
LGA    R    44_B      R    44_B     7.838     0    0.600   0.958    14.803    6.667    2.857
LGA    E    45_B      E    45_B     9.089     0    0.468   1.549     9.912    1.310    2.910
LGA    E    46_B      E    46_B    12.272     0    0.585   1.447    15.868    0.000    0.000
LGA    V    47_B      V    47_B     7.985     0    0.406   1.366    10.307    2.500   12.449

# 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):     3.031          3.050                  3.590           67.566   63.821

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     39    2.09    81.395    83.846     1.781

LGA_LOCAL      RMSD:   2.089  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.506  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.031  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.551320 * X  +  -0.739032 * Y  +  -0.387141 * Z  +  23.981270
  Y_new =  -0.567067 * X  +  -0.008423 * Y  +   0.823629 * Z  + -32.136539
  Z_new =  -0.611949 * X  +   0.673617 * Y  +  -0.414437 * Z  +  19.359089 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.342115  0.658523  2.122347   [DEG: -134.1933   37.7306  121.6015 ]
ZXZ: -2.702197  1.998120 -0.737465   [DEG: -154.8245  114.4838  -42.2536 ]
 
# END of job
