
#######################################################
#                                                     #
#                        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   64 (  513),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , 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:    61       1_B - 61_B        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42      16_B - 57_B        1.00     1.95
  LCS_AVERAGE:     59.39

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B      3   61   61      0    3    4    7   12   16   22   35   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     20   61   61      9   18   20   24   45   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     20   61   61      9   18   30   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     20   61   61      9   18   37   44   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     20   61   61      9   18   20   24   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     20   61   61      9   18   34   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     20   61   61      9   18   35   44   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     20   61   61      8   18   20   21   47   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     20   61   61      9   18   20   38   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     20   61   61      9   18   31   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     20   61   61      9   18   21   44   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     20   61   61      5   18   20   22   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     20   61   61      6   18   20   38   49   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     20   61   61      6   18   20   29   39   53   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     20   61   61      8   18   21   44   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     42   61   61      8   18   36   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     42   61   61      8   18   36   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     42   61   61      5   15   31   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     42   61   61      8   20   35   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     42   61   61      8   24   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     42   61   61      7   24   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     42   61   61      9   33   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     42   61   61     12   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     42   61   61     11   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     42   61   61     23   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     42   61   61     19   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     42   61   61     14   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     42   61   61     16   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     42   61   61     23   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     42   61   61     16   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     42   61   61     25   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     42   61   61     16   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     42   61   61     16   35   38   45   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     41   61   61      8   24   36   44   49   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     41   61   61      8   11   32   39   49   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     41   61   61      8   11   17   39   48   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     40   61   61      8   11   17   33   42   54   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  86.46  (  59.39  100.00  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     25     35     38     45     51     55     59     60     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  40.98  57.38  62.30  73.77  83.61  90.16  96.72  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.55   0.71   1.11   1.39   1.54   1.74   1.80   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90
GDT RMS_ALL_AT   2.26   2.06   2.00   1.94   2.03   1.92   1.92   1.91   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  E     5_B      E     5_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     5.291     0    0.316   0.847     7.642   30.000   47.738
LGA    Y     2_B      Y     2_B     3.104     0    0.198   0.355     5.892   57.262   40.278
LGA    I     3_B      I     3_B     2.066     0    0.042   0.675     4.076   68.810   58.690
LGA    R     4_B      R     4_B     2.523     0    0.028   1.265     9.239   62.976   35.671
LGA    E     5_B      E     5_B     2.588     0    0.022   1.135     6.482   64.881   46.243
LGA    L     6_B      L     6_B     1.767     0    0.039   0.072     4.338   77.143   62.024
LGA    R     7_B      R     7_B     2.715     0    0.027   0.073     7.166   61.071   37.532
LGA    A     8_B      A     8_B     3.655     0    0.027   0.028     4.797   51.905   47.810
LGA    A     9_B      A     9_B     2.432     0    0.016   0.019     3.174   68.810   65.048
LGA    L    10_B      L    10_B     2.106     0    0.019   0.035     4.669   68.929   53.988
LGA    I    11_B      I    11_B     3.173     0    0.042   0.071     6.631   59.167   42.440
