
#######################################################
#                                                     #
#                        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        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      13_A - 37_A        1.00     2.21
  LONGEST_CONTINUOUS_SEGMENT:    25      14_A - 38_A        0.98     2.25
  LCS_AVERAGE:     31.09

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     11   63   63      4    7   21   41   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      4   13   25   52   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     22   63   63      5   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     22   63   63      7   24   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     22   63   63      7   17   39   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     22   63   63      7   14   43   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     22   63   63      7   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     22   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     22   63   63      7   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     22   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     22   63   63      4   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     22   63   63      4   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     25   63   63      4   19   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     25   63   63      5   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     25   63   63      3    5   24   47   57   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     25   63   63      6   24   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     25   63   63      6   25   46   54   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     25   63   63      4   23   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     25   63   63      5   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     25   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     25   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     25   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     25   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     25   63   63      6   25   46   54   57   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     25   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     25   63   63      5   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     25   63   63      4   23   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     25   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     25   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     25   63   63      5   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     25   63   63      4   14   43   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     25   63   63      5   24   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     25   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     25   63   63      4   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     25   63   63      5   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   63   63      6   21   44   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   14   31   47   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    6   17   27   43   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      4    4   17   27   44   53   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      6   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      7   22   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      6   23   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      6   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      6   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     10   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   63   63      4   20   41   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   63   63      6   23   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   63   63     10   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   63   63      5   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   63   63      7   21   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   63   63      3   17   42   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   63   63      5   16   32   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   63   63      5    9   20   36   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   63   63      5   13   32   46   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   63   63      5   14   32   49   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   63   63      5   17   42   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   63   63      5   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   63   63      5   20   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     14   63   63      6   25   46   54   58   60   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.03  (  31.09  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     10     25     46     54     58     60     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  39.68  73.02  85.71  92.06  95.24  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.80   1.07   1.25   1.51   1.55   1.76   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81
GDT RMS_ALL_AT   2.22   2.20   1.98   1.89   1.82   1.84   1.82   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_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
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     2.995     0    0.135   0.194     3.670   67.024   62.286
LGA    H     2_A      H     2_A     2.107     0    0.034   0.667     4.803   69.048   55.333
LGA    I     3_A      I     3_A     0.261     0    0.085   0.927     2.922   90.595   86.369
LGA    D     4_A      D     4_A     0.961     0    0.056   1.061     3.587   85.952   72.917
LGA    C     5_A      C     5_A     1.857     0    0.092   0.225     2.443   72.857   70.159
LGA    D     6_A      D     6_A     1.424     0    0.016   0.239     2.664   83.810   76.369
