
#######################################################
#                                                     #
#                        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        1.99     1.99
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.99     1.99
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        1.00     3.15
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.97     3.10
  LCS_AVERAGE:     37.87

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      7   63   63      2   10   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   63   63      3   16   30   44   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   63   63      3   11   25   44   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     33   63   63      3   10   32   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     33   63   63      4   21   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     33   63   63      4   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     33   63   63      4   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     33   63   63      9   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     33   63   63     10   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     33   63   63      4   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     33   63   63      7   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     33   63   63      4   20   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     33   63   63      3   18   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     33   63   63      4   22   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     33   63   63      4   21   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     33   63   63     10   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     33   63   63      4   19   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     33   63   63     11   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     33   63   63     12   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     33   63   63     11   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     33   63   63     11   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     33   63   63     11   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     33   63   63     11   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     33   63   63     11   23   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     33   63   63      9   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     33   63   63     11   21   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     27   63   63      5   21   32   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     27   63   63      6   24   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   63   63      4   20   33   39   51   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   63   63      3   17   25   38   50   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   63   63      3    6   19   34   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   63   63      6   21   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   63   63      5   20   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   63   63      5   11   26   43   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   63   63      5   20   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   63   63      5   21   32   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   63   63      5    8   25   47   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   63   63      5   10   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   63   63      5   10   22   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   63   63      5    8   31   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   63   63      5   21   32   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   63   63      4   18   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   63   63      5   16   28   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     11   63   63      5   12   23   37   54   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     11   63   63      6    9   21   32   43   55   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     11   63   63      6   11   23   35   46   56   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     11   63   63      6    9   25   40   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   63   63      6   20   30   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   63   63     11   21   34   48   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   63   63      6   15   34   47   54   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   63   63      3   15   32   38   50   58   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   63   63      3   11   24   37   45   55   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.29  (  37.87  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     12     24     34     48     55     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  19.05  38.10  53.97  76.19  87.30  93.65  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    9.13   0.58   0.94   1.44   1.63   1.76   1.94   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99
GDT RMS_ALL_AT   3.67   3.51   2.97   2.11   2.02   2.01   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99   1.99

