
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      30_A - 58_A        4.52    14.91
  LCS_AVERAGE:     43.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.58    15.14
  LCS_AVERAGE:     32.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.81    15.15
  LCS_AVERAGE:     29.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     A     1_A     A     1_A      3   14   17      3    3    3    4   12   20   29   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     13   14   17     22   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     13   14   17     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     13   14   21      4   28   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     13   14   25      3    5   29   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A     13   14   25     22   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   16   25      3    3    3    8   19   21   24   33   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   16   25     14   14   14   14   15   15   22   25   31   35   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   27   31   36   41   43   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   29   31   36   38 
LCS_GDT     P    19_A     P    19_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     F    20_A     F    20_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     K    21_A     K    21_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     K    22_A     K    22_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     G    23_A     G    23_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     E    24_A     E    24_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     I    25_A     I    25_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     L    26_A     L    26_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     R    27_A     R    27_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   24   25   28   28   29 
LCS_GDT     I    28_A     I    28_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   24   25   28   32   35   36 
LCS_GDT     R    29_A     R    29_A     15   16   25     14   14   14   14   15   15   16   18   20   22   22   22   22   23   28   28   33   34   37   42 
LCS_GDT     D    30_A     D    30_A     15   16   29      3    4    7   14   15   15   16   18   20   22   22   24   28   30   35   40   43   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    7   11   15   18   20   22   23   24   28   41   43   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    7   29      3    3    4    5    7   13   16   18   20   22   22   22   38   41   43   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    7   29      3    3    5    6    7    9   11   28   33   39   40   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    5    9   15   32   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      6   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     30   34   35   36   36   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    6   13   19   36   37   37   38   40   41   42   42   42   43   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.40  (  29.49   32.91   43.82 )

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     30     34     35     36     36     36     37     37     38     40     41     42     42     42     43     44     44     45     46     46 
GDT PERCENT_AT  51.72  58.62  60.34  62.07  62.07  62.07  63.79  63.79  65.52  68.97  70.69  72.41  72.41  72.41  74.14  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.28   0.39   0.50   0.65   0.65   0.65   0.91   0.91   1.42   2.07   2.40   2.76   2.76   2.76   3.21   3.64   3.64   3.98   4.38   4.38
GDT RMS_ALL_AT  15.17  15.15  15.16  15.18  15.18  15.18  15.16  15.16  15.12  14.97  14.86  14.84  14.84  14.84  14.79  14.70  14.70  14.58  14.48  14.48

