
#######################################################
#                                                     #
#                        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        1.89     1.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.89     1.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       4_A - 36_A        0.97     3.02
  LONGEST_CONTINUOUS_SEGMENT:    33       5_A - 37_A        0.96     2.96
  LCS_AVERAGE:     37.82

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   12   31   48   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   35   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      4   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     10   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      6   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     10   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     10   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     10   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     10   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     10   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     10   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     10   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      6   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   35   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   18   34   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    9   18   36   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      5   21   35   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      5   19   35   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    9   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   20   35   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    8   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    9   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    9   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   35   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   20   35   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   34   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   48   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   39   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   13   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   20   35   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      4   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   34   40   48   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   27   38   47   55   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  79.27  (  37.82  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    0.34   0.65   0.97   1.40   1.63   1.71   1.85   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89
GDT RMS_ALL_AT   2.26   3.11   2.69   2.03   1.91   1.91   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89   1.89

# 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     1.947     0    0.083   0.083     2.922   75.476   75.476
LGA    S     2_A      S     2_A     2.197     0    0.213   0.799     3.782   70.952   62.857
LGA    S     3_A      S     3_A     2.139     0    0.157   0.467     3.556   68.810   62.619
LGA    F     4_A      F     4_A     1.688     0    0.081   0.212     3.712   72.857   61.082
LGA    C     5_A      C     5_A     1.807     0    0.116   0.790     2.647   72.857   70.238
LGA    D     6_A      D     6_A     1.817     0    0.114   1.116     5.994   72.857   55.774
LGA    S     7_A      S     7_A     2.175     0    0.130   0.233     2.540   62.857   63.492
LGA    K     8_A      K     8_A     1.428     0    0.110   0.749     5.781   79.286   67.831
LGA    C     9_A      C     9_A     1.490     0    0.051   0.061     1.761   77.143   78.571
LGA    G    10_A      G    10_A     1.532     0    0.115   0.115     1.556   75.000   75.000
LGA    V    11_A      V    11_A     1.952     0    0.060   0.074     2.245   70.833   68.231
LGA    R    12_A      R    12_A     1.724     0    0.060   1.372     8.068   72.857   52.554
LGA    C    13_A      C    13_A     1.037     0    0.639   0.716     2.500   77.619   80.397
LGA    S    14_A      S    14_A     1.442     0    0.107   0.622     2.030   77.143   74.365
LGA    K    15_A      K    15_A     1.296     0    0.102   0.644     4.059   81.429   68.571
LGA    A    16_A      A    16_A     1.248     0    0.624   0.560     2.822   75.357   76.571
LGA    G    17_A      G    17_A     2.310     0    0.032   0.032     2.648   64.881   64.881
LGA    Y    18_A      Y    18_A     1.884     0    0.284   1.373     7.732   75.000   52.381
LGA    Q    19_A      Q    19_A     1.242     0    0.108   1.203     4.135   85.952   74.868
LGA    E    20_A      E    20_A     1.586     0    0.026   0.558     3.808   72.976   62.910
