
#######################################################
#                                                     #
#                        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        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       7_A - 30_A        0.98     2.60
  LONGEST_CONTINUOUS_SEGMENT:    24      16_A - 39_A        0.98     2.36
  LCS_AVERAGE:     31.82

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     16   63   63      3    8   28   40   54   57   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     22   63   63      7   14   35   48   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     22   63   63      5   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     22   63   63      3    5   37   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     22   63   63      7   21   37   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     22   63   63      7   18   37   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     24   63   63      7   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     24   63   63      7   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     24   63   63      7   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     24   63   63      6   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     24   63   63      6   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     24   63   63      5   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     24   63   63      5   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     24   63   63      3   15   30   51   57   58   59   60   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     24   63   63      4   22   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     24   63   63      7   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     24   63   63      8   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     24   63   63      5   24   38   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     24   63   63      6   24   38   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     24   63   63      4   20   38   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     24   63   63      4   20   36   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     24   63   63      5   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     24   63   63      6   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     24   63   63      6   20   36   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     24   63   63      6   15   35   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     24   63   63      6   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     24   63   63      6   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     24   63   63      3   17   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     24   63   63      5   24   37   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     24   63   63      6   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   63   63      8   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     24   63   63      4   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   63   63      4   24   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    7   10   25   45   55   58   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    7   10   20   27   42   50   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      6   63   63      3    4   10   20   25   37   50   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      6   15   34   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      6   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      6   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      6   22   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   63   63      8   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      6   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      3   20   35   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      4   15   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     16   63   63      4   20   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     16   63   63      5   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63      7   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      5   22   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      5   17   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      5   14   26   51   56   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      5   16   32   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      4   16   34   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     16   63   63      8   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     16   63   63      8   23   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      3   20   39   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      5   24   36   52   57   58   59   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     15   63   63      3    3   12   21   45   54   59   60   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.27  (  31.82  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      8     24     39     52     57     58     59     61     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  12.70  38.10  61.90  82.54  90.48  92.06  93.65  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.73   1.05   1.28   1.41   1.45   1.52   1.82   1.81   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91
GDT RMS_ALL_AT   2.11   2.60   1.96   1.96   1.93   1.93   1.93   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91

