
#######################################################
#                                                     #
#                        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        1.00     2.95
  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   11   27   48   56   60   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   15   31   46   56   60   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   60   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   60   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   34   48   56   60   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      5   24   34   48   56   60   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   56   60   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   56   60   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      8   24   34   48   56   60   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   56   60   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   56   60   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   56   60   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      6   24   34   48   56   60   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   18   34   48   56   60   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   34   48   56   60   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   56   60   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   60   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      8   24   34   48   56   60   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   34   48   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   56   60   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   23   34   48   56   60   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   56   60   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   23   34   48   56   60   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   56   60   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      3   21   30   48   56   60   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      6   23   34   48   56   60   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      3   19   34   41   54   60   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   54   60   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   18   38   56   60   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   30   48   56   60   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   60   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   60   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   60   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   60   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   24   37   56   60   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   60   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   60   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   60   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   60   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   60   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   60   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   60   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      5    9   24   36   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      5   12   24   38   52   60   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      5   12   27   45   56   60   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   60   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      6   21   34   48   56   60   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      5    9   34   47   56   60   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   12   19   37   44   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     12     24     34     48     56     60     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  88.89  95.24  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.60   0.91   1.43   1.61   1.77   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   3.55   3.47   2.99   2.01   1.94   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   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     1.890     0    0.073   0.073     3.058   73.690   73.690
LGA    S     2_A      S     2_A     2.313     0    0.206   0.815     3.913   68.810   61.429
LGA    S     3_A      S     3_A     2.285     0    0.151   0.471     3.833   68.810   61.429
LGA    F     4_A      F     4_A     1.725     0    0.078   0.238     3.840   72.857   60.390
LGA    C     5_A      C     5_A     1.817     0    0.130   0.808     2.636   72.857   70.238
LGA    D     6_A      D     6_A     1.847     0    0.103   1.117     5.975   72.857   55.774
LGA    S     7_A      S     7_A     2.190     0    0.117   0.237     2.523   62.857   63.492
LGA    K     8_A      K     8_A     1.475     0    0.123   0.773     5.744   77.143   66.878
LGA    C     9_A      C     9_A     1.623     0    0.050   0.080     1.890   75.000   77.143
LGA    G    10_A      G    10_A     1.604     0    0.075   0.075     1.665   75.000   75.000
LGA    V    11_A      V    11_A     2.008     0    0.030   0.086     2.269   68.810   67.075
LGA    R    12_A      R    12_A     1.811     0    0.054   1.365     8.132   72.857   52.554
LGA    C    13_A      C    13_A     1.063     0    0.606   0.691     2.465   79.524   80.159