LGA    L    12_B      L    12_B     2.853     0    0.024   0.149     6.009   62.857   44.940
LGA    L    13_B      L    13_B     2.734     0    0.112   1.382     8.148   61.190   40.417
LGA    A    14_B      A    14_B     3.547     0    0.117   0.126     4.587   48.810   45.333
LGA    L    15_B      L    15_B     3.091     0    0.052   0.121     6.272   57.262   40.833
LGA    K    16_B      K    16_B     1.920     0    0.153   0.322     6.220   72.857   54.074
LGA    K    17_B      K    17_B     1.822     0    0.561   0.842     4.057   59.881   66.243
LGA    Q    18_B      Q    18_B     2.037     0    0.085   1.347     6.587   70.952   54.180
LGA    H    19_B      H    19_B     1.994     0    0.370   0.578     5.418   68.929   53.476
LGA    A    20_B      A    20_B     1.580     0    0.509   0.563     3.253   67.143   66.667
LGA    E    21_B      E    21_B     1.728     0    0.127   0.445     2.014   70.833   74.815
LGA    D    22_B      D    22_B     1.371     0    0.039   0.250     1.587   81.548   82.619
LGA    P    23_B      P    23_B     1.148     0    0.037   0.058     1.631   85.952   81.565
LGA    D    24_B      D    24_B     0.934     0    0.030   0.965     4.942   88.214   71.607
LGA    A    25_B      A    25_B     1.047     0    0.030   0.029     1.337   85.952   85.048
LGA    Q    26_B      Q    26_B     1.037     0    0.031   0.089     2.087   85.952   77.831
LGA    R    27_B      R    27_B     0.880     0    0.040   0.256     2.021   90.476   81.688
LGA    V    28_B      V    28_B     1.210     0    0.015   0.031     1.671   81.429   80.204
LGA    A    29_B      A    29_B     1.228     0    0.029   0.045     1.360   81.429   81.429
LGA    D    30_B      D    30_B     0.945     0    0.028   0.692     1.640   90.476   86.071
LGA    E    31_B      E    31_B     0.916     0    0.026   0.090     1.147   88.214   86.455
LGA    L    32_B      L    32_B     0.946     0    0.022   0.076     1.240   90.476   85.952
LGA    M    33_B      M    33_B     0.919     0    0.015   1.197     4.773   90.476   72.738
LGA    K    34_B      K    34_B     0.749     0    0.003   0.298     2.000   90.476   86.508
LGA    K    35_B      K    35_B     0.298     0    0.021   0.269     0.908  100.000   97.884
LGA    L    36_B      L    36_B     0.635     0    0.013   1.070     3.638   90.476   76.250
LGA    F    37_B      F    37_B     0.976     0    0.020   0.159     2.815   90.476   74.286
LGA    D    38_B      D    38_B     0.548     0    0.071   0.835     3.688   90.476   74.524
LGA    A    39_B      A    39_B     0.563     0    0.008   0.022     0.700   90.476   92.381
LGA    A    40_B      A    40_B     0.768     0    0.091   0.095     1.341   85.952   86.857
LGA    H    41_B      H    41_B     1.054     0    0.032   1.408     3.905   83.690   70.714
LGA    R    42_B      R    42_B     1.081     0    0.013   0.848     3.473   83.690   78.052
LGA    N    43_B      N    43_B     1.308     0    0.085   0.801     3.857   83.690   69.762
LGA    D    44_B      D    44_B     0.759     0    0.022   0.101     0.907   90.476   90.476
LGA    K    45_B      K    45_B     0.670     0    0.032   0.987     8.013   90.476   62.381
LGA    D    46_B      D    46_B     0.569     0    0.020   0.053     0.725   92.857   91.667
LGA    K    47_B      K    47_B     0.415     0    0.020   0.276     1.813  100.000   91.852
LGA    V    48_B      V    48_B     0.396     0    0.018   0.106     0.592   97.619   97.279
LGA    K    49_B      K    49_B     0.490     0    0.012   0.484     1.478   95.238   92.698
LGA    K    50_B      K    50_B     0.571     0    0.008   0.370     1.704   90.476   89.577
LGA    V    51_B      V    51_B     0.395     0    0.032   0.031     0.547  100.000   98.639
LGA    V    52_B      V    52_B     0.336     0    0.033   0.090     0.592  100.000   97.279
LGA    E    53_B      E    53_B     0.419     0    0.019   0.843     2.528  100.000   87.143
LGA    E    54_B      E    54_B     0.380     0    0.040   0.236     1.760   95.238   88.624
LGA    A    55_B      A    55_B     0.763     0    0.016   0.025     1.295   90.595   90.571
LGA    K    56_B      K    56_B     1.181     0    0.006   0.726     2.630   81.548   76.931
LGA    K    57_B      K    57_B     1.234     0    0.019   0.035     1.836   77.143   87.725
LGA    V    58_B      V    58_B     2.223     0    0.141   0.187     3.183   61.190   60.612
LGA    V    59_B      V    59_B     2.859     0    0.071   0.178     3.164   55.476   54.150
LGA    S    60_B      S    60_B     3.202     0    0.194   0.224     4.146   46.905   50.317
LGA    T    61_B      T    61_B     3.814     0    0.161   1.081     4.631   41.905   40.816

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     1.902          1.850                  2.632           77.849   70.616

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   61    4.0     60    1.80    82.377    90.027     3.157

LGA_LOCAL      RMSD:   1.801  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.910  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.902  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.869484 * X  +  -0.479516 * Y  +   0.118581 * Z  +  15.251517
  Y_new =  -0.037179 * X  +  -0.175851 * Y  +  -0.983715 * Z  + -10.273107
  Z_new =   0.492559 * X  +  -0.859733 * Y  +   0.135071 * Z  +   9.178747 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.098859 -0.515028 -1.414962   [DEG: -177.5515  -29.5089  -81.0713 ]
ZXZ:  0.119965  1.435311  2.621322   [DEG:    6.8735   82.2373  150.1907 ]
 
# END of job
