
#######################################################
#                                                     #
#                        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   63 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        2.02     2.02
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62       1_A - 62_A        1.98     2.02
  LCS_AVERAGE:     98.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       7_A - 35_A        0.98     3.74
  LCS_AVERAGE:     34.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     A     1_A     A     1_A     14   62   63      3    5   22   38   52   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     14   62   63      3   19   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     14   62   63      7   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     14   62   63      7   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     26   62   63      7   20   30   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     26   62   63      7   16   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     29   62   63      7   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     29   62   63      5   20   30   41   51   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     29   62   63      6   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     29   62   63      5   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     29   62   63      4   15   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     29   62   63      4   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     29   62   63      4   18   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     29   62   63      4   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     29   62   63      5   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     29   62   63      5   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     29   62   63      6   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     29   62   63      3   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     29   62   63      4   18   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     29   62   63      5   16   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     29   62   63      6   14   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     29   62   63      5   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     29   62   63      7   20   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     27   62   63      7   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   62   63      6   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   62   63      6   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   62   63      5   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     13   62   63      3   18   29   39   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     13   62   63      3   15   29   39   52   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   62   63      3    6   26   39   50   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   62   63      7   18   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   62   63      4    9   26   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     11   62   63      6   19   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     11   62   63      6   15   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     11   62   63      6   15   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     11   62   63      6   19   30   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   62   63      6   14   29   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   62   63      5   10   24   40   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   62   63      5   13   24   33   48   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   62   63      6   14   24   36   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   62   63      3   13   24   40   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   62   63      5   11   24   36   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   62   63      5   14   29   40   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   62   63      3   10   19   32   36   56   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   62   63      6   14   26   36   53   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   62   63      6   14   24   36   52   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   62   63      6   14   24   38   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   62   63      5   12   24   36   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   62   63      5   17   26   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   62   63      5   14   31   41   54   60   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     14   51   63      5   11   17   26   40   51   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.54  (  34.49   98.14  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      7     20     31     41     54     60     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  11.11  31.75  49.21  65.08  85.71  95.24  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.26   0.66   1.07   1.31   1.73   1.90   1.98   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02
GDT RMS_ALL_AT   3.63   3.92   2.71   2.65   2.06   2.03   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02   2.02