LGA    R    21_A      R    21_A     2.240     0    0.053   1.260    11.889   66.786   35.195
LGA    C    22_A      C    22_A     1.536     0    0.063   0.086     1.757   75.000   75.714
LGA    L    23_A      L    23_A     1.114     0    0.055   0.298     2.187   81.429   79.345
LGA    K    24_A      K    24_A     1.970     0    0.064   1.119     9.913   68.810   44.392
LGA    Y    25_A      Y    25_A     2.194     0    0.123   0.574     3.421   62.857   63.095
LGA    C    26_A      C    26_A     1.136     0    0.049   0.107     1.360   83.690   84.444
LGA    G    27_A      G    27_A     0.939     0    0.045   0.045     1.473   85.952   85.952
LGA    I    28_A      I    28_A     1.849     0    0.038   0.750     4.957   75.000   63.036
LGA    C    29_A      C    29_A     1.421     0    0.099   0.128     1.849   83.690   80.079
LGA    C    30_A      C    30_A     0.859     0    0.141   0.152     1.202   88.214   90.556
LGA    E    31_A      E    31_A     0.732     0    0.022   0.868     4.094   90.476   76.984
LGA    K    32_A      K    32_A     1.048     0    0.081   0.773     1.843   88.214   82.593
LGA    C    33_A      C    33_A     1.064     0    0.223   0.230     1.999   79.286   81.508
LGA    H    34_A      H    34_A     1.321     0    0.102   1.276     3.372   79.286   71.095
LGA    C    35_A      C    35_A     1.294     0    0.073   0.608     2.394   81.429   77.222
LGA    V    36_A      V    36_A     1.149     0    0.068   0.300     2.281   81.429   77.823
LGA    P    37_A      P    37_A     1.025     0    0.049   0.323     1.387   85.952   86.599
LGA    S    38_A      S    38_A     1.295     0    0.235   0.658     5.033   83.810   71.032
LGA    G    39_A      G    39_A     1.821     0    0.072   0.072     2.615   66.905   66.905
LGA    T    40_A      T    40_A     3.156     0    0.491   0.396     4.230   50.476   51.429
LGA    Y    41_A      Y    41_A     3.309     0    0.160   0.312     4.078   55.476   47.976
LGA    G    42_A      G    42_A     2.615     0    0.630   0.630     4.747   50.714   50.714
LGA    N    43_A      N    43_A     1.164     0    0.195   0.851     4.158   83.690   67.560
LGA    K    44_A      K    44_A     1.249     0    0.053   1.020     8.208   77.143   56.614
LGA    D    45_A      D    45_A     2.161     0    0.092   1.024     3.853   70.833   62.262
LGA    E    46_A      E    46_A     1.518     0    0.129   0.192     2.687   79.405   69.630
LGA    C    47_A      C    47_A     0.879     0    0.108   0.233     2.416   79.524   77.381
LGA    P    48_A      P    48_A     2.217     0    0.247   0.437     2.762   68.810   69.524
LGA    C    49_A      C    49_A     1.845     0    0.083   0.221     2.226   72.976   73.016
LGA    Y    50_A      Y    50_A     1.874     0    0.084   0.808     5.284   72.857   53.492
LGA    R    51_A      R    51_A     1.177     0    0.041   1.234     5.774   83.690   63.939
LGA    D    52_A      D    52_A     0.238     0    0.085   0.766     3.424   92.857   80.179
LGA    L    53_A      L    53_A     1.075     0    0.029   0.592     3.760   83.690   73.571
LGA    K    54_A      K    54_A     1.470     0    0.041   1.297     6.255   75.119   62.116
LGA    N    55_A      N    55_A     2.607     0    0.086   0.303     2.998   59.048   61.905
LGA    S    56_A      S    56_A     3.918     0    0.150   0.570     6.047   42.024   37.063
LGA    K    57_A      K    57_A     3.397     0    0.041   0.772     6.035   50.000   38.466
LGA    G    58_A      G    58_A     2.246     0    0.043   0.043     2.500   68.810   68.810
LGA    N    59_A      N    59_A     0.920     0    0.042   0.277     2.564   90.595   84.107
LGA    P    60_A      P    60_A     1.727     0    0.074   0.321     2.989   75.000   69.524
LGA    K    61_A      K    61_A     2.326     0    0.040   0.983     3.047   59.167   62.434
LGA    C    62_A      C    62_A     3.186     0    0.111   0.522     4.246   50.119   47.937
LGA    P    63_A      P    63_A     3.602     0    0.329   0.314     4.058   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):     1.891          1.915                  2.800           73.426   66.924

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.89    78.968    89.146     3.164

LGA_LOCAL      RMSD:   1.891  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.891  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.891  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.041790 * X  +   0.994964 * Y  +  -0.091104 * Z  +  -6.247384
  Y_new =   0.949583 * X  +  -0.067910 * Y  +  -0.306071 * Z  +   2.344654
  Z_new =  -0.310717 * X  +  -0.073720 * Y  +  -0.947639 * Z  +  -4.915778 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.526816  0.315947 -3.063956   [DEG:   87.4801   18.1024 -175.5517 ]
ZXZ: -0.289304  2.816557 -1.803747   [DEG:  -16.5759  161.3768 -103.3471 ]
 
# END of job
