
#######################################################
#                                                     #
#                        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        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.98     3.03
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.96     2.97
  LCS_AVERAGE:     37.79

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   28   47   57   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   33   48   57   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   12   33   48   57   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   33   48   57   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   57   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   25   35   48   57   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      6   25   35   48   57   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     11   25   35   48   57   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      9   24   35   48   57   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      5   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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   25   35   48   57   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   22   35   48   57   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      4   21   35   48   57   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   23   35   48   57   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   57   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   25   35   48   57   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   21   35   48   57   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   25   35   48   57   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     10   25   35   48   57   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      6   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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     11   25   35   48   57   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   25   35   48   57   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   25   35   48   57   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   25   35   48   57   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   25   35   48   57   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   24   35   48   57   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   25   35   48   57   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   57   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   34   48   57   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      5   25   35   48   57   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   16   33   40   50   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     13   63   63      3   17   27   39   49   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   18   37   57   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   34   48   57   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      6   19   34   48   57   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   13   28   46   57   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   19   31   48   57   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   34   48   57   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    9   24   37   57   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   28   48   57   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   24   48   57   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   34   48   57   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   19   34   48   57   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   19   33   48   57   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   18   30   47   57   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   13   25   38   57   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      5   10   24   36   45   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   13   25   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      5   12   27   46   57   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   34   48   57   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   57   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      3   16   35   48   57   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   33   40   49   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   11   26   38   47   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.26  (  37.79  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     35     48     57     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  39.68  55.56  76.19  90.48  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    0.35   0.64   0.97   1.41   1.63   1.71   1.85   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90
GDT RMS_ALL_AT   2.27   3.12   2.70   2.02   1.91   1.93   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90

