
#######################################################
#                                                     #
#                        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        2.10     2.10
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        2.00     2.11
  LCS_AVERAGE:     94.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.97     3.61
  LCS_AVERAGE:     36.33

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     11   60   63      3    6   27   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   60   63      3   15   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   60   63      3   12   23   41   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   60   63      3    9   31   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   60   63      4   21   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   60   63      4   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   60   63      4   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   60   63      8   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   60   63     11   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   60   63      4   19   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   60   63      3   10   31   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   60   63      3   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   60   63      3   21   31   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   60   63      8   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   60   63      3   23   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   60   63      9   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   60   63     10   24   32   43   53   57   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   60   63      9   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   60   63     10   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   60   63     10   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   60   63     13   24   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   60   63     10   23   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   60   63     10   21   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   60   63      9   21   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   60   63     10   21   31   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   60   63      8   21   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   60   63      9   20   32   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   60   63      4   23   32   39   51   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   60   63      3   19   25   35   51   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   60   63      3    8   18   36   51   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   60   63      5   17   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   60   63      4   16   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   60   63      4    8   25   36   52   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   60   63      4   14   29   41   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   60   63      5   17   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   60   63      4    7   21   34   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   60   63      4   10   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   60   63      4   10   23   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   60   63      4    7   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   60   63      5   17   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   60   63      5   17   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   60   63      4   15   25   41   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   60   63      4   12   21   34   49   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   60   63      6   10   21   32   40   50   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   60   63      6   10   21   33   42   54   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   60   63      6    9   21   36   49   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   60   63      6   16   29   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   60   63     10   21   31   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   58   63      6    9   28   43   53   58   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   55   63      6   18   32   38   49   55   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   42   63      3   14   31   37   44   52   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.98  (  36.33   94.61  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     32     43     53     58     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  38.10  50.79  68.25  84.13  92.06  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    0.31   0.63   0.92   1.39   1.64   1.85   2.01   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10
GDT RMS_ALL_AT   3.74   3.87   3.48   2.51   2.20   2.12   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10

