
#######################################################
#                                                     #
#                        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        2.10     2.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    59       2_B - 60_B        2.00     2.11
  LONGEST_CONTINUOUS_SEGMENT:    59       3_B - 61_B        1.96     2.12
  LCS_AVERAGE:     96.64

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40      20_B - 59_B        0.99     2.28
  LCS_AVERAGE:     55.82

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   56   61      7   14   19   21   24   40   47   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   59   61     10   17   20   21   24   37   54   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   59   61     12   18   26   39   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   59   61     12   18   29   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   59   61     12   18   20   21   30   50   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   59   61     12   18   21   36   46   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   59   61     12   18   25   39   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   59   61     12   18   20   36   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   59   61     12   18   20   24   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   59   61     12   18   22   35   45   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   59   61     12   18   22   37   45   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   59   61     12   18   20   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   59   61     12   19   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   59   61     12   18   20   30   44   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   59   61     12   18   20   30   44   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   59   61     12   18   28   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   59   61     11   18   20   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   59   61      8   18   20   31   44   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     21   59   61      5   17   23   38   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     40   59   61      4   19   29   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     40   59   61      9   25   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     40   59   61     11   29   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     40   59   61     11   29   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     40   59   61     11   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     40   59   61     20   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     40   59   61     12   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     40   59   61     13   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     40   59   61     14   30   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     40   59   61     22   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     40   59   61     21   30   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     40   59   61     21   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     40   59   61     24   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     40   59   61     23   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     40   59   61      9   31   38   40   47   53   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     40   59   61      7   28   36   40   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     40   59   61      7   16   33   39   46   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     39   59   61      7   10   28   38   44   52   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     39   59   61      3   10   28   34   42   50   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  84.15  (  55.82   96.64  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     24     31     38     40     47     53     57     60     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  39.34  50.82  62.30  65.57  77.05  86.89  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
GDT RMS_LOCAL    0.28   0.57   0.87   0.96   1.40   1.71   1.86   2.03   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10
GDT RMS_ALL_AT   2.67   2.38   2.26   2.27   2.19   2.20   2.13   2.11   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_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     4.763     0    0.303   0.831     6.865   31.310   44.286
LGA    Y     2_B      Y     2_B     4.540     0    0.189   1.263    10.493   40.476   21.429
LGA    I     3_B      I     3_B     2.381     0    0.031   0.064     4.446   66.786   54.345
LGA    R     4_B      R     4_B     2.631     0    0.018   0.463     9.262   62.976   33.680
LGA    E     5_B      E     5_B     3.263     0    0.036   1.003    10.360   61.071   31.905
LGA    L     6_B      L     6_B     2.837     0    0.048   0.103     5.920   62.857   46.726
LGA    R     7_B      R     7_B     2.906     0    0.014   0.071     8.098   59.048   33.680
LGA    A     8_B      A     8_B     3.271     0    0.025   0.025     4.453   57.262   53.238
LGA    A     9_B      A     9_B     2.413     0    0.011   0.024     3.535   68.810   63.714
LGA    L    10_B      L    10_B     2.792     0    0.024   0.051     5.483   59.286   45.536
LGA    I    11_B      I    11_B     3.563     0    0.020   0.102     6.483   51.905   37.381
