
#######################################################
#                                                     #
#                        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        1.96     1.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.96     1.96
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.92     3.26
  LCS_AVERAGE:     36.66

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   26   46   55   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   15   31   46   55   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   31   46   55   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   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   63   63      4   21   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   63   63      6   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   63   63      4   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   63   63      9   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   63   63      4   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   63   63      7   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   63   63      4   18   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   63   63      3   14   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   63   63      4   22   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   63   63      4   21   29   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   63   63      9   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   63   63      4   18   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   63   63     11   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   63   63     13   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   63   63     11   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   63   63     11   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   63   63     11   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   63   63     11   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   63   63     11   23   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   63   63     11   24   33   46   55   59   62   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   63   63     10   21   33   46   55   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   46   55   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   33   46   55   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   33   40   52   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   18   26   39   50   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   35   55   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   31   46   55   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   20   31   46   55   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   10   28   44   55   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   20   29   46   55   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   31   46   55   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   23   35   55   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   46   55   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   23   46   55   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   31   46   55   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   31   46   55   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      5   18   31   46   55   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   17   28   46   55   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   23   36   54   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    9   23   34   44   57   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   23   36   50   58   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   11   26   43   55   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      9   20   31   46   55   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   33   46   55   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      5    9   33   46   54   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   11   32   39   49   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   23   37   44   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  78.89  (  36.66  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     33     46     55     59     62     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  20.63  38.10  52.38  73.02  87.30  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   0.58   0.89   1.42   1.63   1.75   1.91   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96
GDT RMS_ALL_AT   3.55   3.50   3.11   2.05   1.98   1.97   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96

