
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , 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:    71       1_B - 71_B        1.06     1.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.06     1.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    68       1_B - 68_B        0.98     1.07
  LONGEST_CONTINUOUS_SEGMENT:    68       2_B - 69_B        0.99     1.07
  LCS_AVERAGE:     95.26

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     G     1_B     G     1_B     68   71   71      4   35   55   69   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     68   71   71     23   47   63   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     68   71   71     18   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     68   71   71     21   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     68   71   71     20   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     68   71   71     18   44   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     68   71   71     15   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     68   71   71     20   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     68   71   71     22   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     68   71   71     22   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     68   71   71     21   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     68   71   71     22   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     68   71   71     22   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     68   71   71     22   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     68   71   71     17   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     68   71   71      6   45   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     68   71   71     24   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     68   71   71     13   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     68   71   71     17   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     68   71   71     17   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     68   71   71     17   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     68   71   71     17   46   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     68   71   71      9   30   60   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     68   71   71     15   31   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     68   71   71     22   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     68   71   71     19   36   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     68   71   71     19   36   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     68   71   71     19   30   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     68   71   71     19   40   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     68   71   71     19   47   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     68   71   71     19   26   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     68   71   71     19   43   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     68   71   71     19   45   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     68   71   71     19   37   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     68   71   71     19   26   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     68   71   71     19   26   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     68   71   71     13   25   38   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     55   71   71      5   26   38   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     55   71   71      5   26   66   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.42  (  95.26  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     24     47     66     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  33.80  66.20  92.96  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.63   0.96   1.03   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06
GDT RMS_ALL_AT   1.45   1.15   1.07   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06   1.06