LGA    S    14_A      S    14_A     1.438     0    0.075   0.573     1.989   79.286   77.143
LGA    K    15_A      K    15_A     1.301     0    0.097   0.655     4.275   81.429   68.571
LGA    A    16_A      A    16_A     1.302     0    0.623   0.561     2.845   75.357   76.571
LGA    G    17_A      G    17_A     2.394     0    0.055   0.055     2.881   62.857   62.857
LGA    Y    18_A      Y    18_A     1.940     0    0.315   1.377     7.553   72.976   52.063
LGA    Q    19_A      Q    19_A     1.468     0    0.110   0.988     2.750   83.690   73.280
LGA    E    20_A      E    20_A     1.757     0    0.027   0.811     4.475   72.976   59.048
LGA    R    21_A      R    21_A     2.251     0    0.056   1.164    10.219   66.786   36.364
LGA    C    22_A      C    22_A     1.486     0    0.088   0.107     1.773   77.143   77.143
LGA    L    23_A      L    23_A     1.149     0    0.043   0.285     2.308   81.429   78.274
LGA    K    24_A      K    24_A     1.903     0    0.064   1.134     9.958   70.833   45.291
LGA    Y    25_A      Y    25_A     2.146     0    0.109   0.619     3.536   68.810   65.238
LGA    C    26_A      C    26_A     1.061     0    0.032   0.097     1.381   83.690   84.444
LGA    G    27_A      G    27_A     0.931     0    0.046   0.046     1.407   85.952   85.952
LGA    I    28_A      I    28_A     1.794     0    0.031   0.750     4.904   75.000   63.036
LGA    C    29_A      C    29_A     1.372     0    0.112   0.130     1.918   83.690   80.079
LGA    C    30_A      C    30_A     0.788     0    0.127   0.136     1.144   88.214   90.556
LGA    E    31_A      E    31_A     0.716     0    0.032   0.788     3.766   90.476   77.672
LGA    K    32_A      K    32_A     0.990     0    0.065   0.803     1.834   90.476   83.598
LGA    C    33_A      C    33_A     0.958     0    0.230   0.242     1.960   83.810   86.032
LGA    H    34_A      H    34_A     1.286     0    0.094   1.273     3.355   79.286   69.333
LGA    C    35_A      C    35_A     1.258     0    0.056   0.618     2.356   81.429   77.222
LGA    V    36_A      V    36_A     1.144     0    0.067   0.294     2.245   81.429   77.823
LGA    P    37_A      P    37_A     0.995     0    0.067   0.336     1.350   88.214   87.891
LGA    S    38_A      S    38_A     1.443     0    0.223   0.610     5.125   81.548   69.524
LGA    G    39_A      G    39_A     1.739     0    0.073   0.073     2.404   68.810   68.810
LGA    T    40_A      T    40_A     2.964     0    0.462   0.396     4.016   52.262   53.401
LGA    Y    41_A      Y    41_A     3.215     0    0.193   0.326     4.100   55.476   47.460
LGA    G    42_A      G    42_A     2.558     0    0.629   0.629     4.693   50.714   50.714
LGA    N    43_A      N    43_A     1.267     0    0.191   0.817     4.132   83.690   67.560
LGA    K    44_A      K    44_A     1.243     0    0.060   1.014     8.173   77.143   56.614
LGA    D    45_A      D    45_A     2.199     0    0.085   1.041     4.020   70.833   59.702
LGA    E    46_A      E    46_A     1.520     0    0.107   0.185     2.543   79.405   70.476
LGA    C    47_A      C    47_A     0.854     0    0.084   0.246     2.364   79.524   77.381
LGA    P    48_A      P    48_A     2.286     0    0.231   0.440     2.854   68.810   69.524
LGA    C    49_A      C    49_A     1.840     0    0.070   0.201     2.187   72.976   73.016
LGA    Y    50_A      Y    50_A     1.796     0    0.081   0.826     5.454   72.857   53.611
LGA    R    51_A      R    51_A     1.143     0    0.041   1.246     5.985   83.690   63.939
LGA    D    52_A      D    52_A     0.124     0    0.129   0.811     3.623   97.619   79.643
LGA    L    53_A      L    53_A     1.032     0    0.036   0.755     3.324   81.548   72.381
LGA    K    54_A      K    54_A     1.477     0    0.048   1.282     6.197   73.095   61.217
LGA    N    55_A      N    55_A     2.620     0    0.081   0.283     3.019   57.262   61.012
LGA    S    56_A      S    56_A     3.954     0    0.157   0.566     6.153   40.476   35.079
LGA    K    57_A      K    57_A     3.500     0    0.022   0.777     6.196   50.000   38.466
LGA    G    58_A      G    58_A     2.245     0    0.031   0.031     2.527   66.905   66.905
LGA    N    59_A      N    59_A     0.930     0    0.027   0.316     2.716   90.595   84.107
LGA    P    60_A      P    60_A     1.774     0    0.060   0.311     3.043   75.000   68.503
LGA    K    61_A      K    61_A     2.483     0    0.023   0.962     3.236   59.167   59.153
LGA    C    62_A      C    62_A     3.313     0    0.091   0.508     4.228   48.452   46.825
LGA    P    63_A      P    63_A     3.796     0    0.463   0.456     4.385   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                  2.788           73.428   66.653

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.91    78.571    88.896     3.129

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 =   0.473400 * X  +   0.684866 * Y  +   0.553941 * Z  +  -9.532396
  Y_new =   0.623330 * X  +   0.183874 * Y  +  -0.760033 * Z  +   2.322064
  Z_new =  -0.622376 * X  +   0.705088 * Y  +  -0.339852 * Z  +  -5.347708 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.921262  0.671775  2.019940   [DEG:   52.7845   38.4898  115.7340 ]
ZXZ:  0.629820  1.917556 -0.723170   [DEG:   36.0860  109.8678  -41.4346 ]
 
# END of job