# 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     1.989     0    0.059   0.059     3.070   73.690   73.690
LGA    S     2_A      S     2_A     2.230     0    0.219   0.804     3.812   68.810   61.429
LGA    S     3_A      S     3_A     2.148     0    0.160   0.498     3.682   68.810   62.619
LGA    F     4_A      F     4_A     1.710     0    0.077   0.214     3.739   72.857   60.390
LGA    C     5_A      C     5_A     1.835     0    0.120   0.791     2.653   72.857   70.238
LGA    D     6_A      D     6_A     1.834     0    0.119   1.122     6.020   72.857   55.238
LGA    S     7_A      S     7_A     2.180     0    0.106   0.556     4.264   64.762   60.159
LGA    K     8_A      K     8_A     1.438     0    0.108   0.729     5.628   79.286   67.831
LGA    C     9_A      C     9_A     1.491     0    0.048   0.059     1.735   77.143   78.571
LGA    G    10_A      G    10_A     1.522     0    0.116   0.116     1.555   75.000   75.000
LGA    V    11_A      V    11_A     1.928     0    0.058   0.069     2.207   70.833   69.388
LGA    R    12_A      R    12_A     1.700     0    0.063   1.373     8.062   72.857   52.554
LGA    C    13_A      C    13_A     1.017     0    0.646   0.721     2.521   77.619   80.397
LGA    S    14_A      S    14_A     1.416     0    0.051   0.639     2.025   79.286   75.794
LGA    K    15_A      K    15_A     1.310     0    0.110   0.647     4.108   81.429   68.571
LGA    A    16_A      A    16_A     1.257     0    0.633   0.569     2.821   75.357   76.571
LGA    G    17_A      G    17_A     2.376     0    0.031   0.031     2.684   62.857   62.857
LGA    Y    18_A      Y    18_A     1.901     0    0.290   1.363     7.647   72.976   52.579
LGA    Q    19_A      Q    19_A     1.224     0    0.119   0.976     2.353   88.214   78.836
LGA    E    20_A      E    20_A     1.648     0    0.026   0.647     4.144   72.976   61.323
LGA    R    21_A      R    21_A     2.262     0    0.044   1.139    10.096   66.786   36.364
LGA    C    22_A      C    22_A     1.526     0    0.063   0.084     1.756   75.000   75.714
LGA    L    23_A      L    23_A     1.122     0    0.054   0.297     2.219   81.429   79.345
LGA    K    24_A      K    24_A     1.974     0    0.064   1.130    10.017   68.810   44.339
LGA    Y    25_A      Y    25_A     2.202     0    0.121   0.635     3.602   62.857   62.698
LGA    C    26_A      C    26_A     1.128     0    0.047   0.106     1.361   83.690   84.444
LGA    G    27_A      G    27_A     0.950     0    0.044   0.044     1.480   85.952   85.952
LGA    I    28_A      I    28_A     1.868     0    0.036   0.751     4.998   75.000   63.036
LGA    C    29_A      C    29_A     1.437     0    0.098   0.130     1.851   83.690   80.079
LGA    C    30_A      C    30_A     0.867     0    0.142   0.152     1.210   88.214   90.556
LGA    E    31_A      E    31_A     0.748     0    0.020   0.861     4.057   90.476   76.984
LGA    K    32_A      K    32_A     1.075     0    0.081   0.776     1.948   83.690   80.582
LGA    C    33_A      C    33_A     1.079     0    0.223   0.228     2.019   77.262   80.159
LGA    H    34_A      H    34_A     1.330     0    0.105   1.263     3.263   79.286   70.238
LGA    C    35_A      C    35_A     1.299     0    0.074   0.609     2.391   81.429   77.222
LGA    V    36_A      V    36_A     1.149     0    0.068   0.308     2.285   81.429   77.823
LGA    P    37_A      P    37_A     1.020     0    0.047   0.319     1.366   85.952   86.599
LGA    S    38_A      S    38_A     1.310     0    0.232   0.658     5.041   81.548   69.524
LGA    G    39_A      G    39_A     1.814     0    0.062   0.062     2.471   68.810   68.810
LGA    T    40_A      T    40_A     3.155     0    0.469   0.374     4.212   50.476   51.429
LGA    Y    41_A      Y    41_A     3.274     0    0.157   0.309     3.988   55.476   48.492
LGA    G    42_A      G    42_A     2.572     0    0.630   0.630     4.699   50.714   50.714
LGA    N    43_A      N    43_A     1.132     0    0.203   0.874     4.264   83.690   67.560
LGA    K    44_A      K    44_A     1.223     0    0.057   1.022     8.148   77.143   57.407
LGA    D    45_A      D    45_A     2.101     0    0.091   1.024     3.785   70.833   62.262
LGA    E    46_A      E    46_A     1.487     0    0.130   0.189     2.625   81.548   71.429
LGA    C    47_A      C    47_A     0.879     0    0.109   0.235     2.412   81.548   78.730
LGA    P    48_A      P    48_A     2.200     0    0.244   0.433     2.727   72.976   71.905
LGA    C    49_A      C    49_A     1.831     0    0.110   0.225     2.185   72.976   73.016
LGA    Y    50_A      Y    50_A     1.883     0    0.080   0.804     5.303   72.857   53.492
LGA    R    51_A      R    51_A     1.180     0    0.039   1.235     5.698   83.690   63.939
LGA    D    52_A      D    52_A     0.292     0    0.089   0.766     3.427   92.857   80.179
LGA    L    53_A      L    53_A     1.105     0    0.029   0.762     4.203   81.548   71.726
LGA    K    54_A      K    54_A     1.509     0    0.039   1.287     6.129   70.952   59.365
LGA    N    55_A      N    55_A     2.664     0    0.088   0.297     3.048   55.476   60.119
LGA    S    56_A      S    56_A     3.960     0    0.152   0.568     6.086   42.024   36.111
LGA    K    57_A      K    57_A     3.403     0    0.039   0.774     5.983   50.000   39.577
LGA    G    58_A      G    58_A     2.263     0    0.041   0.041     2.514   66.905   66.905
LGA    N    59_A      N    59_A     0.899     0    0.038   0.285     2.554   90.595   85.238
LGA    P    60_A      P    60_A     1.701     0    0.075   0.320     2.968   75.000   69.524
LGA    K    61_A      K    61_A     2.317     0    0.038   0.993     3.066   61.190   63.333
LGA    C    62_A      C    62_A     3.192     0    0.113   0.524     4.228   50.119   47.937
LGA    P    63_A      P    63_A     3.637     0    0.324   0.309     4.083   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):     1.897          1.920                  2.757           73.267   66.813

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.90    78.968    89.146     3.155

LGA_LOCAL      RMSD:   1.897  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.897  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.897  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.235370 * X  +  -0.754415 * Y  +  -0.612748 * Z  +  -8.676739
  Y_new =   0.727655 * X  +   0.281161 * Y  +  -0.625673 * Z  +   2.206623
  Z_new =   0.644298 * X  +  -0.593133 * Y  +   0.482777 * Z  +  -8.068921 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.883638 -0.700105 -0.887611   [DEG:  107.9245  -40.1130  -50.8564 ]
ZXZ: -0.774961  1.066974  2.314871   [DEG:  -44.4020   61.1331  132.6323 ]
 
# END of job
