
#######################################################
#                                                     #
#                        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   70 (  573),  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        2.36     2.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    53       9_B - 61_B        1.95     2.39
  LCS_AVERAGE:     80.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43      19_B - 61_B        0.86     2.41
  LCS_AVERAGE:     59.85

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     21   22   61      6   15   21   21   21   22   30   54   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   22   61     17   19   21   28   39   46   48   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   22   61     17   19   36   42   44   45   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   22   61     17   19   21   21   21   45   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   22   61     17   19   21   21   21   25   48   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   22   61     17   19   21   21   34   42   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   22   61     17   19   30   42   44   45   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   22   61     17   19   21   21   21   27   42   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   53   61     17   19   21   28   39   46   48   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   53   61     17   19   21   29   41   45   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   53   61     17   19   21   21   44   45   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   53   61     17   19   21   21   21   27   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   53   61     17   19   21   21   34   46   48   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   53   61     17   19   21   21   30   45   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   53   61     17   19   21   21   21   22   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   53   61     16   19   21   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   53   61     17   19   21   21   33   45   48   53   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   53   61     17   19   21   21   21   22   39   56   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     43   53   61     17   19   21   21   21   45   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     43   53   61     12   19   37   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     43   53   61     26   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     43   53   61      4   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     43   53   61     21   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     43   53   61     13   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     43   53   61     13   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     43   53   61     29   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     43   53   61     29   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     43   53   61     29   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     43   53   61     28   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     43   53   61     31   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     43   53   61     28   40   41   43   44   46   50   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  80.02  (  59.85   80.22  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     31     40     41     43     44     46     50     58     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  50.82  65.57  67.21  70.49  72.13  75.41  81.97  95.08 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.45   0.48   0.71   0.81   1.20   1.50   2.11   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36
GDT RMS_ALL_AT   2.43   2.42   2.42   2.45   2.44   2.50   2.43   2.38   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36   2.36

