
#######################################################
#                                                     #
#                        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        2.12     2.12
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    56       1_A - 56_A        1.95     2.14
  LONGEST_CONTINUOUS_SEGMENT:    56       5_A - 60_A        2.00     2.14
  LCS_AVERAGE:     88.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.99     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   56   63      3   16   28   44   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   56   63      3   16   29   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   56   63      3   13   25   42   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   56   63      3   13   30   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   56   63      4   21   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   56   63      5   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   56   63      4   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   56   63      8   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   56   63      9   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   56   63      5   21   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   56   63      3    8   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   56   63      4   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   56   63      4   21   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   56   63      8   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   56   63      4   19   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   56   63     10   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   56   63      9   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   56   63      8   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   56   63     10   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   56   63     10   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   56   63     13   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   56   63     10   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   56   63     10   21   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   56   63      8   23   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   56   63     10   21   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   56   63     10   21   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   56   63      8   20   31   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   56   63      5   20   31   39   51   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   56   63      3   12   24   34   48   57   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   56   63      3    7   18   34   50   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   56   63      4   17   28   43   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   56   63      4   17   28   43   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   56   63      4    8   23   35   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   56   63      4   13   28   41   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   56   63      4   17   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   56   63      4    8   20   36   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   56   63      4   11   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   56   63      4   11   23   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   56   63      4    9   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   56   63      4   17   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   56   63      4   17   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   56   63      4   15   25   40   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   56   63      3   11   23   33   47   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   56   63      3   11   22   31   41   48   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   56   63      5   11   22   33   41   50   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   56   63      5   10   22   34   50   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   56   63      5   17   25   41   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   56   63     10   21   30   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   55   63      5    9   28   45   54   58   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   51   63      5   21   31   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   17   31   37   45   53   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  74.91  (  36.33   88.38  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     23     31     45     54     58     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  36.51  49.21  71.43  85.71  92.06  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.63   0.89   1.44   1.68   1.85   1.92   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12
GDT RMS_ALL_AT   3.74   3.77   3.46   2.47   2.20   2.14   2.15   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12   2.12