LGA    L    12_B      L    12_B     2.766     0    0.033   1.436     8.097   62.976   41.786
LGA    L    13_B      L    13_B     1.810     0    0.080   1.107     7.777   75.000   49.464
LGA    A    14_B      A    14_B     3.408     0    0.023   0.026     4.644   52.024   47.905
LGA    L    15_B      L    15_B     3.778     0    0.031   0.208     7.530   50.119   33.274
LGA    K    16_B      K    16_B     2.041     0    0.053   0.148     6.454   70.952   50.476
LGA    K    17_B      K    17_B     1.995     0    0.018   1.088     2.952   70.952   66.825
LGA    Q    18_B      Q    18_B     3.127     0    0.021   1.421     8.714   57.262   36.296
LGA    H    19_B      H    19_B     2.677     0    0.149   0.437     6.963   59.167   39.476
LGA    A    20_B      A    20_B     2.491     0    0.418   0.466     3.532   66.786   62.095
LGA    E    21_B      E    21_B     1.632     0    0.054   0.481     1.899   75.000   80.582
LGA    D    22_B      D    22_B     1.241     0    0.016   0.266     1.480   83.690   84.821
LGA    P    23_B      P    23_B     1.215     0    0.065   0.340     1.441   85.952   84.014
LGA    D    24_B      D    24_B     0.994     0    0.023   0.976     5.331   85.952   68.929
LGA    A    25_B      A    25_B     1.462     0    0.033   0.031     1.818   81.429   79.714
LGA    Q    26_B      Q    26_B     1.392     0    0.041   0.439     2.781   81.429   71.376
LGA    R    27_B      R    27_B     0.939     0    0.055   0.256     2.474   83.690   76.883
LGA    V    28_B      V    28_B     1.603     0    0.024   0.042     2.254   75.000   72.925
LGA    A    29_B      A    29_B     1.777     0    0.016   0.034     1.961   72.857   72.857
LGA    D    30_B      D    30_B     1.228     0    0.021   0.702     1.734   81.429   79.286
LGA    E    31_B      E    31_B     1.133     0    0.022   0.130     1.527   81.429   80.476
LGA    L    32_B      L    32_B     1.385     0    0.066   1.392     5.072   81.429   63.155
LGA    M    33_B      M    33_B     1.311     0    0.013   1.163     4.705   81.429   67.381
LGA    K    34_B      K    34_B     1.009     0    0.041   1.427     8.116   85.952   61.481
LGA    K    35_B      K    35_B     0.375     0    0.012   0.306     1.716   97.619   91.852
LGA    L    36_B      L    36_B     0.666     0    0.017   0.070     1.099   90.476   89.345
LGA    F    37_B      F    37_B     1.130     0    0.015   0.189     2.979   85.952   72.641
LGA    D    38_B      D    38_B     0.608     0    0.029   0.170     0.775   90.476   94.048
LGA    A    39_B      A    39_B     0.640     0    0.015   0.019     0.989   90.476   90.476
LGA    A    40_B      A    40_B     1.088     0    0.083   0.088     1.770   81.548   81.524
LGA    H    41_B      H    41_B     1.346     0    0.036   1.405     3.784   79.286   68.048
LGA    R    42_B      R    42_B     1.448     0    0.015   0.997     2.994   77.143   76.147
LGA    N    43_B      N    43_B     1.759     0    0.076   0.800     3.837   72.857   64.226
LGA    D    44_B      D    44_B     1.289     0    0.018   0.159     1.388   81.429   81.429
LGA    K    45_B      K    45_B     1.359     0    0.021   0.300     2.989   81.429   74.127
LGA    D    46_B      D    46_B     1.226     0    0.015   0.917     4.597   83.690   66.012
LGA    K    47_B      K    47_B     0.747     0    0.011   0.926     4.903   90.476   76.296
LGA    V    48_B      V    48_B     0.746     0    0.027   0.087     1.010   90.476   89.184
LGA    K    49_B      K    49_B     0.774     0    0.060   1.022     7.001   92.857   67.249
LGA    K    50_B      K    50_B     0.551     0    0.010   0.184     1.093   95.238   89.577
LGA    V    51_B      V    51_B     0.344     0    0.023   0.042     0.481  100.000  100.000
LGA    V    52_B      V    52_B     0.522     0    0.013   0.069     0.766   92.857   91.837
LGA    E    53_B      E    53_B     0.509     0    0.016   0.403     1.132   92.857   90.582
LGA    E    54_B      E    54_B     0.473     0    0.007   0.922     4.475   95.238   76.667
LGA    A    55_B      A    55_B     0.834     0    0.014   0.023     1.242   85.952   86.857
LGA    K    56_B      K    56_B     1.257     0    0.005   0.385     1.994   81.548   80.529
LGA    K    57_B      K    57_B     1.384     0    0.033   0.594     1.841   77.143   79.630
LGA    V    58_B      V    58_B     2.143     0    0.110   0.147     3.058   61.190   62.789
LGA    V    59_B      V    59_B     2.736     0    0.070   0.145     3.096   57.262   57.211
LGA    S    60_B      S    60_B     3.243     0    0.233   0.254     3.885   50.119   51.270
LGA    T    61_B      T    61_B     3.520     0    0.012   0.071     4.088   43.452   45.306

# 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):     2.103          1.984                  3.106           74.471   66.103

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   61    4.0     60    2.03    78.689    87.275     2.812

LGA_LOCAL      RMSD:   2.034  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.107  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.103  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.205972 * X  +  -0.956234 * Y  +   0.207828 * Z  +  14.591498
  Y_new =  -0.503464 * X  +  -0.078562 * Y  +  -0.860437 * Z  +  -9.763602
  Z_new =   0.839107 * X  +  -0.281860 * Y  +  -0.465248 * Z  +   5.753840 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.959131 -0.995639 -2.596900   [DEG: -112.2499  -57.0459 -148.7914 ]
ZXZ:  0.236998  2.054711  1.894859   [DEG:   13.5790  117.7262  108.5674 ]
 
# END of job