# Checking swapping
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    53_B      E    53_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     5.566     0    0.536   1.415     8.229   25.833   17.321
LGA    Y     2_B      Y     2_B     4.943     0    0.062   0.142    10.923   39.048   16.825
LGA    I     3_B      I     3_B     2.298     0    0.060   0.067     5.882   68.929   49.762
LGA    R     4_B      R     4_B     3.644     0    0.048   0.663    12.576   50.357   21.602
LGA    E     5_B      E     5_B     4.606     0    0.048   0.932    11.283   42.024   21.376
LGA    L     6_B      L     6_B     3.701     0    0.028   0.138     8.144   50.119   32.143
LGA    R     7_B      R     7_B     3.305     0    0.019   0.130    11.241   55.476   25.455
LGA    A     8_B      A     8_B     3.953     0    0.056   0.059     5.794   50.119   44.381
LGA    A     9_B      A     9_B     3.707     0    0.029   0.037     5.422   53.690   48.190
LGA    L    10_B      L    10_B     3.801     0    0.016   0.026     8.507   48.452   30.119
LGA    I    11_B      I    11_B     4.010     0    0.013   0.035     8.191   50.357   31.369
LGA    L    12_B      L    12_B     3.388     0    0.043   0.059     8.082   59.167   37.143
LGA    L    13_B      L    13_B     3.656     0    0.011   0.062     8.672   50.357   30.060
LGA    A    14_B      A    14_B     4.758     0    0.032   0.035     6.382   39.048   34.667
LGA    L    15_B      L    15_B     4.122     0    0.081   1.380    10.397   50.357   28.512
LGA    K    16_B      K    16_B     2.645     0    0.040   0.739    13.580   64.881   34.550
LGA    K    17_B      K    17_B     4.796     0    0.039   0.677    13.622   34.762   17.090
LGA    Q    18_B      Q    18_B     5.713     0    0.011   1.341    12.211   29.048   14.550
LGA    H    19_B      H    19_B     3.508     0    0.239   0.533    10.008   50.357   26.000
LGA    A    20_B      A    20_B     2.834     0    0.646   0.600     5.057   71.310   62.286
LGA    E    21_B      E    21_B     1.301     0    0.139   0.336     2.144   83.810   76.825
LGA    D    22_B      D    22_B     1.530     0    0.087   0.270     3.423   79.286   67.381
LGA    P    23_B      P    23_B     0.673     0    0.076   0.320     1.180   90.476   87.891
LGA    D    24_B      D    24_B     1.175     0    0.092   0.192     2.173   81.429   76.131
LGA    A    25_B      A    25_B     1.124     0    0.036   0.039     1.197   85.952   85.048
LGA    Q    26_B      Q    26_B     0.578     0    0.059   0.987     4.306   90.476   77.407
LGA    R    27_B      R    27_B     0.505     0    0.020   0.174     0.807   92.857   93.074
LGA    V    28_B      V    28_B     0.671     0    0.011   0.028     0.798   90.476   90.476
LGA    A    29_B      A    29_B     0.655     0    0.025   0.025     0.672   90.476   90.476
LGA    D    30_B      D    30_B     0.438     0    0.039   0.641     2.470   97.619   88.690
LGA    E    31_B      E    31_B     0.370     0    0.025   0.146     0.593  100.000   97.884
LGA    L    32_B      L    32_B     0.396     0    0.032   0.150     0.719  100.000   98.810
LGA    M    33_B      M    33_B     0.411     0    0.046   0.909     2.418  100.000   92.083
LGA    K    34_B      K    34_B     0.341     0    0.060   0.885     5.649  100.000   74.974
LGA    K    35_B      K    35_B     0.216     0    0.023   0.309     0.883  100.000   96.825
LGA    L    36_B      L    36_B     0.229     0    0.019   1.361     3.022  100.000   85.000
LGA    F    37_B      F    37_B     0.564     0    0.016   0.265     1.409   95.238   88.095
LGA    D    38_B      D    38_B     0.464     0    0.017   0.204     0.893   97.619   96.429
LGA    A    39_B      A    39_B     0.466     0    0.035   0.043     0.545   95.238   96.190
LGA    A    40_B      A    40_B     0.494     0    0.105   0.122     0.989   92.857   94.286
LGA    H    41_B      H    41_B     0.665     0    0.059   0.937     2.542   90.476   78.524
LGA    R    42_B      R    42_B     0.853     0    0.014   0.833     3.139   88.214   80.519
LGA    N    43_B      N    43_B     0.804     0    0.067   0.172     1.257   90.476   87.083
LGA    D    44_B      D    44_B     0.662     0    0.033   0.101     0.801   92.857   91.667
LGA    K    45_B      K    45_B     0.798     0    0.026   0.220     1.913   90.476   85.556
LGA    D    46_B      D    46_B     0.810     0    0.022   0.222     1.846   90.476   86.012
LGA    K    47_B      K    47_B     0.151     0    0.034   0.222     1.518  100.000   93.862
LGA    V    48_B      V    48_B     0.291     0    0.022   0.040     0.734  100.000   95.918
LGA    K    49_B      K    49_B     0.465     0    0.036   0.962     6.270  100.000   70.688
LGA    K    50_B      K    50_B     0.553     0    0.035   0.337     1.879   95.238   90.635
LGA    V    51_B      V    51_B     0.470     0    0.026   0.040     0.750  100.000   95.918
LGA    V    52_B      V    52_B     0.292     0    0.016   0.104     0.663  100.000   98.639
LGA    E    53_B      E    53_B     0.232     0    0.022   0.923     3.539  100.000   83.175
LGA    E    54_B      E    54_B     0.551     0    0.054   0.366     2.070   97.619   89.841
LGA    A    55_B      A    55_B     0.553     0    0.015   0.018     0.602   95.238   94.286
LGA    K    56_B      K    56_B     0.273     0    0.036   0.414     1.834  100.000   93.810
LGA    K    57_B      K    57_B     0.257     0    0.015   0.042     1.386  100.000   92.698
LGA    V    58_B      V    58_B     0.740     0    0.154   0.249     1.898   90.595   85.442
LGA    V    59_B      V    59_B     0.867     0    0.051   0.143     1.049   90.476   89.184
LGA    S    60_B      S    60_B     0.507     0    0.204   0.236     0.781   92.857   93.651
LGA    T    61_B      T    61_B     0.506     0    0.044   0.090     0.722   90.476   93.197

# 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):     2.359          2.063                  3.843           79.393   69.634

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     58    2.11    82.787    83.191     2.625

LGA_LOCAL      RMSD:   2.109  Number of atoms:   58  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.377  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.359  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.681177 * X  +   0.243606 * Y  +   0.690401 * Z  +   0.970380
  Y_new =   0.009865 * X  +   0.945987 * Y  +  -0.324056 * Z  + -11.028638
  Z_new =  -0.732052 * X  +  -0.213929 * Y  +  -0.646788 * Z  +   1.937688 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  3.127111  0.821329 -2.822164   [DEG:  179.1703   47.0587 -161.6981 ]
ZXZ:  1.131949  2.274162 -1.855111   [DEG:   64.8559  130.2999 -106.2900 ]
 
# END of job
