
#######################################################
#                                                     #
#                        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        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    44      18_B - 61_B        0.94     2.07
  LCS_AVERAGE:     61.17

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     20   61   61      7   14   19   20   20   25   56   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     20   61   61     11   20   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     20   61   61     10   17   19   20   24   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     20   61   61     10   17   19   20   28   42   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     20   61   61     11   17   22   39   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     20   61   61     10   17   35   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     20   61   61     11   17   19   20   48   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     20   61   61     11   17   19   36   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     20   61   61     10   17   23   40   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     20   61   61     10   17   19   20   40   56   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     20   61   61     11   17   19   20   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     20   61   61     11   17   24   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     20   61   61     11   17   19   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     20   61   61     11   17   19   20   51   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     20   61   61     11   17   40   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     20   61   61     11   17   24   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     20   61   61     11   17   19   20   31   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     44   61   61     10   17   19   42   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     44   61   61      5   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     44   61   61      5   14   19   42   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     44   61   61     11   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     44   61   61     12   21   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     44   61   61     12   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     44   61   61     12   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     44   61   61     12   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     44   61   61     13   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     44   61   61     16   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     44   61   61     12   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     44   61   61     15   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     44   61   61      6   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     44   61   61      9   33   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     44   61   61     22   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     44   61   61     11   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     44   61   61     19   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     44   61   61     20   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     44   61   61     20   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     44   61   61     10   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     44   61   61     11   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     44   61   61     11   39   42   45   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  87.06  (  61.17  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     22     39     42     45     52     57     60     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  36.07  63.93  68.85  73.77  85.25  93.44  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.68   0.74   0.98   1.36   1.60   1.77   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88
GDT RMS_ALL_AT   2.40   2.11   2.10   1.99   1.95   1.91   1.89   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88

