
#######################################################
#                                                     #
#                        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        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.91     1.91
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.99     2.96
  LCS_AVERAGE:     37.24

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      0   10   28   48   56   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   32   46   56   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   27   46   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     31   63   63      3    9   32   48   56   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   22   35   48   56   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   35   48   56   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   35   48   56   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     13   24   35   48   56   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      7   24   35   48   56   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   35   48   56   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      7   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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   19   35   48   56   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   19   35   48   56   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   21   35   48   56   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   29   48   56   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      9   24   35   48   56   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   16   35   48   56   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   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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     13   24   35   48   56   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   35   48   56   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   35   48   56   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   35   48   56   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   35   48   56   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   35   48   56   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      7   24   35   48   56   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   35   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   63   63      4   21   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   63   63      5   24   35   48   56   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   19   34   41   53   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   19   27   41   53   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   37   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     11   63   63      6   21   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     11   63   63      5   19   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     10   63   63      5    9   27   45   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     10   63   63      5   19   29   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     10   63   63      5   21   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     10   63   63      5    8   23   38   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     10   63   63      5   11   28   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     10   63   63      5   11   24   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     10   63   63      5    9   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     11   63   63     11   21   32   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     11   63   63      4   19   31   48   56   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     11   63   63      5   18   29   48   56   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   24   39   56   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   23   37   44   59   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   12   24   38   52   59   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   12   27   45   56   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     11   21   31   48   56   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      9   21   35   48   56   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    9   35   46   56   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   24   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   46   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.08  (  37.24  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     13     24     35     48     56     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  38.10  55.56  76.19  88.89  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    0.34   0.59   0.99   1.42   1.61   1.72   1.87   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91
GDT RMS_ALL_AT   3.48   3.38   2.71   2.01   1.94   1.93   1.92   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91   1.91