# Checking swapping
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_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     2.177     0    0.163   0.163     2.738   71.190   71.190
LGA    S     2_A      S     2_A     2.334     0    0.148   0.212     3.142   68.810   62.540
LGA    S     3_A      S     3_A     2.519     0    0.144   0.696     5.769   60.952   52.540
LGA    F     4_A      F     4_A     1.959     0    0.077   0.359     3.548   68.810   61.558
LGA    C     5_A      C     5_A     2.156     0    0.095   0.814     3.062   66.786   63.651
LGA    D     6_A      D     6_A     2.141     0    0.105   0.553     3.386   64.762   62.976
LGA    S     7_A      S     7_A     2.610     0    0.119   0.237     2.910   60.952   60.952
LGA    K     8_A      K     8_A     1.653     0    0.105   0.779     5.309   72.857   66.296
LGA    C     9_A      C     9_A     1.624     0    0.063   0.087     1.781   72.857   74.286
LGA    G    10_A      G    10_A     1.633     0    0.079   0.079     1.648   75.000   75.000
LGA    V    11_A      V    11_A     2.234     0    0.024   0.107     2.579   64.762   63.673
LGA    R    12_A      R    12_A     2.012     0    0.037   1.362     7.709   66.786   52.511
LGA    C    13_A      C    13_A     1.201     0    0.657   0.747     2.425   79.524   77.302
LGA    S    14_A      S    14_A     1.553     0    0.040   0.111     1.879   77.143   77.143
LGA    K    15_A      K    15_A     1.878     0    0.289   1.104     6.496   72.857   57.460
LGA    A    16_A      A    16_A     1.506     0    0.618   0.558     3.158   67.143   70.000
LGA    G    17_A      G    17_A     2.405     0    0.047   0.047     2.679   60.952   60.952
LGA    Y    18_A      Y    18_A     2.645     0    0.323   1.236     6.402   61.071   48.651
LGA    Q    19_A      Q    19_A     1.490     0    0.091   1.000     3.298   81.429   74.339
LGA    E    20_A      E    20_A     2.220     0    0.023   0.434     3.372   64.881   58.995
LGA    R    21_A      R    21_A     2.701     0    0.050   1.388    12.914   60.952   30.736
LGA    C    22_A      C    22_A     1.705     0    0.085   0.182     1.924   72.857   74.286
LGA    L    23_A      L    23_A     1.402     0    0.042   1.005     4.760   77.143   65.893
LGA    K    24_A      K    24_A     2.059     0    0.063   0.963     8.589   66.786   44.709
LGA    Y    25_A      Y    25_A     2.258     0    0.126   0.541     3.168   62.857   65.119
LGA    C    26_A      C    26_A     1.272     0    0.023   0.176     1.434   81.429   81.429
LGA    G    27_A      G    27_A     1.062     0    0.020   0.020     1.421   83.690   83.690
LGA    I    28_A      I    28_A     1.779     0    0.021   0.759     4.900   75.000   63.869
LGA    C    29_A      C    29_A     1.462     0    0.107   0.648     4.093   81.548   72.698
LGA    C    30_A      C    30_A     0.844     0    0.099   0.105     1.167   88.214   92.143
LGA    E    31_A      E    31_A     0.869     0    0.068   0.770     2.490   85.952   78.836
LGA    K    32_A      K    32_A     1.211     0    0.056   0.572     3.190   81.429   70.688
LGA    C    33_A      C    33_A     1.247     0    0.129   0.158     1.970   79.286   81.508
LGA    H    34_A      H    34_A     1.468     0    0.104   1.075     3.117   77.143   71.571
LGA    C    35_A      C    35_A     1.355     0    0.028   0.199     1.877   81.429   78.571
LGA    V    36_A      V    36_A     1.275     0    0.070   0.285     2.424   81.429   76.599
LGA    P    37_A      P    37_A     0.873     0    0.029   0.216     1.059   88.214   89.184
LGA    S    38_A      S    38_A     1.227     0    0.294   0.679     4.872   81.548   70.397
LGA    G    39_A      G    39_A     1.786     0    0.029   0.029     2.550   66.905   66.905
LGA    T    40_A      T    40_A     3.147     0    0.542   0.427     4.187   48.571   52.517
LGA    Y    41_A      Y    41_A     3.277     0    0.201   1.336    11.034   55.476   30.198
LGA    G    42_A      G    42_A     2.636     0    0.663   0.663     4.540   50.714   50.714
LGA    N    43_A      N    43_A     1.483     0    0.238   0.997     3.450   81.429   73.274
LGA    K    44_A      K    44_A     1.367     0    0.025   0.955     7.754   77.143   56.878
LGA    D    45_A      D    45_A     2.357     0    0.125   0.869     4.040   66.786   56.786
LGA    E    46_A      E    46_A     1.951     0    0.076   0.186     2.521   72.976   68.466
LGA    C    47_A      C    47_A     1.261     0    0.054   0.607     2.554   72.976   71.746
LGA    P    48_A      P    48_A     2.178     0    0.162   0.418     2.554   70.833   70.680
LGA    C    49_A      C    49_A     1.604     0    0.097   0.240     1.862   77.143   78.651
LGA    Y    50_A      Y    50_A     1.681     0    0.125   0.795     5.460   75.000   54.802
LGA    R    51_A      R    51_A     0.995     0    0.015   1.302     6.315   85.952   62.814
LGA    D    52_A      D    52_A     0.251     0    0.046   0.759     3.347  100.000   85.774
LGA    L    53_A      L    53_A     0.899     0    0.103   0.919     4.739   88.333   75.476
LGA    K    54_A      K    54_A     1.604     0    0.045   1.211     6.375   70.952   59.365
LGA    N    55_A      N    55_A     3.046     0    0.062   0.119     3.493   51.786   50.893
LGA    S    56_A      S    56_A     4.536     0    0.026   0.143     5.735   32.857   29.841
LGA    K    57_A      K    57_A     4.518     0    0.200   0.853     6.124   34.286   29.471
LGA    G    58_A      G    58_A     3.044     0    0.039   0.039     3.415   57.381   57.381
LGA    N    59_A      N    59_A     1.292     0    0.019   1.150     5.159   86.190   67.738
LGA    P    60_A      P    60_A     1.417     0    0.085   0.365     3.183   77.143   69.728
LGA    K    61_A      K    61_A     2.539     0    0.059   0.957     3.580   55.833   61.164
LGA    C    62_A      C    62_A     3.565     0    0.145   0.564     4.463   43.452   42.381
LGA    P    63_A      P    63_A     3.967     0    0.368   0.338     4.176   41.786   40.680

# 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):     2.121          2.127                  3.040           70.291   64.258

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.12    76.984    84.593     2.836

LGA_LOCAL      RMSD:   2.121  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.121  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.121  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.876543 * X  +  -0.312585 * Y  +  -0.366010 * Z  +   3.302165
  Y_new =  -0.287938 * X  +  -0.268813 * Y  +   0.919147 * Z  +  -0.676599
  Z_new =  -0.385699 * X  +   0.911060 * Y  +   0.145622 * Z  +  -1.621288 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.824205  0.395966  1.412300   [DEG: -161.8150   22.6872   80.9188 ]
ZXZ: -2.762634  1.424655 -0.400474   [DEG: -158.2873   81.6267  -22.9455 ]
 
# END of job
