
#######################################################
#                                                     #
#                        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        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.88     1.88
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.99     3.00
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.98     2.94
  LCS_AVERAGE:     37.84

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      8   63   63      2   10   30   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   32   48   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   12   32   48   56   60   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   33   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      5   21   33   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      4   25   33   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   25   33   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     11   25   33   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      9   25   33   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      6   25   33   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     10   25   33   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     11   25   33   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     10   25   33   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   20   33   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   33   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   33   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     10   25   33   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   13   33   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     10   25   33   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     11   25   33   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      6   25   33   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     11   25   33   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     11   25   33   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     11   25   33   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     11   25   33   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     11   25   33   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     11   25   33   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     11   25   33   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     11   25   33   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     10   25   33   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     10   25   33   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     10   25   33   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     10   25   33   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     10   24   33   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     10   25   33   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     10   21   33   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     26   63   63      5   21   31   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     26   63   63      5   24   33   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   20   33   41   55   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   20   28   39   52   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    7   22   37   56   60   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   31   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     12   63   63      6   20   33   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     12   63   63      5   10   28   46   56   60   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   31   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     12   63   63      5   20   33   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     12   63   63      5    8   22   35   56   60   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    9   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     12   63   63      5    9   23   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     12   63   63      5    8   33   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     12   63   63      5   20   33   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     12   63   63      5   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     12   63   63      4   19   31   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      4   12   26   38   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   12   25   36   46   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   14   26   38   53   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   13   27   46   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      9   20   33   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     10   21   33   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      3   10   33   48   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   10   32   39   51   59   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   10   18   37   46   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.28  (  37.84  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     11     25     33     48     56     60     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  52.38  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    0.30   0.61   0.89   1.41   1.59   1.74   1.83   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88
GDT RMS_ALL_AT   3.39   3.27   2.96   1.98   1.91   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88   1.88