# 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     1.923     0    0.076   0.076     2.912   75.476   75.476
LGA    S     2_A      S     2_A     2.293     0    0.209   0.797     3.835   68.810   61.429
LGA    S     3_A      S     3_A     2.317     0    0.158   0.472     3.836   68.810   61.429
LGA    F     4_A      F     4_A     1.753     0    0.078   0.233     3.766   72.857   60.390
LGA    C     5_A      C     5_A     1.853     0    0.108   0.788     2.632   72.857   70.238
LGA    D     6_A      D     6_A     1.855     0    0.117   1.110     5.989   72.857   55.774
LGA    S     7_A      S     7_A     2.241     0    0.132   0.239     2.589   62.857   63.492
LGA    K     8_A      K     8_A     1.478     0    0.112   0.756     5.590   77.143   66.878
LGA    C     9_A      C     9_A     1.588     0    0.053   0.062     1.860   75.000   77.143
LGA    G    10_A      G    10_A     1.630     0    0.109   0.109     1.658   75.000   75.000
LGA    V    11_A      V    11_A     2.046     0    0.059   0.078     2.356   64.762   64.762
LGA    R    12_A      R    12_A     1.804     0    0.062   1.363     8.176   72.857   52.554
LGA    C    13_A      C    13_A     1.096     0    0.641   0.719     2.476   79.524   80.159
LGA    S    14_A      S    14_A     1.484     0    0.078   0.627     2.038   79.286   75.794
LGA    K    15_A      K    15_A     1.343     0    0.115   0.653     4.291   81.429   67.619
LGA    A    16_A      A    16_A     1.308     0    0.627   0.564     2.819   75.357   76.571
LGA    G    17_A      G    17_A     2.445     0    0.037   0.037     2.841   62.857   62.857
LGA    Y    18_A      Y    18_A     1.932     0    0.302   1.373     7.613   72.976   51.706
LGA    Q    19_A      Q    19_A     1.372     0    0.132   0.991     2.616   85.952   76.032
LGA    E    20_A      E    20_A     1.771     0    0.028   0.762     4.460   72.976   59.048
LGA    R    21_A      R    21_A     2.366     0    0.049   1.150    10.432   66.786   35.584
LGA    C    22_A      C    22_A     1.546     0    0.062   0.085     1.762   75.000   75.714
LGA    L    23_A      L    23_A     1.153     0    0.054   0.291     2.270   79.286   77.202
LGA    K    24_A      K    24_A     2.030     0    0.060   1.127    10.109   66.786   43.439
LGA    Y    25_A      Y    25_A     2.238     0    0.119   0.617     3.664   62.857   61.349
LGA    C    26_A      C    26_A     1.137     0    0.049   0.105     1.366   83.690   84.444
LGA    G    27_A      G    27_A     0.975     0    0.045   0.045     1.529   83.810   83.810
LGA    I    28_A      I    28_A     1.897     0    0.041   0.753     4.992   72.857   61.964
LGA    C    29_A      C    29_A     1.476     0    0.100   0.127     1.931   81.548   78.651
LGA    C    30_A      C    30_A     0.882     0    0.141   0.154     1.229   88.214   90.556
LGA    E    31_A      E    31_A     0.772     0    0.021   0.861     4.047   90.476   76.138
LGA    K    32_A      K    32_A     1.093     0    0.079   0.822     2.021   83.690   79.683
LGA    C    33_A      C    33_A     1.091     0    0.229   0.232     2.052   77.262   80.159
LGA    H    34_A      H    34_A     1.343     0    0.103   1.276     3.271   79.286   70.238
LGA    C    35_A      C    35_A     1.314     0    0.069   0.614     2.420   81.429   77.222
LGA    V    36_A      V    36_A     1.204     0    0.067   0.293     2.288   81.429   76.599
LGA    P    37_A      P    37_A     1.053     0    0.045   0.321     1.372   85.952   86.599
LGA    S    38_A      S    38_A     1.379     0    0.232   0.658     5.127   81.548   69.524
LGA    G    39_A      G    39_A     1.780     0    0.078   0.078     2.605   66.905   66.905
LGA    T    40_A      T    40_A     3.041     0    0.477   0.392     4.187   50.476   51.429
LGA    Y    41_A      Y    41_A     3.222     0    0.152   0.319     4.025   55.476   47.976
LGA    G    42_A      G    42_A     2.630     0    0.631   0.631     4.732   50.714   50.714
LGA    N    43_A      N    43_A     1.261     0    0.197   0.863     4.222   83.690   67.560
LGA    K    44_A      K    44_A     1.248     0    0.054   1.012     8.150   77.143   56.614
LGA    D    45_A      D    45_A     2.136     0    0.089   1.031     3.888   70.833   62.262
LGA    E    46_A      E    46_A     1.509     0    0.126   0.169     2.765   79.405   69.630
LGA    C    47_A      C    47_A     0.860     0    0.106   0.239     2.426   79.524   77.381
LGA    P    48_A      P    48_A     2.230     0    0.237   0.430     2.750   68.810   69.524
LGA    C    49_A      C    49_A     1.842     0    0.107   0.217     2.176   72.976   73.016
LGA    Y    50_A      Y    50_A     1.872     0    0.083   0.811     5.327   72.857   54.563
LGA    R    51_A      R    51_A     1.164     0    0.051   1.247     5.761   83.690   63.939
LGA    D    52_A      D    52_A     0.199     0    0.121   0.789     3.417   92.857   80.179
LGA    L    53_A      L    53_A     1.045     0    0.030   0.744     4.103   83.690   73.869
LGA    K    54_A      K    54_A     1.532     0    0.034   0.977     2.657   70.952   68.519
LGA    N    55_A      N    55_A     2.734     0    0.090   0.254     3.166   55.476   60.119
LGA    S    56_A      S    56_A     4.142     0    0.132   0.563     6.230   37.262   32.937
LGA    K    57_A      K    57_A     3.627     0    0.034   0.775     6.127   45.000   36.243
LGA    G    58_A      G    58_A     2.476     0    0.049   0.049     2.731   64.881   64.881
LGA    N    59_A      N    59_A     0.978     0    0.029   0.906     3.370   90.595   81.071
LGA    P    60_A      P    60_A     1.806     0    0.077   0.330     3.126   75.000   68.503
LGA    K    61_A      K    61_A     2.510     0    0.041   0.970     3.277   57.262   58.307
LGA    C    62_A      C    62_A     3.327     0    0.103   0.527     4.271   48.452   46.825
LGA    P    63_A      P    63_A     3.767     0    0.306   0.291     4.229   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):     1.955          1.977                  2.797           72.496   66.184

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.96    77.778    88.353     3.066

LGA_LOCAL      RMSD:   1.955  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.955  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.955  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.421666 * X  +   0.740170 * Y  +   0.523781 * Z  +  -8.948886
  Y_new =   0.607444 * X  +   0.198283 * Y  +  -0.769217 * Z  +   1.720191
  Z_new =  -0.673208 * X  +   0.642521 * Y  +  -0.366003 * Z  +  -5.939778 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.963998  0.738539  2.088590   [DEG:   55.2330   42.3152  119.6674 ]
ZXZ:  0.597811  1.945507 -0.808718   [DEG:   34.2520  111.4693  -46.3361 ]
 
# END of job