# Checking swapping
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_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     2.102     0    0.132   0.132     2.740   71.190   71.190
LGA    S     2_A      S     2_A     2.341     0    0.149   0.765     3.507   68.810   61.429
LGA    S     3_A      S     3_A     2.510     0    0.154   0.334     4.650   60.952   54.206
LGA    F     4_A      F     4_A     1.833     0    0.069   0.327     3.711   70.833   61.039
LGA    C     5_A      C     5_A     2.073     0    0.087   0.104     2.729   70.833   67.540
LGA    D     6_A      D     6_A     2.117     0    0.103   1.055     5.967   64.762   51.726
LGA    S     7_A      S     7_A     2.616     0    0.113   0.552     4.782   60.952   55.397
LGA    K     8_A      K     8_A     1.712     0    0.123   1.091     5.953   72.857   64.233
LGA    C     9_A      C     9_A     1.655     0    0.066   0.106     1.783   72.857   72.857
LGA    G    10_A      G    10_A     1.612     0    0.089   0.089     1.636   75.000   75.000
LGA    V    11_A      V    11_A     2.215     0    0.015   1.229     4.879   64.762   62.381
LGA    R    12_A      R    12_A     1.986     0    0.052   1.333     8.011   68.810   51.515
LGA    C    13_A      C    13_A     1.208     0    0.659   0.742     2.448   79.524   77.302
LGA    S    14_A      S    14_A     1.497     0    0.062   0.604     1.939   79.286   77.143
LGA    K    15_A      K    15_A     1.653     0    0.221   0.808     2.753   75.000   75.979
LGA    A    16_A      A    16_A     1.459     0    0.621   0.561     2.989   73.214   74.857
LGA    G    17_A      G    17_A     2.557     0    0.073   0.073     2.649   59.048   59.048
LGA    Y    18_A      Y    18_A     2.234     0    0.381   1.331     8.940   64.881   45.675
LGA    Q    19_A      Q    19_A     1.317     0    0.070   0.992     2.540   81.429   74.974
LGA    E    20_A      E    20_A     2.454     0    0.027   1.017     8.772   62.976   38.148
LGA    R    21_A      R    21_A     2.864     0    0.061   1.242    10.804   59.048   32.554
LGA    C    22_A      C    22_A     1.702     0    0.082   0.174     1.924   72.857   74.286
LGA    L    23_A      L    23_A     1.377     0    0.030   1.002     4.445   77.143   68.512
LGA    K    24_A      K    24_A     2.078     0    0.052   1.099     9.156   66.786   42.540
LGA    Y    25_A      Y    25_A     2.258     0    0.122   0.524     3.254   62.857   63.016
LGA    C    26_A      C    26_A     1.255     0    0.020   0.191     1.472   81.429   81.429
LGA    G    27_A      G    27_A     1.010     0    0.019   0.019     1.355   83.690   83.690
LGA    I    28_A      I    28_A     1.787     0    0.026   0.321     3.283   77.143   65.357
LGA    C    29_A      C    29_A     1.446     0    0.096   0.639     4.109   83.690   74.127
LGA    C    30_A      C    30_A     0.799     0    0.084   0.801     2.331   88.214   86.270
LGA    E    31_A      E    31_A     0.818     0    0.069   0.962     3.819   85.952   75.556
LGA    K    32_A      K    32_A     1.220     0    0.059   0.592     3.253   83.690   72.487
LGA    C    33_A      C    33_A     1.275     0    0.109   0.229     1.950   79.286   80.000
LGA    H    34_A      H    34_A     1.486     0    0.112   1.110     3.290   77.143   72.429
LGA    C    35_A      C    35_A     1.350     0    0.021   0.195     1.853   81.429   78.571
LGA    V    36_A      V    36_A     1.271     0    0.065   0.280     2.406   81.429   76.599
LGA    P    37_A      P    37_A     0.901     0    0.030   0.334     1.046   88.214   91.905
LGA    S    38_A      S    38_A     1.251     0    0.271   0.687     4.907   81.548   70.397
LGA    G    39_A      G    39_A     1.722     0    0.036   0.036     2.504   66.905   66.905
LGA    T    40_A      T    40_A     3.050     0    0.540   0.430     4.146   50.476   54.558
LGA    Y    41_A      Y    41_A     3.183     0    0.200   1.138    11.728   55.476   28.810
LGA    G    42_A      G    42_A     2.615     0    0.654   0.654     4.573   50.714   50.714
LGA    N    43_A      N    43_A     1.268     0    0.178   0.991     4.583   83.690   66.845
LGA    K    44_A      K    44_A     1.352     0    0.017   1.161     7.741   77.143   58.148
LGA    D    45_A      D    45_A     2.355     0    0.133   1.275     7.112   68.810   50.476
LGA    E    46_A      E    46_A     1.942     0    0.068   0.399     3.349   72.976   66.825
LGA    C    47_A      C    47_A     1.235     0    0.042   0.627     2.599   72.976   71.746
LGA    P    48_A      P    48_A     2.232     0    0.186   0.440     2.627   70.833   70.680
LGA    C    49_A      C    49_A     1.706     0    0.061   0.742     2.299   79.405   77.302
LGA    Y    50_A      Y    50_A     1.723     0    0.118   0.837     5.256   72.857   55.159
LGA    R    51_A      R    51_A     1.129     0    0.033   1.309     6.117   83.690   63.290
LGA    D    52_A      D    52_A     0.158     0    0.053   0.769     3.131  100.000   88.036
LGA    L    53_A      L    53_A     0.977     0    0.102   1.354     5.079   85.952   68.869
LGA    K    54_A      K    54_A     1.648     0    0.050   1.232     5.239   70.952   56.772
LGA    N    55_A      N    55_A     2.955     0    0.054   0.114     3.448   55.476   57.262
LGA    S    56_A      S    56_A     4.526     0    0.022   0.754     7.592   34.405   28.492
LGA    K    57_A      K    57_A     4.231     0    0.143   1.199     5.623   38.690   40.370
LGA    G    58_A      G    58_A     3.017     0    0.047   0.047     3.303   55.476   55.476
LGA    N    59_A      N    59_A     1.124     0    0.017   1.109     3.453   86.190   81.012
LGA    P    60_A      P    60_A     1.552     0    0.077   0.197     2.706   75.000   69.524
LGA    K    61_A      K    61_A     2.565     0    0.056   0.994     3.558   55.833   59.259
LGA    C    62_A      C    62_A     3.567     0    0.122   0.530     4.402   43.452   42.381
LGA    P    63_A      P    63_A     4.024     0    0.462   0.616     4.234   38.690   43.605

# 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):     2.099          2.106                  3.098           70.724   64.030

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.10    76.587    86.156     2.865

LGA_LOCAL      RMSD:   2.099  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.099  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.099  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.898271 * X  +  -0.297140 * Y  +  -0.323755 * Z  +   3.406286
  Y_new =  -0.254733 * X  +  -0.248245 * Y  +   0.934604 * Z  +  -1.341944
  Z_new =  -0.358079 * X  +   0.921999 * Y  +   0.147300 * Z  +  -2.719586 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.865266  0.366210  1.412374   [DEG: -164.1676   20.9823   80.9230 ]
ZXZ: -2.808121  1.422958 -0.370443   [DEG: -160.8935   81.5295  -21.2248 ]
 
# END of job