# Checking swapping
#   possible swapping detected:  F     4_A      F     4_A
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    46_A      E    46_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     1.880     0    0.063   0.063     2.936   75.476   75.476
LGA    S     2_A      S     2_A     2.481     0    0.218   0.802     4.040   66.786   57.937
LGA    S     3_A      S     3_A     2.442     0    0.156   0.485     4.047   68.810   60.397
LGA    F     4_A      F     4_A     1.889     0    0.080   0.236     4.017   70.833   57.835
LGA    C     5_A      C     5_A     1.932     0    0.115   0.798     2.691   72.857   68.889
LGA    D     6_A      D     6_A     1.908     0    0.120   1.118     6.088   72.857   54.524
LGA    S     7_A      S     7_A     2.251     0    0.132   0.232     2.606   62.857   63.492
LGA    K     8_A      K     8_A     1.444     0    0.111   0.741     5.598   79.286   67.831
LGA    C     9_A      C     9_A     1.514     0    0.054   0.066     1.839   75.000   77.143
LGA    G    10_A      G    10_A     1.595     0    0.119   0.119     1.636   75.000   75.000
LGA    V    11_A      V    11_A     2.057     0    0.052   0.093     2.448   66.786   65.918
LGA    R    12_A      R    12_A     1.802     0    0.059   1.356     8.182   72.857   51.991
LGA    C    13_A      C    13_A     1.093     0    0.640   0.717     2.452   79.524   81.667
LGA    S    14_A      S    14_A     1.568     0    0.108   0.620     2.043   72.857   71.508
LGA    K    15_A      K    15_A     1.408     0    0.098   0.666     4.499   81.429   66.772
LGA    A    16_A      A    16_A     1.337     0    0.618   0.555     2.851   75.357   76.571
LGA    G    17_A      G    17_A     2.307     0    0.045   0.045     2.791   64.881   64.881
LGA    Y    18_A      Y    18_A     2.026     0    0.273   1.374     7.452   68.929   50.278
LGA    Q    19_A      Q    19_A     1.328     0    0.114   1.219     4.146   85.952   74.868
LGA    E    20_A      E    20_A     1.663     0    0.026   0.744     4.208   72.976   61.323
LGA    R    21_A      R    21_A     2.352     0    0.049   1.280    12.192   66.786   34.502
LGA    C    22_A      C    22_A     1.605     0    0.062   0.083     1.819   75.000   75.714
LGA    L    23_A      L    23_A     1.189     0    0.053   0.295     2.196   79.286   78.274
LGA    K    24_A      K    24_A     2.061     0    0.063   1.120    10.016   66.786   43.439
LGA    Y    25_A      Y    25_A     2.286     0    0.115   0.576     3.560   62.857   60.635
LGA    C    26_A      C    26_A     1.213     0    0.047   0.098     1.450   81.429   82.937
LGA    G    27_A      G    27_A     1.052     0    0.049   0.049     1.607   81.548   81.548
LGA    I    28_A      I    28_A     1.970     0    0.050   0.758     5.048   72.857   60.357
LGA    C    29_A      C    29_A     1.504     0    0.110   0.130     2.050   79.405   75.873
LGA    C    30_A      C    30_A     0.851     0    0.134   0.150     1.225   88.214   90.556
LGA    E    31_A      E    31_A     0.781     0    0.019   0.871     3.838   90.476   77.566
LGA    K    32_A      K    32_A     1.097     0    0.069   0.890     2.269   88.214   79.735
LGA    C    33_A      C    33_A     1.007     0    0.229   0.230     2.042   77.262   80.159
LGA    H    34_A      H    34_A     1.248     0    0.082   1.289     3.778   79.286   67.381
LGA    C    35_A      C    35_A     1.286     0    0.073   0.602     2.441   81.429   77.222
LGA    V    36_A      V    36_A     1.159     0    0.073   0.303     2.281   81.429   77.823
LGA    P    37_A      P    37_A     0.979     0    0.046   0.325     1.291   88.214   87.891
LGA    S    38_A      S    38_A     1.321     0    0.236   0.656     5.012   81.548   69.524
LGA    G    39_A      G    39_A     1.834     0    0.064   0.064     2.559   66.905   66.905
LGA    T    40_A      T    40_A     3.143     0    0.469   0.377     4.262   50.476   51.429
LGA    Y    41_A      Y    41_A     3.295     0    0.148   0.302     4.055   55.476   47.976
LGA    G    42_A      G    42_A     2.626     0    0.631   0.631     4.696   50.714   50.714
LGA    N    43_A      N    43_A     1.097     0    0.192   0.873     4.281   83.690   67.560
LGA    K    44_A      K    44_A     1.153     0    0.044   1.003     8.105   77.143   56.614
LGA    D    45_A      D    45_A     2.044     0    0.085   1.028     3.971   70.833   62.262
LGA    E    46_A      E    46_A     1.421     0    0.127   0.169     2.600   83.810   75.132
LGA    C    47_A      C    47_A     0.787     0    0.103   0.239     2.386   81.548   78.730
LGA    P    48_A      P    48_A     2.127     0    0.235   0.430     2.648   72.976   71.905
LGA    C    49_A      C    49_A     1.760     0    0.086   0.214     2.143   75.119   74.444
LGA    Y    50_A      Y    50_A     1.781     0    0.084   0.797     5.124   72.857   55.595
LGA    R    51_A      R    51_A     1.159     0    0.053   1.201     5.676   83.690   64.372
LGA    D    52_A      D    52_A     0.228     0    0.100   0.770     3.674  100.000   80.833
LGA    L    53_A      L    53_A     1.046     0    0.030   0.814     3.261   81.548   73.452
LGA    K    54_A      K    54_A     1.560     0    0.042   1.281     5.877   70.952   59.841
LGA    N    55_A      N    55_A     2.809     0    0.086   0.335     3.297   55.476   59.167
LGA    S    56_A      S    56_A     4.398     0    0.152   0.558     6.529   35.952   30.556
LGA    K    57_A      K    57_A     3.948     0    0.038   0.772     6.632   43.333   32.751
LGA    G    58_A      G    58_A     2.687     0    0.040   0.040     2.967   60.952   60.952
LGA    N    59_A      N    59_A     1.234     0    0.046   0.280     3.005   86.190   78.869
LGA    P    60_A      P    60_A     1.799     0    0.087   0.323     3.240   72.857   67.279
LGA    K    61_A      K    61_A     2.490     0    0.040   0.964     3.314   59.167   58.201
LGA    C    62_A      C    62_A     3.403     0    0.118   0.505     4.320   46.667   45.635
LGA    P    63_A      P    63_A     3.789     0    0.324   0.307     4.183   41.786   43.401

# 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):     1.988          2.009                  2.879           72.436   65.714

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.99    78.571    88.694     3.017

LGA_LOCAL      RMSD:   1.988  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.988  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.988  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.522366 * X  +  -0.827712 * Y  +  -0.205006 * Z  +  -8.974136
  Y_new =   0.625782 * X  +   0.535414 * Y  +  -0.567212 * Z  +   2.268409
  Z_new =   0.579251 * X  +   0.168003 * Y  +   0.797649 * Z  +  -7.466510 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.875228 -0.617809  0.207589   [DEG:   50.1469  -35.3979   11.8940 ]
ZXZ: -0.346818  0.647409  1.288506   [DEG:  -19.8712   37.0938   73.8260 ]
 
# END of job