# 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     1.909     0    0.062   0.062     3.106   73.690   73.690
LGA    S     2_A      S     2_A     2.313     0    0.204   0.812     3.922   68.810   61.429
LGA    S     3_A      S     3_A     2.294     0    0.158   0.474     3.882   68.810   61.429
LGA    F     4_A      F     4_A     1.711     0    0.076   0.237     3.860   72.857   60.390
LGA    C     5_A      C     5_A     1.824     0    0.127   0.802     2.641   72.857   70.238
LGA    D     6_A      D     6_A     1.861     0    0.106   1.112     5.973   72.857   55.774
LGA    S     7_A      S     7_A     2.207     0    0.119   0.238     2.538   62.857   63.492
LGA    K     8_A      K     8_A     1.481     0    0.119   0.767     5.726   77.143   66.878
LGA    C     9_A      C     9_A     1.587     0    0.045   0.079     1.819   75.000   77.143
LGA    G    10_A      G    10_A     1.583     0    0.097   0.097     1.656   75.000   75.000
LGA    V    11_A      V    11_A     2.011     0    0.031   0.077     2.236   68.810   67.075
LGA    R    12_A      R    12_A     1.812     0    0.052   1.363     8.142   72.857   52.554
LGA    C    13_A      C    13_A     1.052     0    0.606   0.694     2.447   79.524   80.159
LGA    S    14_A      S    14_A     1.439     0    0.075   0.575     1.991   79.286   77.143
LGA    K    15_A      K    15_A     1.313     0    0.099   0.658     4.281   81.429   68.571
LGA    A    16_A      A    16_A     1.325     0    0.619   0.557     2.850   75.357   76.571
LGA    G    17_A      G    17_A     2.402     0    0.045   0.045     2.843   62.857   62.857
LGA    Y    18_A      Y    18_A     1.946     0    0.317   1.373     7.542   72.976   52.063
LGA    Q    19_A      Q    19_A     1.463     0    0.107   0.985     2.742   83.690   73.280
LGA    E    20_A      E    20_A     1.751     0    0.025   0.806     4.479   72.976   59.048
LGA    R    21_A      R    21_A     2.250     0    0.055   1.167    10.221   66.786   36.364
LGA    C    22_A      C    22_A     1.489     0    0.093   0.111     1.774   77.143   77.143
LGA    L    23_A      L    23_A     1.152     0    0.041   0.292     2.287   81.429   78.274
LGA    K    24_A      K    24_A     1.891     0    0.070   1.133     9.962   70.833   45.291
LGA    Y    25_A      Y    25_A     2.139     0    0.112   0.621     3.543   68.810   65.238
LGA    C    26_A      C    26_A     1.063     0    0.033   0.101     1.365   83.690   84.444
LGA    G    27_A      G    27_A     0.929     0    0.043   0.043     1.403   85.952   85.952
LGA    I    28_A      I    28_A     1.804     0    0.029   0.752     4.907   75.000   63.036
LGA    C    29_A      C    29_A     1.380     0    0.110   0.126     1.923   83.690   80.079
LGA    C    30_A      C    30_A     0.811     0    0.127   0.137     1.168   88.214   90.556
LGA    E    31_A      E    31_A     0.718     0    0.026   0.798     3.797   90.476   77.672
LGA    K    32_A      K    32_A     0.989     0    0.076   0.796     1.850   90.476   83.598
LGA    C    33_A      C    33_A     0.977     0    0.227   0.238     1.994   81.548   84.524
LGA    H    34_A      H    34_A     1.265     0    0.102   1.277     3.461   79.286   70.190
LGA    C    35_A      C    35_A     1.249     0    0.061   0.619     2.352   81.429   77.222
LGA    V    36_A      V    36_A     1.153     0    0.069   0.306     2.273   81.429   77.823
LGA    P    37_A      P    37_A     0.992     0    0.068   0.323     1.336   88.214   87.891
LGA    S    38_A      S    38_A     1.422     0    0.216   0.606     5.118   81.548   69.524
LGA    G    39_A      G    39_A     1.754     0    0.070   0.070     2.449   68.810   68.810
LGA    T    40_A      T    40_A     2.973     0    0.460   0.383     4.008   52.262   53.401
LGA    Y    41_A      Y    41_A     3.210     0    0.185   0.331     4.078   57.381   48.611
LGA    G    42_A      G    42_A     2.553     0    0.630   0.630     4.701   50.714   50.714
LGA    N    43_A      N    43_A     1.249     0    0.187   0.845     4.185   83.690   67.560
LGA    K    44_A      K    44_A     1.229     0    0.054   1.021     8.195   77.143   56.614
LGA    D    45_A      D    45_A     2.192     0    0.083   1.040     4.002   70.833   60.595
LGA    E    46_A      E    46_A     1.511     0    0.095   0.167     2.526   79.405   70.476
LGA    C    47_A      C    47_A     0.845     0    0.083   0.244     2.379   79.524   77.381
LGA    P    48_A      P    48_A     2.277     0    0.229   0.434     2.843   68.810   69.524
LGA    C    49_A      C    49_A     1.850     0    0.073   0.204     2.188   72.976   73.016
LGA    Y    50_A      Y    50_A     1.798     0    0.086   0.831     5.424   72.857   53.611
LGA    R    51_A      R    51_A     1.145     0    0.037   1.248     5.987   83.690   63.939
LGA    D    52_A      D    52_A     0.128     0    0.122   0.799     3.619   97.619   79.643
LGA    L    53_A      L    53_A     1.030     0    0.041   0.757     3.342   83.690   73.452
LGA    K    54_A      K    54_A     1.462     0    0.046   1.274     6.179   73.095   61.217
LGA    N    55_A      N    55_A     2.615     0    0.078   0.262     3.021   57.262   61.012
LGA    S    56_A      S    56_A     3.966     0    0.154   0.564     6.143   40.476   35.079
LGA    K    57_A      K    57_A     3.516     0    0.020   0.778     6.202   48.333   37.725
LGA    G    58_A      G    58_A     2.273     0    0.034   0.034     2.554   66.905   66.905
LGA    N    59_A      N    59_A     0.944     0    0.028   0.327     2.754   90.595   84.107
LGA    P    60_A      P    60_A     1.753     0    0.067   0.303     3.016   75.000   68.503
LGA    K    61_A      K    61_A     2.479     0    0.023   0.958     3.218   59.167   59.153
LGA    C    62_A      C    62_A     3.308     0    0.093   0.515     4.226   48.452   46.825
LGA    P    63_A      P    63_A     3.787     0    0.474   0.462     4.365   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):     1.914          1.936                  2.789           73.430   66.681

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.91    78.571    88.917     3.128

LGA_LOCAL      RMSD:   1.914  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.914  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.914  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.473559 * X  +   0.685033 * Y  +   0.553598 * Z  +  -9.531105
  Y_new =   0.623312 * X  +   0.183418 * Y  +  -0.760158 * Z  +   2.321733
  Z_new =  -0.622274 * X  +   0.705044 * Y  +  -0.340130 * Z  +  -5.347365 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.921086  0.671644  2.020284   [DEG:   52.7743   38.4824  115.7538 ]
ZXZ:  0.629446  1.917851 -0.723120   [DEG:   36.0646  109.8848  -41.4317 ]
 
# END of job