# Checking swapping
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  D    24_B      D    24_B
#   possible swapping detected:  D    30_B      D    30_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  F    37_B      F    37_B
#   possible swapping detected:  D    38_B      D    38_B
#   possible swapping detected:  D    44_B      D    44_B
#   possible swapping detected:  D    46_B      D    46_B
#   possible swapping detected:  E    53_B      E    53_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     5.076     0    0.566   1.188     6.550   33.214   37.500
LGA    Y     2_B      Y     2_B     1.712     0    0.074   1.391    10.199   77.143   40.714
LGA    I     3_B      I     3_B     3.317     0    0.067   0.062     7.083   53.690   36.845
LGA    R     4_B      R     4_B     4.149     0    0.068   0.950     8.102   45.119   26.753
LGA    E     5_B      E     5_B     2.984     0    0.056   0.727     6.281   59.048   40.635
LGA    L     6_B      L     6_B     2.519     0    0.047   1.404     8.513   64.881   43.036
LGA    R     7_B      R     7_B     2.909     0    0.046   0.787     7.586   62.857   34.848
LGA    A     8_B      A     8_B     2.853     0    0.064   0.059     4.090   60.952   56.190
LGA    A     9_B      A     9_B     2.876     0    0.062   0.067     4.124   60.952   56.190
LGA    L    10_B      L    10_B     3.388     0    0.070   1.032     7.292   55.476   39.524
LGA    I    11_B      I    11_B     2.568     0    0.084   0.110     5.988   66.905   49.405
LGA    L    12_B      L    12_B     2.311     0    0.072   0.084     5.719   70.833   50.119
LGA    L    13_B      L    13_B     2.620     0    0.034   1.430     6.598   62.976   52.083
LGA    A    14_B      A    14_B     2.743     0    0.049   0.053     3.540   62.857   58.952
LGA    L    15_B      L    15_B     1.722     0    0.053   0.184     4.551   79.286   60.774
LGA    K    16_B      K    16_B     2.228     0    0.018   0.963     3.344   67.024   62.487
LGA    K    17_B      K    17_B     3.400     0    0.021   0.777     9.290   53.571   32.698
LGA    Q    18_B      Q    18_B     2.330     0    0.039   1.586     5.725   68.810   55.450
LGA    H    19_B      H    19_B     0.844     0    0.208   1.177     5.225   85.952   65.000
LGA    A    20_B      A    20_B     2.522     0    0.619   0.616     4.288   55.952   54.762
LGA    E    21_B      E    21_B     1.240     0    0.404   1.105     6.606   77.262   55.556
LGA    D    22_B      D    22_B     1.589     0    0.079   0.279     2.427   77.143   75.060
LGA    P    23_B      P    23_B     0.987     0    0.093   0.359     1.839   83.690   82.789
LGA    D    24_B      D    24_B     0.926     0    0.059   0.506     1.790   85.952   83.750
LGA    A    25_B      A    25_B     1.167     0    0.046   0.034     1.231   81.429   81.429
LGA    Q    26_B      Q    26_B     1.132     0    0.048   0.727     2.911   81.429   79.735
LGA    R    27_B      R    27_B     1.364     0    0.044   0.850     4.435   81.429   64.329
LGA    V    28_B      V    28_B     1.352     0    0.057   0.062     1.504   81.429   80.204
LGA    A    29_B      A    29_B     1.197     0    0.063   0.063     1.244   81.429   81.429
LGA    D    30_B      D    30_B     1.247     0    0.056   0.738     2.651   81.429   74.286
LGA    E    31_B      E    31_B     1.523     0    0.000   0.075     1.998   79.286   75.714
LGA    L    32_B      L    32_B     1.112     0    0.029   0.154     1.246   81.429   81.429
LGA    M    33_B      M    33_B     1.115     0    0.045   0.112     1.186   81.429   83.690
LGA    K    34_B      K    34_B     1.382     0    0.035   0.278     2.635   81.429   75.873
LGA    K    35_B      K    35_B     1.034     0    0.039   0.299     2.039   85.952   81.640
LGA    L    36_B      L    36_B     0.754     0    0.019   0.061     0.926   90.476   92.857
LGA    F    37_B      F    37_B     1.300     0    0.027   0.127     1.847   81.429   75.974
LGA    D    38_B      D    38_B     1.185     0    0.049   1.049     4.771   81.429   69.107
LGA    A    39_B      A    39_B     0.864     0    0.041   0.037     1.068   85.952   86.857
LGA    A    40_B      A    40_B     1.199     0    0.099   0.090     1.820   77.143   78.000
LGA    H    41_B      H    41_B     1.776     0    0.117   0.972     4.328   72.976   62.476
LGA    R    42_B      R    42_B     1.133     0    0.129   1.086     4.712   81.429   76.320
LGA    N    43_B      N    43_B     1.684     0    0.068   0.847     2.359   72.857   73.988
LGA    D    44_B      D    44_B     1.251     0    0.150   1.033     2.331   86.190   81.726
LGA    K    45_B      K    45_B     1.056     0    0.047   0.315     2.590   88.214   78.942
LGA    D    46_B      D    46_B     1.076     0    0.029   1.162     5.280   85.952   66.488
LGA    K    47_B      K    47_B     0.218     0    0.067   0.614     4.055   97.619   77.831
LGA    V    48_B      V    48_B     0.199     0    0.052   0.137     0.530  100.000   98.639
LGA    K    49_B      K    49_B     0.762     0    0.006   0.987     6.601   90.476   63.016
LGA    K    50_B      K    50_B     0.872     0    0.044   0.860     6.287   90.476   66.190
LGA    V    51_B      V    51_B     0.596     0    0.034   0.073     0.753   92.857   91.837
LGA    V    52_B      V    52_B     0.586     0    0.048   0.100     0.704   92.857   91.837
LGA    E    53_B      E    53_B     1.046     0    0.042   0.338     2.480   85.952   78.730
LGA    E    54_B      E    54_B     1.009     0    0.036   0.958     3.666   88.214   76.455
LGA    A    55_B      A    55_B     0.316     0    0.000   0.000     0.488  100.000  100.000
LGA    K    56_B      K    56_B     0.866     0    0.060   0.408     2.250   90.476   82.646
LGA    K    57_B      K    57_B     1.012     0    0.051   0.084     1.739   85.952   81.534
LGA    V    58_B      V    58_B     0.452     0    0.082   1.081     3.091   97.619   86.258
LGA    V    59_B      V    59_B     0.885     0    0.065   0.155     1.554   90.595   85.442
LGA    S    60_B      S    60_B     1.198     0    0.233   0.601     3.401   88.333   80.794
LGA    T    61_B      T    61_B     0.917     0    0.053   0.073     1.226   88.214   89.252

# 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):     1.883          1.738                  2.869           77.923   68.919

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    1.88    84.426    91.523     3.077

LGA_LOCAL      RMSD:   1.883  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.882  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.883  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.143727 * X  +   0.660295 * Y  +   0.737125 * Z  + -262.523193
  Y_new =   0.773077 * X  +   0.539927 * Y  +  -0.332914 * Z  + -221.100235
  Z_new =  -0.617815 * X  +   0.522005 * Y  +  -0.588061 * Z  + 159.127136 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.754614  0.665961  2.415630   [DEG:  100.5320   38.1567  138.4054 ]
ZXZ:  1.146581  2.199455 -0.869258   [DEG:   65.6943  126.0195  -49.8048 ]
 
# END of job