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    23_B      E    23_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  F    67_B      F    67_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.106     0    0.198   0.198     2.406   73.095   73.095
LGA    S     2_B      S     2_B     1.397     0    0.088   0.734     4.109   81.548   72.698
LGA    V     3_B      V     3_B     0.834     0    0.061   1.230     3.972   88.214   77.483
LGA    S     4_B      S     4_B     0.842     0    0.074   0.554     2.356   90.476   84.683
LGA    K     5_B      K     5_B     0.708     0    0.144   0.265     2.467   88.214   81.852
LGA    W     6_B      W     6_B     0.790     0    0.023   0.110     1.725   90.476   84.116
LGA    S     7_B      S     7_B     0.802     0    0.077   0.095     1.044   90.476   87.460
LGA    T     8_B      T     8_B     0.320     0    0.040   0.962     2.642  100.000   87.755
LGA    D     9_B      D     9_B     0.809     0    0.036   0.805     3.708   92.857   76.310
LGA    E    10_B      E    10_B     1.034     0    0.047   0.762     2.058   88.214   85.661
LGA    V    11_B      V    11_B     0.457     0    0.033   0.120     0.719   92.857   94.558
LGA    S    12_B      S    12_B     0.957     0    0.035   0.712     1.948   85.952   83.016
LGA    E    13_B      E    13_B     1.393     0    0.049   0.457     2.473   81.429   75.820
LGA    F    14_B      F    14_B     1.026     0    0.040   0.070     1.384   88.214   85.541
LGA    I    15_B      I    15_B     0.732     0    0.030   0.119     0.893   90.476   91.667
LGA    Q    16_B      Q    16_B     1.173     0    0.082   0.636     3.237   81.429   69.048
LGA    S    17_B      S    17_B     1.082     0    0.082   0.083     1.222   85.952   85.952
LGA    L    18_B      L    18_B     0.674     0    0.021   0.071     1.046   88.214   92.917
LGA    P    19_B      P    19_B     0.976     0    0.515   0.833     3.908   74.286   81.224
LGA    G    20_B      G    20_B     0.864     0    0.097   0.097     1.958   81.548   81.548
LGA    C    21_B      C    21_B     0.877     0    0.111   0.142     1.084   88.214   88.968
LGA    E    22_B      E    22_B     0.863     0    0.086   0.267     1.372   90.476   88.466
LGA    E    23_B      E    23_B     0.626     0    0.184   0.655     2.737   88.214   74.656
LGA    H    24_B      H    24_B     0.472     0    0.143   0.228     1.505  100.000   89.810
LGA    G    25_B      G    25_B     0.567     0    0.032   0.032     0.600   90.476   90.476
LGA    K    26_B      K    26_B     0.774     0    0.028   0.780     5.189   90.476   67.778
LGA    V    27_B      V    27_B     0.981     0    0.029   1.120     3.345   90.476   79.728
LGA    F    28_B      F    28_B     0.600     0    0.028   0.070     0.694   90.476   93.074
LGA    K    29_B      K    29_B     0.679     0    0.023   0.886     1.954   90.476   85.556
LGA    D    30_B      D    30_B     1.102     0    0.080   0.116     1.434   88.214   84.821
LGA    E    31_B      E    31_B     1.037     0    0.115   0.215     2.292   85.952   80.688
LGA    Q    32_B      Q    32_B     1.191     0    0.038   0.782     2.361   85.952   81.640
LGA    I    33_B      I    33_B     0.464     0    0.141   0.512     1.284   97.619   95.298
LGA    D    34_B      D    34_B     0.578     0    0.036   0.160     1.358   95.238   89.464
LGA    G    35_B      G    35_B     0.377     0    0.025   0.025     0.498  100.000  100.000
LGA    E    36_B      E    36_B     0.705     0    0.038   0.947     2.178   90.476   84.603
LGA    A    37_B      A    37_B     0.721     0    0.036   0.043     0.916   90.476   90.476
LGA    F    38_B      F    38_B     0.353     0    0.037   0.410     1.546  100.000   90.736
LGA    L    39_B      L    39_B     0.296     0    0.116   0.123     0.925   95.238   96.429
LGA    L    40_B      L    40_B     0.398     0    0.176   1.080     2.342   92.976   85.298
LGA    M    41_B      M    41_B     0.369     0    0.028   0.632     1.795  100.000   93.036
LGA    T    42_B      T    42_B     0.524     0    0.046   0.047     0.793   92.857   91.837
LGA    Q    43_B      Q    43_B     1.144     0    0.043   1.197     4.062   81.429   66.772
LGA    T    44_B      T    44_B     1.305     0    0.034   0.924     3.695   81.429   72.381
LGA    D    45_B      D    45_B     0.824     0    0.028   0.095     0.926   90.476   90.476
LGA    I    46_B      I    46_B     0.504     0    0.073   0.087     1.421   90.476   89.345
LGA    V    47_B      V    47_B     1.169     0    0.014   1.052     3.779   83.690   72.585
LGA    K    48_B      K    48_B     1.739     0    0.104   1.205    10.484   75.000   46.243
LGA    I    49_B      I    49_B     1.623     0    0.029   0.619     2.812   77.143   71.012
LGA    M    50_B      M    50_B     0.751     0    0.092   0.757     1.689   95.238   89.524
LGA    S    51_B      S    51_B     0.232     0    0.076   0.076     0.794   97.619   96.825
LGA    I    52_B      I    52_B     0.256     0    0.034   1.051     2.199   95.238   84.405
LGA    K    53_B      K    53_B     0.731     0    0.044   0.958     5.846   90.476   75.661
LGA    E    54_B      E    54_B     1.126     0    0.027   1.095     3.590   81.429   75.291
LGA    G    55_B      G    55_B     1.541     0    0.047   0.047     1.541   77.143   77.143
LGA    P    56_B      P    56_B     1.319     0    0.039   0.292     1.406   81.429   81.429
LGA    A    57_B      A    57_B     0.908     0    0.036   0.035     1.089   88.214   88.667
LGA    E    58_B      E    58_B     1.265     0    0.023   0.710     4.218   81.429   66.878
LGA    K    59_B      K    59_B     1.645     0    0.031   0.648     2.115   77.143   73.862
LGA    I    60_B      I    60_B     1.140     0    0.035   0.606     2.199   85.952   81.607
LGA    F    61_B      F    61_B     0.681     0    0.048   0.290     1.081   92.857   89.697
LGA    N    62_B      N    62_B     0.794     0    0.053   0.832     2.794   90.476   79.940
LGA    S    63_B      S    63_B     1.401     0    0.026   0.067     1.607   79.286   77.143
LGA    I    64_B      I    64_B     1.262     0    0.032   0.190     1.458   81.429   81.429
LGA    L    65_B      L    65_B     0.838     0    0.036   1.404     3.761   90.476   75.357
LGA    M    66_B      M    66_B     1.195     0    0.034   0.801     2.128   81.429   79.345
LGA    F    67_B      F    67_B     1.621     0    0.027   0.842     3.812   75.000   68.225
LGA    K    68_B      K    68_B     1.581     0    0.038   0.940     2.819   72.857   73.016
LGA    A    69_B      A    69_B     1.991     0    0.094   0.092     2.241   70.833   69.619
LGA    A    70_B      A    70_B     2.106     0    0.166   0.168     2.106   68.810   69.619
LGA    E    71_B      E    71_B     1.815     0    0.464   0.941     3.135   67.143   66.984

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.057          1.077                  1.634           86.898   81.771

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.06    91.197    96.707     6.135

LGA_LOCAL      RMSD:   1.057  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.057  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.057  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.753135 * X  +  -0.628361 * Y  +  -0.194807 * Z  +  19.576717
  Y_new =   0.186703 * X  +   0.488098 * Y  +  -0.852586 * Z  +  72.456520
  Z_new =   0.630817 * X  +   0.605741 * Y  +   0.484921 * Z  +   5.234450 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.243003 -0.682605  0.895725   [DEG:   13.9230  -39.1104   51.3213 ]
ZXZ: -0.224633  1.064524  0.805674   [DEG:  -12.8705   60.9927   46.1617 ]
 
# END of job
