
#######################################################
#                                                     #
#                        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:    37      21_B - 57_B        1.00     2.19
  LCS_AVERAGE:     51.57

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      6   13   19   21   41   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     20   61   61      6   17   33   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     20   61   61      7   17   19   21   41   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     20   61   61     12   17   19   21   43   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     20   61   61     12   17   26   41   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     20   61   61     12   17   19   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     20   61   61     12   17   19   35   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     20   61   61     12   17   23   40   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     20   61   61     12   17   28   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     20   61   61     12   17   19   29   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     20   61   61     12   17   19   35   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     20   61   61     12   17   32   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     20   61   61     12   17   20   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     20   61   61     10   17   19   36   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     20   61   61     12   17   32   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     20   61   61     12   17   35   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     20   61   61     12   17   19   22   43   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     20   61   61     12   17   19   33   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     23   61   61      6   20   36   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     23   61   61      6   15   19   31   53   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     37   61   61      9   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     37   61   61      4   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     37   61   61     13   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     37   61   61     13   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     37   61   61     13   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     37   61   61     13   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     37   61   61     13   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     37   61   61     13   24   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     37   61   61     13   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     37   61   61     13   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     37   61   61     13   26   39   45   53   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     37   61   61     13   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     37   61   61     16   25   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     37   61   61     16   25   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     37   61   61      5   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     37   61   61      5    9   38   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     37   61   61      5   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     37   61   61     15   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     37   61   61     12   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     37   61   61     16   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     37   61   61     11   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     37   61   61     11   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     37   61   61     11   26   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     36   61   61     11   16   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     36   61   61     11   16   20   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     36   61   61     11   16   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     36   61   61      4   16   39   45   54   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  83.86  (  51.57  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     16     26     39     45     54     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  26.23  42.62  63.93  73.77  88.52  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.68   1.03   1.25   1.61   1.81   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   1.88
GDT RMS_ALL_AT   3.07   2.59   2.16   2.04   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   1.88