# Checking swapping
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_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     3.631     0    0.063   0.098     4.443   45.119   47.524
LGA    H     2_A      H     2_A     2.323     0    0.039   1.216     4.985   66.905   57.524
LGA    I     3_A      I     3_A     0.549     0    0.704   0.884     3.222   75.833   76.964
LGA    D     4_A      D     4_A     1.552     0    0.154   1.000     3.335   72.857   67.024
LGA    C     5_A      C     5_A     1.545     0    0.069   0.149     1.891   75.000   74.286
LGA    D     6_A      D     6_A     1.395     0    0.060   0.654     3.258   81.429   75.357
LGA    K     7_A      K     7_A     0.437     0    0.046   1.270     4.656   95.238   82.169
LGA    E     8_A      E     8_A     0.559     0    0.057   0.347     0.927   92.857   92.593
LGA    C     9_A      C     9_A     0.875     0    0.046   0.074     1.334   90.476   87.460
LGA    N    10_A      N    10_A     0.575     0    0.079   0.651     2.413   90.476   86.131
LGA    R    11_A      R    11_A     1.070     0    0.022   1.208     8.671   83.690   49.524
LGA    R    12_A      R    12_A     0.876     0    0.042   1.201     5.373   90.476   75.671
LGA    C    13_A      C    13_A     0.783     0    0.217   0.245     3.007   90.595   82.302
LGA    S    14_A      S    14_A     0.916     0    0.062   0.654     2.806   80.119   78.016
LGA    K    15_A      K    15_A     2.995     0    0.104   1.010     5.271   57.262   50.741
LGA    A    16_A      A    16_A     1.419     0    0.027   0.032     1.858   75.000   78.095
LGA    S    17_A      S    17_A     1.824     0    0.147   0.657     3.563   70.833   65.238
LGA    A    18_A      A    18_A     1.611     0    0.031   0.032     1.826   75.000   74.571
LGA    H    19_A      H    19_A     1.485     0    0.139   0.392     2.466   75.119   73.857
LGA    D    20_A      D    20_A     1.210     0    0.191   0.193     1.587   81.429   80.357
LGA    R    21_A      R    21_A     1.332     0    0.071   0.903     3.548   83.690   72.727
LGA    C    22_A      C    22_A     1.031     0    0.102   0.170     1.262   83.690   85.952
LGA    L    23_A      L    23_A     0.979     0    0.117   0.203     1.549   88.214   83.750
LGA    K    24_A      K    24_A     2.307     0    0.061   0.463     5.719   66.786   51.958
LGA    Y    25_A      Y    25_A     2.358     0    0.014   0.713     3.227   64.762   64.325
LGA    C    26_A      C    26_A     1.943     0    0.071   0.196     2.228   68.810   68.810
LGA    G    27_A      G    27_A     2.042     0    0.162   0.162     2.880   64.881   64.881
LGA    I    28_A      I    28_A     1.723     0    0.046   0.694     4.376   72.857   65.357
LGA    C    29_A      C    29_A     1.711     0    0.053   0.100     1.953   75.000   74.286
LGA    C    30_A      C    30_A     1.847     0    0.022   0.051     2.244   72.857   70.159
LGA    E    31_A      E    31_A     1.863     0    0.033   0.220     3.446   72.857   63.439
LGA    K    32_A      K    32_A     1.231     0    0.049   0.732     3.522   81.429   75.291
LGA    C    33_A      C    33_A     1.059     0    0.615   0.543     3.919   69.762   69.603
LGA    N    34_A      N    34_A     1.314     0    0.178   0.701     3.566   86.071   71.845
LGA    C    35_A      C    35_A     1.484     0    0.101   0.883     1.811   81.429   78.571
LGA    V    36_A      V    36_A     0.712     0    0.139   0.182     1.003   90.476   91.905
LGA    P    37_A      P    37_A     0.736     0    0.026   0.275     1.081   90.476   89.184
LGA    P    38_A      P    38_A     1.317     0    0.058   0.104     1.569   81.429   80.204
LGA    G    39_A      G    39_A     1.855     0    0.181   0.181     2.807   66.905   66.905
LGA    T    40_A      T    40_A     4.121     0    0.614   0.569     5.785   36.786   35.442
LGA    Y    41_A      Y    41_A     4.888     0    0.197   0.664    12.333   35.714   15.476
LGA    G    42_A      G    42_A     4.930     0    0.579   0.579     5.722   29.048   29.048
LGA    N    43_A      N    43_A     1.661     0    0.275   0.309     2.454   75.119   85.179
LGA    E    44_A      E    44_A     0.864     0    0.127   0.806     1.944   88.214   85.503
LGA    D    45_A      D    45_A     0.459     0    0.122   0.720     3.782   97.619   79.821
LGA    S    46_A      S    46_A     0.821     0    0.150   0.237     1.377   90.476   87.460
LGA    C    47_A      C    47_A     0.893     0    0.045   0.517     2.890   88.214   81.905
LGA    P    48_A      P    48_A     1.084     0    0.052   0.332     1.628   81.548   85.374
LGA    C    49_A      C    49_A     1.978     0    0.019   0.232     3.247   72.976   67.778
LGA    Y    50_A      Y    50_A     1.638     0    0.079   0.964     4.918   75.000   65.079
LGA    A    51_A      A    51_A     1.704     0    0.138   0.151     1.988   72.857   72.857
LGA    N    52_A      N    52_A     1.142     0    0.163   0.359     1.872   85.952   80.476
LGA    L    53_A      L    53_A     1.046     0    0.043   0.955     3.298   81.429   77.560
LGA    K    54_A      K    54_A     1.238     0    0.059   1.238     4.457   81.429   73.968
LGA    N    55_A      N    55_A     1.451     0    0.070   1.241     4.960   75.119   67.917
LGA    S    56_A      S    56_A     2.830     0    0.131   0.663     5.209   55.595   49.762
LGA    K    57_A      K    57_A     1.972     0    0.178   0.562     4.539   68.810   62.116
LGA    G    58_A      G    58_A     1.775     0    0.618   0.618     3.753   65.476   65.476
LGA    G    59_A      G    59_A     0.870     0    0.285   0.285     3.072   78.095   78.095
LGA    H    60_A      H    60_A     1.077     0    0.121   1.422     6.969   88.214   56.952
LGA    K    61_A      K    61_A     1.429     0    0.043   0.779     1.977   77.143   78.624
LGA    C    62_A      C    62_A     2.271     0    0.430   0.908     3.748   59.524   60.159
LGA    P    63_A      P    63_A     4.505     0    0.625   0.579     6.479   45.476   35.374

# 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):     1.908          1.964                  2.636           75.142   70.190

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     61    1.82    79.365    89.327     3.180

LGA_LOCAL      RMSD:   1.818  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.914  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.908  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.087443 * X  +   0.098520 * Y  +   0.991286 * Z  +   8.425812
  Y_new =  -0.863267 * X  +   0.504074 * Y  +   0.026053 * Z  +   3.016043
  Z_new =  -0.497115 * X  +  -0.858023 * Y  +   0.129127 * Z  +  -0.697957 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.469847  0.520270 -1.421424   [DEG:  -84.2160   29.8093  -81.4416 ]
ZXZ:  1.597072  1.441308 -2.616479   [DEG:   91.5055   82.5809 -149.9132 ]
 
# END of job
