
#######################################################
#                                                     #
#                        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 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  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        2.08     2.08
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_A - 61_A        1.98     2.09
  LCS_AVERAGE:     96.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.97     3.74
  LCS_AVERAGE:     37.49

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     G     1_A     G     1_A      8   61   63      3   11   28   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   61   63      3   15   28   42   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   61   63      3   10   24   37   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   61   63      3   10   28   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   61   63      4   20   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   61   63      5   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   61   63      6   24   31   41   54   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   61   63     11   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   61   63      6   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   61   63      5   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   61   63     11   24   31   42   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   61   63     11   24   31   42   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   61   63     11   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   61   63      3   22   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   61   63      3   17   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   61   63      4   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   61   63      4    4   31   42   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   61   63      4   24   31   43   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   61   63      4   19   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   61   63     10   24   31   43   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   61   63      6   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   61   63     11   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   61   63     11   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   61   63     11   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   61   63     11   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   61   63     12   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   61   63     13   24   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   61   63      7   22   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   61   63     13   21   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   61   63     13   21   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     24   61   63     13   21   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     24   61   63     13   21   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   61   63      3    9   16   34   54   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   61   63     13   21   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     24   61   63      3   12   25   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     21   61   63      6   17   29   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     21   61   63      9   20   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     19   61   63      7   20   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     14   61   63      4   13   26   40   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     14   61   63      4   16   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     14   61   63      5   17   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     14   61   63      4    7   15   32   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   61   63      4   12   28   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   61   63      4   12   24   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     14   61   63      4   10   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     14   61   63      9   20   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   61   63      5   17   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   61   63      4   15   26   43   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   61   63      4    9   23   35   50   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   61   63      6    9   22   34   42   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   61   63      6   12   23   35   43   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   61   63      6   13   26   37   51   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   61   63      7   17   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   61   63     13   21   31   44   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   61   63      6    9   28   42   55   59   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   59   63      3   24   31   36   46   56   60   62   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   56   63      4   11   31   35   41   50   58   61   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  78.05  (  37.49   96.65  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     13     24     31     44     55     59     60     62     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  38.10  49.21  69.84  87.30  93.65  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
GDT RMS_LOCAL    0.38   0.63   0.91   1.49   1.69   1.83   1.87   2.02   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08
GDT RMS_ALL_AT   2.54   4.05   3.74   2.14   2.14   2.10   2.11   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     2.116     0    0.096   0.096     2.709   71.190   71.190
LGA    S     2_A      S     2_A     2.522     0    0.196   0.824     3.533   62.857   57.460
LGA    S     3_A      S     3_A     2.726     0    0.125   0.326     4.974   60.952   54.206
LGA    F     4_A      F     4_A     1.832     0    0.104   0.387     3.177   70.833   63.593