# Checking swapping
#   possible swapping detected:  D     4_A      D     4_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     2.744     0    0.049   0.076     3.313   57.262   57.238
LGA    H     2_A      H     2_A     1.487     0    0.012   1.073     2.760   83.810   73.333
LGA    I     3_A      I     3_A     0.437     0    0.057   0.993     2.745   88.333   82.024
LGA    D     4_A      D     4_A     1.593     0    0.052   1.270     4.852   77.262   66.905
LGA    C     5_A      C     5_A     2.096     0    0.069   0.200     2.334   66.786   67.460
LGA    D     6_A      D     6_A     2.120     0    0.014   1.112     5.074   68.810   59.167
LGA    K     7_A      K     7_A     1.395     0    0.079   0.562     3.009   79.286   78.042
LGA    E     8_A      E     8_A     1.421     0    0.061   0.548     2.349   77.143   75.767
LGA    C     9_A      C     9_A     1.805     0    0.041   0.053     1.814   72.857   72.857
LGA    N    10_A      N    10_A     1.812     0    0.088   0.224     2.451   72.857   68.810
LGA    R    11_A      R    11_A     2.863     0    0.026   0.971     6.850   57.143   39.610
LGA    R    12_A      R    12_A     2.428     0    0.051   0.900     3.114   64.762   64.372
LGA    C    13_A      C    13_A     1.672     0    0.214   0.236     3.299   79.405   72.063
LGA    S    14_A      S    14_A     1.196     0    0.029   0.666     1.862   85.952   84.524
LGA    K    15_A      K    15_A     1.498     0    0.143   0.989     4.012   77.143   62.328
LGA    A    16_A      A    16_A     1.401     0    0.017   0.031     1.768   77.143   79.810
LGA    S    17_A      S    17_A     2.540     0    0.023   0.682     4.461   60.952   55.159
LGA    A    18_A      A    18_A     2.432     0    0.098   0.096     2.699   64.762   63.238
LGA    H    19_A      H    19_A     1.584     0    0.139   1.166     2.752   70.833   68.143
LGA    D    20_A      D    20_A     1.875     0    0.172   0.161     2.465   72.857   68.810
LGA    R    21_A      R    21_A     2.377     0    0.066   1.174     9.594   68.810   39.134
LGA    C    22_A      C    22_A     1.515     0    0.118   0.181     1.817   75.000   75.714
LGA    L    23_A      L    23_A     0.873     0    0.109   1.273     4.127   88.214   79.286
LGA    K    24_A      K    24_A     2.417     0    0.055   0.490     7.035   66.786   47.937
LGA    Y    25_A      Y    25_A     2.467     0    0.032   0.603     3.087   62.857   62.302
LGA    C    26_A      C    26_A     1.925     0    0.051   0.188     2.073   70.833   71.508
LGA    G    27_A      G    27_A     1.837     0    0.134   0.134     2.565   66.905   66.905
LGA    I    28_A      I    28_A     1.941     0    0.043   0.685     5.022   72.857   62.083
LGA    C    29_A      C    29_A     1.833     0    0.040   0.711     1.889   72.857   74.286
LGA    C    30_A      C    30_A     1.780     0    0.025   0.053     2.217   72.857   70.159
LGA    E    31_A      E    31_A     1.794     0    0.034   0.511     4.094   72.857   62.169
LGA    K    32_A      K    32_A     1.265     0    0.054   0.891     4.463   81.429   71.958
LGA    C    33_A      C    33_A     1.110     0    0.600   0.518     3.484   71.429   69.286
LGA    N    34_A      N    34_A     0.837     0    0.193   0.701     3.412   88.214   76.726
LGA    C    35_A      C    35_A     1.110     0    0.018   0.513     2.272   88.214   83.175
LGA    V    36_A      V    36_A     0.732     0    0.071   1.341     2.684   90.476   80.952
LGA    P    37_A      P    37_A     0.656     0    0.025   0.121     0.676   92.857   93.197
LGA    P    38_A      P    38_A     0.940     0    0.032   0.141     1.102   90.476   87.891
LGA    G    39_A      G    39_A     0.631     0    0.196   0.196     0.946   90.476   90.476
LGA    T    40_A      T    40_A     2.307     0    0.619   1.297     3.717   59.524   59.864
LGA    Y    41_A      Y    41_A     2.734     0    0.160   0.751    10.245   50.357   27.619
LGA    G    42_A      G    42_A     3.270     0    0.181   0.181     4.023   50.357   50.357
LGA    N    43_A      N    43_A     1.654     0    0.277   0.481     2.114   72.976   74.048
LGA    E    44_A      E    44_A     1.214     0    0.073   1.031     3.729   85.952   73.704
LGA    D    45_A      D    45_A     1.779     0    0.158   1.066     6.530   72.976   53.452
LGA    S    46_A      S    46_A     2.160     0    0.093   0.726     2.515   68.810   66.190
LGA    C    47_A      C    47_A     1.112     0    0.061   0.355     2.374   85.952   80.238
LGA    P    48_A      P    48_A     0.794     0    0.039   0.299     1.638   86.190   86.735
LGA    C    49_A      C    49_A     1.630     0    0.047   0.255     2.704   72.976   70.317
LGA    Y    50_A      Y    50_A     2.168     0    0.023   1.090     4.465   66.786   65.635
LGA    A    51_A      A    51_A     3.019     0    0.209   0.226     3.407   53.571   52.857
LGA    N    52_A      N    52_A     2.282     0    0.071   0.345     2.477   64.762   65.774
LGA    L    53_A      L    53_A     1.941     0    0.049   0.994     2.899   66.786   68.929
LGA    K    54_A      K    54_A     2.346     0    0.120   1.284     3.935   68.810   65.238
LGA    N    55_A      N    55_A     1.670     0    0.029   0.251     3.019   63.214   71.250
LGA    S    56_A      S    56_A     3.830     0    0.138   0.669     6.200   43.810   38.254
LGA    K    57_A      K    57_A     2.604     0    0.139   0.738     5.666   57.143   51.799
LGA    G    58_A      G    58_A     3.058     0    0.129   0.129     3.256   53.571   53.571
LGA    G    59_A      G    59_A     2.166     0    0.062   0.062     2.279   66.786   66.786
LGA    H    60_A      H    60_A     2.349     0    0.130   1.317     9.271   66.786   38.810
LGA    K    61_A      K    61_A     1.571     0    0.015   0.757     2.043   70.833   76.825
LGA    C    62_A      C    62_A     2.577     0    0.047   0.113     3.228   55.476   58.651
LGA    P    63_A      P    63_A     3.952     0    0.253   0.409     4.260   43.452   42.585

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     2.023          2.048                  2.739           71.232   66.417

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.02    74.206    86.585     2.967

LGA_LOCAL      RMSD:   2.023  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.023  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.023  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.447711 * X  +  -0.865584 * Y  +  -0.224321 * Z  + -12.192864
  Y_new =  -0.810317 * X  +  -0.498820 * Y  +   0.307514 * Z  +   0.185148
  Z_new =  -0.378075 * X  +   0.044093 * Y  +  -0.924724 * Z  + -11.214002 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.066025  0.387716  3.093946   [DEG:  -61.0788   22.2145  177.2701 ]
ZXZ: -2.511365  2.751107 -1.454696   [DEG: -143.8906  157.6268  -83.3479 ]
 
# END of job