# 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     1.847     0    0.050   0.050     2.826   77.738   77.738
LGA    S     2_A      S     2_A     2.245     0    0.208   0.791     3.837   68.810   61.429
LGA    S     3_A      S     3_A     2.194     0    0.141   0.681     5.593   68.810   58.968
LGA    F     4_A      F     4_A     1.665     0    0.082   0.231     3.636   72.857   61.082
LGA    C     5_A      C     5_A     1.847     0    0.122   0.793     2.657   72.857   70.238
LGA    D     6_A      D     6_A     1.854     0    0.109   1.101     5.965   72.857   55.774
LGA    S     7_A      S     7_A     2.222     0    0.118   0.597     4.450   62.857   58.889
LGA    K     8_A      K     8_A     1.446     0    0.106   0.705     5.355   79.286   68.360
LGA    C     9_A      C     9_A     1.484     0    0.051   0.064     1.728   77.143   78.571
LGA    G    10_A      G    10_A     1.500     0    0.119   0.119     1.542   77.143   77.143
LGA    V    11_A      V    11_A     1.891     0    0.060   0.079     2.190   72.857   70.544
LGA    R    12_A      R    12_A     1.661     0    0.052   1.369     8.196   75.000   53.333
LGA    C    13_A      C    13_A     0.995     0    0.634   0.713     2.455   81.786   83.175
LGA    S    14_A      S    14_A     1.397     0    0.090   0.626     2.112   79.286   77.222
LGA    K    15_A      K    15_A     1.253     0    0.095   0.644     4.035   81.429   69.312
LGA    A    16_A      A    16_A     1.249     0    0.621   0.557     2.790   75.357   76.571
LGA    G    17_A      G    17_A     2.345     0    0.038   0.038     2.732   64.881   64.881
LGA    Y    18_A      Y    18_A     1.933     0    0.306   1.367     7.524   72.976   52.063
LGA    Q    19_A      Q    19_A     1.481     0    0.123   1.119     3.806   83.690   73.704
LGA    E    20_A      E    20_A     1.802     0    0.029   0.735     4.599   72.976   58.413
LGA    R    21_A      R    21_A     2.309     0    0.049   1.165    10.595   66.786   35.108
LGA    C    22_A      C    22_A     1.502     0    0.061   0.079     1.727   75.000   75.714
LGA    L    23_A      L    23_A     1.106     0    0.055   0.299     2.215   81.429   78.274
LGA    K    24_A      K    24_A     1.916     0    0.066   1.119     9.854   70.833   45.291
LGA    Y    25_A      Y    25_A     2.129     0    0.118   0.661     3.534   68.810   65.873
LGA    C    26_A      C    26_A     1.130     0    0.049   0.107     1.338   83.690   84.444
LGA    G    27_A      G    27_A     0.886     0    0.050   0.050     1.401   85.952   85.952
LGA    I    28_A      I    28_A     1.721     0    0.044   0.752     4.743   77.143   64.940
LGA    C    29_A      C    29_A     1.386     0    0.100   0.121     1.858   83.690   80.079
LGA    C    30_A      C    30_A     0.863     0    0.135   0.143     1.189   88.214   90.556
LGA    E    31_A      E    31_A     0.726     0    0.018   0.880     4.006   90.476   77.831
LGA    K    32_A      K    32_A     1.057     0    0.060   0.890     2.045   85.952   78.730
LGA    C    33_A      C    33_A     1.106     0    0.227   0.233     2.000   79.286   81.508
LGA    H    34_A      H    34_A     1.330     0    0.102   1.222     3.064   79.286   71.714
LGA    C    35_A      C    35_A     1.261     0    0.080   0.612     2.364   81.429   77.222
LGA    V    36_A      V    36_A     1.159     0    0.066   0.276     2.279   81.429   76.599
LGA    P    37_A      P    37_A     0.917     0    0.027   0.289     1.181   88.214   87.891
LGA    S    38_A      S    38_A     1.434     0    0.243   0.658     5.194   81.548   68.254
LGA    G    39_A      G    39_A     1.657     0    0.061   0.061     2.358   68.810   68.810
LGA    T    40_A      T    40_A     2.854     0    0.476   0.378     4.051   52.262   54.422
LGA    Y    41_A      Y    41_A     3.044     0    0.149   0.302     3.813   59.167   50.833
LGA    G    42_A      G    42_A     2.446     0    0.635   0.635     4.630   52.619   52.619
LGA    N    43_A      N    43_A     1.308     0    0.189   0.810     4.425   83.690   67.560
LGA    K    44_A      K    44_A     1.263     0    0.056   1.044     8.143   77.143   57.407
LGA    D    45_A      D    45_A     2.144     0    0.091   1.038     3.784   70.833   62.262
LGA    E    46_A      E    46_A     1.467     0    0.129   0.160     2.773   83.810   72.434
LGA    C    47_A      C    47_A     0.819     0    0.103   0.232     2.329   81.548   78.730
LGA    P    48_A      P    48_A     2.241     0    0.248   0.436     2.784   68.810   69.524
LGA    C    49_A      C    49_A     1.862     0    0.093   0.219     2.194   72.976   73.016
LGA    Y    50_A      Y    50_A     1.957     0    0.079   0.777     5.196   72.857   55.595
LGA    R    51_A      R    51_A     1.245     0    0.040   1.221     5.568   83.690   63.939
LGA    D    52_A      D    52_A     0.278     0    0.095   0.778     3.364   92.857   80.179
LGA    L    53_A      L    53_A     1.093     0    0.031   0.699     4.077   83.690   72.798
LGA    K    54_A      K    54_A     1.465     0    0.034   1.263     5.981   73.095   61.693
LGA    N    55_A      N    55_A     2.684     0    0.093   0.275     3.033   57.262   59.107
LGA    S    56_A      S    56_A     3.890     0    0.160   0.570     6.145   42.024   37.063
LGA    K    57_A      K    57_A     3.313     0    0.036   0.775     5.957   51.786   39.735
LGA    G    58_A      G    58_A     2.119     0    0.039   0.039     2.385   68.810   68.810
LGA    N    59_A      N    59_A     0.622     0    0.034   0.297     2.190   90.595   88.512
LGA    P    60_A      P    60_A     1.653     0    0.079   0.323     2.824   75.000   70.680
LGA    K    61_A      K    61_A     2.392     0    0.037   0.970     3.131   59.167   60.794
LGA    C    62_A      C    62_A     3.274     0    0.106   0.533     4.278   48.452   46.825
LGA    P    63_A      P    63_A     3.732     0    0.308   0.289     4.216   43.452   44.354

# 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):     1.877          1.898                  2.770           73.876   67.160

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.88    78.968    88.903     3.186

LGA_LOCAL      RMSD:   1.877  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.877  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.877  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.849847 * X  +   0.526434 * Y  +  -0.025046 * Z  +  -9.803468
  Y_new =  -0.240705 * X  +  -0.429980 * Y  +  -0.870160 * Z  +   3.554099
  Z_new =  -0.468851 * X  +  -0.733474 * Y  +   0.492133 * Z  +  -2.749161 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.865588  0.487989 -0.979826   [DEG: -164.1861   27.9597  -56.1399 ]
ZXZ: -0.028775  1.056258 -2.572834   [DEG:   -1.6487   60.5191 -147.4125 ]
 
# END of job