# Checking swapping
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  D    22_B      D    22_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     4.103     0    0.575   1.246     5.950   43.214   51.190
LGA    Y     2_B      Y     2_B     1.558     0    0.078   0.335    10.196   75.000   37.778
LGA    I     3_B      I     3_B     3.037     0    0.071   0.083     6.421   57.262   41.964
LGA    R     4_B      R     4_B     3.642     0    0.025   0.862     8.082   51.905   28.442
LGA    E     5_B      E     5_B     2.644     0    0.042   0.778     5.112   64.881   47.037
LGA    L     6_B      L     6_B     2.176     0    0.111   0.168     5.985   70.833   52.917
LGA    R     7_B      R     7_B     2.514     0    0.060   0.960     9.166   64.881   37.835
LGA    A     8_B      A     8_B     2.335     0    0.055   0.056     3.151   68.810   65.048
LGA    A     9_B      A     9_B     2.114     0    0.039   0.042     3.039   68.810   65.048
LGA    L    10_B      L    10_B     2.675     0    0.032   0.038     5.488   62.976   47.381
LGA    I    11_B      I    11_B     2.336     0    0.058   0.101     4.672   70.833   55.655
LGA    L    12_B      L    12_B     1.812     0    0.076   0.093     4.649   77.143   58.988
LGA    L    13_B      L    13_B     2.256     0    0.078   0.076     4.208   66.786   56.845
LGA    A    14_B      A    14_B     2.474     0    0.047   0.048     3.035   66.786   63.429
LGA    L    15_B      L    15_B     1.440     0    0.045   0.208     3.434   83.690   70.595
LGA    K    16_B      K    16_B     1.890     0    0.046   0.778     4.992   70.952   56.614
LGA    K    17_B      K    17_B     3.300     0    0.051   1.182    12.427   53.690   31.164
LGA    Q    18_B      Q    18_B     2.799     0    0.090   1.441     4.490   55.357   51.958
LGA    H    19_B      H    19_B     1.315     0    0.221   0.436     5.783   75.000   53.905
LGA    A    20_B      A    20_B     2.906     0    0.676   0.609     4.900   50.714   49.238
LGA    E    21_B      E    21_B     1.359     0    0.495   1.044     5.279   77.262   63.333
LGA    D    22_B      D    22_B     1.590     0    0.124   0.400     2.540   77.143   71.012
LGA    P    23_B      P    23_B     0.947     0    0.125   0.387     1.320   83.690   85.306
LGA    D    24_B      D    24_B     1.460     0    0.061   0.473     2.107   77.143   75.060
LGA    A    25_B      A    25_B     1.311     0    0.030   0.028     1.413   81.429   81.429
LGA    Q    26_B      Q    26_B     1.038     0    0.000   1.105     3.904   81.429   68.307
LGA    R    27_B      R    27_B     1.566     0    0.064   0.845     4.593   75.000   60.173
LGA    V    28_B      V    28_B     1.643     0    0.033   0.064     1.849   72.857   72.857
LGA    A    29_B      A    29_B     1.366     0    0.045   0.049     1.507   79.286   79.714
LGA    D    30_B      D    30_B     1.568     0    0.035   0.761     2.916   75.000   68.988
LGA    E    31_B      E    31_B     2.050     0    0.032   0.156     2.734   66.786   64.815
LGA    L    32_B      L    32_B     1.689     0    0.036   0.104     1.791   72.857   72.857
LGA    M    33_B      M    33_B     1.612     0    0.019   0.098     1.789   72.857   73.929
LGA    K    34_B      K    34_B     2.069     0    0.024   0.281     3.345   68.810   63.228
LGA    K    35_B      K    35_B     1.800     0    0.064   0.291     3.373   77.143   67.884
LGA    L    36_B      L    36_B     0.963     0    0.042   1.387     3.928   83.690   72.857
LGA    F    37_B      F    37_B     1.713     0    0.033   0.144     2.368   75.000   69.221
LGA    D    38_B      D    38_B     1.549     0    0.043   1.150     4.810   77.143   65.893
LGA    A    39_B      A    39_B     0.813     0    0.051   0.048     1.081   88.214   88.667
LGA    A    40_B      A    40_B     1.278     0    0.118   0.115     1.964   77.143   78.000
LGA    H    41_B      H    41_B     2.034     0    0.095   0.995     4.545   68.810   58.000
LGA    R    42_B      R    42_B     1.093     0    0.219   0.735     1.736   81.429   83.160
LGA    N    43_B      N    43_B     2.198     0    0.067   0.824     2.379   66.786   69.940
LGA    D    44_B      D    44_B     1.803     0    0.202   1.035     2.239   82.024   75.417
LGA    K    45_B      K    45_B     1.843     0    0.059   0.303     4.352   72.857   60.423
LGA    D    46_B      D    46_B     1.838     0    0.049   1.179     6.269   75.000   54.940
LGA    K    47_B      K    47_B     0.872     0    0.039   0.291     3.333   88.214   77.513
LGA    V    48_B      V    48_B     0.499     0    0.045   0.115     0.658   95.238   94.558
LGA    K    49_B      K    49_B     1.203     0    0.033   0.974     7.266   81.429   55.820
LGA    K    50_B      K    50_B     1.459     0    0.062   0.859     7.774   81.429   55.238
LGA    V    51_B      V    51_B     0.767     0    0.036   0.060     1.257   92.857   89.252
LGA    V    52_B      V    52_B     0.474     0    0.052   0.948     2.848   95.238   83.673
LGA    E    53_B      E    53_B     1.054     0    0.023   0.418     3.259   88.214   74.497
LGA    E    54_B      E    54_B     0.974     0    0.010   0.957     3.507   90.476   80.265
LGA    A    55_B      A    55_B     0.936     0    0.042   0.046     1.250   88.214   86.857
LGA    K    56_B      K    56_B     1.099     0    0.044   0.396     2.790   85.952   77.884
LGA    K    57_B      K    57_B     0.680     0    0.041   0.039     3.148   95.238   78.571
LGA    V    58_B      V    58_B     1.345     0    0.091   0.214     3.115   79.405   71.020
LGA    V    59_B      V    59_B     2.034     0    0.073   0.235     3.078   70.833   63.946
LGA    S    60_B      S    60_B     1.309     0    0.195   0.238     1.544   83.690   81.508
LGA    T    61_B      T    61_B     0.959     0    0.039   0.103     1.292   83.690   86.599

# 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):     1.880          1.793                  2.922           75.187   65.994

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    1.88    79.098    90.085     3.081

LGA_LOCAL      RMSD:   1.880  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.880  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.880  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.401151 * X  +  -0.608626 * Y  +  -0.684582 * Z  + -16.302021
  Y_new =   0.861634 * X  +   0.002949 * Y  +  -0.507522 * Z  + -54.521175
  Z_new =   0.310910 * X  +  -0.793452 * Y  +   0.523230 * Z  +  72.951195 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.006523 -0.316150 -0.987817   [DEG:  114.9653  -18.1141  -56.5977 ]
ZXZ: -0.932847  1.020160  2.768137   [DEG:  -53.4482   58.4509  158.6025 ]
 
# END of job