LGA    K     7_A      K     7_A     0.361     0    0.082   0.556     2.161   92.857   83.862
LGA    E     8_A      E     8_A     1.066     0    0.047   0.418     1.614   81.548   85.503
LGA    C     9_A      C     9_A     1.354     0    0.074   0.087     1.747   81.429   78.571
LGA    N    10_A      N    10_A     0.596     0    0.110   0.263     1.239   88.214   88.214
LGA    R    11_A      R    11_A     1.354     0    0.027   1.122     5.457   81.429   66.840
LGA    R    12_A      R    12_A     1.398     0    0.019   1.433     6.404   81.429   63.377
LGA    C    13_A      C    13_A     1.209     0    0.264   0.284     3.034   79.286   74.762
LGA    S    14_A      S    14_A     1.205     0    0.056   0.668     3.473   73.452   70.873
LGA    K    15_A      K    15_A     3.230     0    0.154   1.022     4.694   57.262   52.169
LGA    A    16_A      A    16_A     1.960     0    0.051   0.059     2.367   70.833   72.952
LGA    S    17_A      S    17_A     2.091     0    0.026   0.699     4.064   68.810   62.857
LGA    A    18_A      A    18_A     1.804     0    0.079   0.082     1.944   72.857   72.857
LGA    H    19_A      H    19_A     1.565     0    0.195   1.051     3.690   70.833   67.857
LGA    D    20_A      D    20_A     1.187     0    0.192   0.426     1.970   81.429   79.286
LGA    R    21_A      R    21_A     1.368     0    0.059   1.207     7.118   83.690   58.615
LGA    C    22_A      C    22_A     1.008     0    0.084   0.124     1.277   85.952   87.460
LGA    L    23_A      L    23_A     0.909     0    0.067   0.174     1.581   88.214   83.750
LGA    K    24_A      K    24_A     2.056     0    0.091   0.416     4.584   68.810   58.942
LGA    Y    25_A      Y    25_A     2.001     0    0.020   0.757     3.184   70.833   67.698
LGA    C    26_A      C    26_A     1.594     0    0.084   0.194     1.853   72.857   74.286
LGA    G    27_A      G    27_A     1.700     0    0.184   0.184     2.676   68.929   68.929
LGA    I    28_A      I    28_A     1.674     0    0.098   0.708     4.520   75.000   65.714
LGA    C    29_A      C    29_A     1.529     0    0.049   0.655     1.536   77.143   77.143
LGA    C    30_A      C    30_A     1.415     0    0.028   0.056     1.971   81.429   78.571
LGA    E    31_A      E    31_A     1.411     0    0.031   0.637     3.813   81.429   69.894
LGA    K    32_A      K    32_A     0.995     0    0.043   1.044     5.987   90.476   67.778
LGA    C    33_A      C    33_A     0.731     0    0.597   0.520     3.456   75.952   73.730
LGA    N    34_A      N    34_A     1.037     0    0.231   0.366     3.140   86.071   72.738
LGA    C    35_A      C    35_A     1.016     0    0.019   0.373     1.500   85.952   83.016
LGA    V    36_A      V    36_A     0.804     0    0.148   0.177     1.675   90.476   85.374
LGA    P    37_A      P    37_A     0.584     0    0.073   0.148     0.703   92.857   95.918
LGA    P    38_A      P    38_A     1.531     0    0.028   0.104     1.953   77.143   76.531
LGA    G    39_A      G    39_A     2.070     0    0.177   0.177     2.477   66.786   66.786
LGA    T    40_A      T    40_A     4.356     0    0.557   0.503     5.411   37.619   35.034
LGA    Y    41_A      Y    41_A     4.421     0    0.159   1.039     6.478   35.714   29.802
LGA    G    42_A      G    42_A     4.187     0    0.595   0.595     5.348   35.952   35.952
LGA    N    43_A      N    43_A     1.191     0    0.289   0.303     1.840   77.143   79.286
LGA    E    44_A      E    44_A     0.415     0    0.113   0.565     2.796  100.000   80.952
LGA    D    45_A      D    45_A     1.118     0    0.088   1.042     5.753   83.690   63.274
LGA    S    46_A      S    46_A     1.472     0    0.128   0.730     1.844   79.286   77.143
LGA    C    47_A      C    47_A     0.832     0    0.076   0.329     1.584   92.857   87.619
LGA    P    48_A      P    48_A     0.459     0    0.071   0.315     1.301   92.976   93.265
LGA    C    49_A      C    49_A     1.819     0    0.029   0.245     3.264   72.976   67.778
LGA    Y    50_A      Y    50_A     0.922     0    0.115   0.377     2.566   88.214   82.500
LGA    A    51_A      A    51_A     0.967     0    0.130   0.136     1.544   83.810   85.143
LGA    N    52_A      N    52_A     1.202     0    0.127   0.169     2.404   85.952   78.393
LGA    L    53_A      L    53_A     1.048     0    0.058   0.792     2.712   81.429   80.714
LGA    K    54_A      K    54_A     1.321     0    0.123   1.231     4.614   81.429   70.476
LGA    N    55_A      N    55_A     1.825     0    0.065   0.144     2.611   69.048   71.012
LGA    S    56_A      S    56_A     3.692     0    0.168   0.511     6.099   42.024   37.063
LGA    K    57_A      K    57_A     2.783     0    0.159   0.518     5.304   57.143   51.429
LGA    G    58_A      G    58_A     2.426     0    0.128   0.128     2.426   64.762   64.762
LGA    G    59_A      G    59_A     1.366     0    0.027   0.027     1.701   83.810   83.810
LGA    H    60_A      H    60_A     1.134     0    0.152   1.137     5.945   83.690   58.238
LGA    K    61_A      K    61_A     1.357     0    0.043   0.762     1.826   79.286   82.540
LGA    C    62_A      C    62_A     1.760     0    0.035   0.059     2.244   75.000   71.587
LGA    P    63_A      P    63_A     1.481     0    0.318   0.452     2.079   72.976   74.150

# 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):     1.807          1.828                  2.349           76.631   71.400

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.81    81.349    91.228     3.303

LGA_LOCAL      RMSD:   1.807  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.807  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.807  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.312375 * X  +  -0.855646 * Y  +   0.412665 * Z  + -10.626311
  Y_new =   0.221392 * X  +   0.488014 * Y  +   0.844292 * Z  +   0.474333
  Z_new =  -0.923801 * X  +  -0.172375 * Y  +   0.341876 * Z  + -12.128171 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.616565  1.177891 -0.467005   [DEG:   35.3266   67.4882  -26.7574 ]
ZXZ:  2.686969  1.221884 -1.755268   [DEG:  153.9520   70.0088 -100.5695 ]
 
# END of job