LGA    C     5_A      C     5_A     2.139     0    0.127   0.794     2.877   66.786   64.841
LGA    D     6_A      D     6_A     2.301     0    0.114   1.117     6.377   64.762   49.524
LGA    S     7_A      S     7_A     2.912     0    0.112   0.261     3.145   55.357   54.762
LGA    K     8_A      K     8_A     2.005     0    0.133   0.837     6.109   68.810   60.952
LGA    C     9_A      C     9_A     1.695     0    0.068   0.101     1.898   72.857   75.714
LGA    G    10_A      G    10_A     1.791     0    0.104   0.104     1.923   72.857   72.857
LGA    V    11_A      V    11_A     2.487     0    0.028   0.074     2.921   64.762   61.497
LGA    R    12_A      R    12_A     2.242     0    0.058   1.381     8.272   64.762   48.009
LGA    C    13_A      C    13_A     1.291     0    0.577   0.672     2.179   75.119   75.794
LGA    S    14_A      S    14_A     1.906     0    0.136   0.569     2.232   68.810   67.460
LGA    K    15_A      K    15_A     1.936     0    0.037   0.671     5.220   70.833   56.984
LGA    A    16_A      A    16_A     1.800     0    0.623   0.561     3.155   67.143   68.286
LGA    G    17_A      G    17_A     2.450     0    0.031   0.031     2.863   60.952   60.952
LGA    Y    18_A      Y    18_A     2.554     0    0.277   1.370     7.375   64.881   47.024
LGA    Q    19_A      Q    19_A     1.391     0    0.096   1.163     4.039   81.429   72.011
LGA    E    20_A      E    20_A     2.038     0    0.029   0.770     4.676   64.881   54.815
LGA    R    21_A      R    21_A     2.698     0    0.069   1.296    10.347   60.952   35.455
LGA    C    22_A      C    22_A     1.814     0    0.084   0.105     2.064   70.833   70.159
LGA    L    23_A      L    23_A     1.208     0    0.044   0.288     2.358   81.429   79.345
LGA    K    24_A      K    24_A     2.003     0    0.066   1.221    10.786   66.786   42.169
LGA    Y    25_A      Y    25_A     2.331     0    0.124   0.513     3.035   62.857   64.960
LGA    C    26_A      C    26_A     1.381     0    0.025   0.113     1.597   79.286   78.571
LGA    G    27_A      G    27_A     0.948     0    0.048   0.048     1.369   85.952   85.952
LGA    I    28_A      I    28_A     1.809     0    0.038   0.751     4.777   75.000   63.036
LGA    C    29_A      C    29_A     1.559     0    0.118   0.122     2.334   79.405   75.873
LGA    C    30_A      C    30_A     0.929     0    0.121   0.126     1.308   88.214   90.556
LGA    E    31_A      E    31_A     0.795     0    0.042   0.785     3.312   90.476   78.307
LGA    K    32_A      K    32_A     1.163     0    0.042   1.306     5.116   83.690   69.365
LGA    C    33_A      C    33_A     1.154     0    0.213   0.219     2.161   75.119   78.730
LGA    H    34_A      H    34_A     1.453     0    0.102   1.222     3.908   79.286   67.952
LGA    C    35_A      C    35_A     1.203     0    0.023   0.166     1.630   81.429   78.571
LGA    V    36_A      V    36_A     1.142     0    0.131   0.920     3.908   85.952   74.966
LGA    P    37_A      P    37_A     1.364     0    0.118   0.144     1.779   81.429   78.980
LGA    S    38_A      S    38_A     1.847     0    0.132   0.348     2.451   68.810   68.810
LGA    G    39_A      G    39_A     2.583     0    0.316   0.316     2.636   60.952   60.952
LGA    T    40_A      T    40_A     0.675     0    0.282   0.380     3.281   82.143   71.497
LGA    Y    41_A      Y    41_A     1.496     0    0.609   1.130     3.901   72.024   62.976
LGA    G    42_A      G    42_A     1.578     0    0.084   0.084     2.039   75.119   75.119
LGA    N    43_A      N    43_A     1.114     0    0.163   0.920     4.399   83.690   67.560
LGA    K    44_A      K    44_A     1.018     0    0.071   0.735     6.411   81.429   62.328
LGA    D    45_A      D    45_A     1.959     0    0.154   1.106     6.749   72.857   53.095
LGA    E    46_A      E    46_A     1.525     0    0.079   0.169     2.569   79.405   72.222
LGA    C    47_A      C    47_A     1.130     0    0.015   0.581     2.334   77.143   75.794
LGA    P    48_A      P    48_A     2.301     0    0.207   0.451     2.804   70.833   70.680
LGA    C    49_A      C    49_A     1.595     0    0.092   0.182     1.954   79.405   80.159
LGA    Y    50_A      Y    50_A     1.721     0    0.082   0.832     5.491   72.857   53.016
LGA    R    51_A      R    51_A     1.285     0    0.047   1.288     6.226   83.690   63.074
LGA    D    52_A      D    52_A     0.449     0    0.105   0.794     3.928  100.000   79.881
LGA    L    53_A      L    53_A     0.789     0    0.063   0.811     2.959   90.595   80.893
LGA    K    54_A      K    54_A     1.603     0    0.034   1.266     5.844   69.048   59.683
LGA    N    55_A      N    55_A     3.013     0    0.061   0.219     3.485   53.690   55.417
LGA    S    56_A      S    56_A     4.567     0    0.071   0.533     6.581   33.095   28.651
LGA    K    57_A      K    57_A     4.036     0    0.024   0.751     6.439   41.786   32.487
LGA    G    58_A      G    58_A     2.690     0    0.040   0.040     3.038   61.190   61.190
LGA    N    59_A      N    59_A     0.893     0    0.050   0.263     2.430   90.833   82.024
LGA    P    60_A      P    60_A     1.715     0    0.077   0.319     3.177   75.000   68.503
LGA    K    61_A      K    61_A     2.876     0    0.068   0.987     3.738   53.810   58.413
LGA    C    62_A      C    62_A     3.855     0    0.152   0.495     4.645   40.476   40.397
LGA    P    63_A      P    63_A     4.342     0    0.439   0.405     4.600   35.714   38.095

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     2.080          2.096                  2.893           71.183   64.663

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     62    2.02    76.587    86.791     2.918

LGA_LOCAL      RMSD:   2.025  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.082  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.080  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.953208 * X  +  -0.171244 * Y  +  -0.249139 * Z  +   3.486284
  Y_new =  -0.135788 * X  +  -0.493777 * Y  +   0.858921 * Z  +  -2.346501
  Z_new =  -0.270104 * X  +   0.852561 * Y  +   0.447419 * Z  +  -9.286652 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.000091  0.273501  1.087511   [DEG: -171.8925   15.6705   62.3098 ]
ZXZ: -2.859279  1.106919 -0.306812   [DEG: -163.8246   63.4218  -17.5790 ]
 
# END of job