# Checking swapping
#   possible swapping detected:  Y     3_A      Y     3_A
#   possible swapping detected:  F     8_A      F     8_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     7.390     0    0.424   0.466     8.969   17.619   15.048
LGA    E     2_A      E     2_A     0.498     0    0.654   1.003     6.094   87.500   61.640
LGA    Y     3_A      Y     3_A     0.382     0    0.045   0.166     1.132  100.000   92.937
LGA    V     4_A      V     4_A     0.237     0    0.042   0.089     0.359  100.000  100.000
LGA    R     5_A      R     5_A     0.307     0    0.033   1.357     2.743  100.000   84.935
LGA    A     6_A      A     6_A     0.456     0    0.031   0.045     0.484  100.000  100.000
LGA    L     7_A      L     7_A     0.498     0    0.108   0.169     0.907   95.238   96.429
LGA    F     8_A      F     8_A     0.518     0    0.024   0.108     0.738   92.857   91.342
LGA    D     9_A      D     9_A     0.434     0    0.070   0.890     3.613   95.238   80.774
LGA    H    10_A      H    10_A     0.608     0    0.068   1.132     2.421   90.476   83.524
LGA    T    11_A      T    11_A     0.365     0    0.094   0.170     0.845   95.238   93.197
LGA    G    12_A      G    12_A     1.640     0    0.061   0.061     1.640   79.405   79.405
LGA    H    13_A      H    13_A     2.569     0    0.527   0.987     5.675   57.500   47.857
LGA    D    14_A      D    14_A     1.041     0    0.059   1.342     4.947   61.071   59.167
LGA    E    15_A      E    15_A     7.151     0    0.641   1.349    13.103   15.357    7.143
LGA    Q    16_A      Q    16_A     8.743     0    0.645   1.241    13.900    2.619    1.376
LGA    E    17_A      E    17_A    12.072     0    0.098   1.062    15.743    0.000    0.000
LGA    L    18_A      L    18_A    19.245     0    0.071   1.386    23.522    0.000    0.000
LGA    P    19_A      P    19_A    24.656     0    0.024   0.201    27.472    0.000    0.000
LGA    F    20_A      F    20_A    30.594     0    0.035   1.438    32.670    0.000    0.000
LGA    K    21_A      K    21_A    37.328     0    0.038   0.701    39.799    0.000    0.000
LGA    K    22_A      K    22_A    40.288     0    0.025   0.967    48.215    0.000    0.000
LGA    G    23_A      G    23_A    42.214     0    0.040   0.040    42.226    0.000    0.000
LGA    E    24_A      E    24_A    38.581     0    0.033   1.046    39.318    0.000    0.000
LGA    I    25_A      I    25_A    36.314     0    0.039   0.620    41.030    0.000    0.000
LGA    L    26_A      L    26_A    30.013     0    0.022   0.123    31.986    0.000    0.000
LGA    R    27_A      R    27_A    28.294     0    0.024   0.366    32.176    0.000    0.000
LGA    I    28_A      I    28_A    21.267     0    0.071   0.153    24.021    0.000    0.000
LGA    R    29_A      R    29_A    21.032     0    0.618   1.241    27.839    0.000    0.000
LGA    D    30_A      D    30_A    16.997     0    0.670   1.064    19.276    0.000    0.000
LGA    K    31_A      K    31_A    14.955     0    0.265   0.306    22.279    0.000    0.000
LGA    P    32_A      P    32_A    13.519     0    0.103   0.307    16.277    0.000    0.000
LGA    E    33_A      E    33_A    10.676     0    0.716   1.131    12.153    0.476    0.212
LGA    E    34_A      E    34_A     7.101     0    0.247   1.161     8.296   17.500   12.116
LGA    Q    35_A      Q    35_A     0.791     0    0.636   1.099     6.882   82.143   56.931
LGA    L    36_A      L    36_A     0.453     0    0.089   0.702     1.735   92.976   88.512
LGA    W    37_A      W    37_A     0.550     0    0.021   0.233     1.324   95.238   89.898
LGA    N    38_A      N    38_A     0.538     0    0.043   0.896     2.919   95.238   84.345
LGA    A    39_A      A    39_A     0.193     0    0.039   0.042     0.268  100.000  100.000
LGA    E    40_A      E    40_A     0.135     0    0.011   0.727     2.066  100.000   87.037
LGA    N    41_A      N    41_A     0.174     0    0.035   0.307     1.580   97.619   94.226
LGA    V    42_A      V    42_A     0.597     0    0.059   1.118     3.259   92.857   82.381
LGA    E    43_A      E    43_A     0.206     0    0.208   0.738     2.405   92.976   81.217
LGA    G    44_A      G    44_A     0.310     0    0.052   0.052     0.435  100.000  100.000
LGA    K    45_A      K    45_A     0.446     0    0.059   0.964     4.718  100.000   75.238
LGA    R    46_A      R    46_A     0.192     0    0.044   0.232     0.756  100.000   96.537
LGA    G    47_A      G    47_A     0.311     0    0.020   0.020     0.341  100.000  100.000
LGA    L    48_A      L    48_A     0.422     0    0.016   0.050     0.540   97.619   98.810
LGA    I    49_A      I    49_A     0.525     0    0.015   0.572     1.581   97.619   91.845
LGA    H    50_A      H    50_A     0.570     0    0.023   1.143     3.327   90.476   81.476
LGA    V    51_A      V    51_A     0.610     0    0.036   1.070     2.977   95.238   84.762
LGA    V    52_A      V    52_A     0.364     0    0.093   1.094     2.898   97.619   87.279
LGA    L    53_A      L    53_A     0.402     0    0.130   0.134     1.179  100.000   94.107
LGA    V    54_A      V    54_A     0.300     0    0.024   0.096     0.540   97.619   97.279
LGA    E    55_A      E    55_A     0.161     0    0.025   0.390     1.947  100.000   95.926
LGA    K    56_A      K    56_A     0.543     0    0.036   0.863     3.060   92.857   82.328
LGA    Y    57_A      Y    57_A     0.439     0    0.589   0.582     2.514   90.833   80.556
LGA    G    58_A      G    58_A     3.750     0    0.314   0.314     5.588   35.833   35.833

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    13.000         12.925                 13.311           59.532   54.718

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    0.91    65.086    57.229     3.656

LGA_LOCAL      RMSD:   0.912  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.163  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  13.000  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.116708 * X  +   0.944320 * Y  +  -0.307633 * Z  + -39.855122
  Y_new =   0.656219 * X  +  -0.159184 * Y  +  -0.737588 * Z  +  16.106714
  Z_new =  -0.745490 * X  +  -0.287958 * Y  +  -0.601103 * Z  +  -2.084577 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.746806  0.841270 -2.694846   [DEG:  100.0846   48.2012 -154.4033 ]
ZXZ: -0.395143  2.215677 -1.939407   [DEG:  -22.6400  126.9490 -111.1199 ]
 
# END of job
