
#######################################################
#                                                     #
#                        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 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  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        1.84     1.84
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.84     1.84
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       7_A - 35_A        1.00     2.46
  LCS_AVERAGE:     36.43

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     A     1_A     A     1_A     26   63   63      6   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     26   63   63      5   26   40   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     26   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     26   63   63      5   21   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     26   63   63      7   21   40   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     26   63   63      7   16   34   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     29   63   63      7   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     29   63   63     10   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     29   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     29   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     29   63   63      5   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     29   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     29   63   63      5   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     29   63   63     11   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     29   63   63      3   17   40   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     29   63   63     11   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     29   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     29   63   63      4   24   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     29   63   63     10   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     29   63   63     11   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     29   63   63     11   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     29   63   63     11   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     29   63   63     11   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     29   63   63      6   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     29   63   63      6   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     29   63   63      5   21   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     29   63   63      4   18   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     29   63   63      5   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     29   63   63      5   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     29   63   63      6   18   40   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     29   63   63      5   18   35   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     29   63   63      5   21   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     29   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     29   63   63      5   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     29   63   63      6   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     26   63   63     11   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     26   63   63     11   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     26   63   63     11   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     26   63   63      7   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      9   63   63      3    6   11   23   42   57   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      9   63   63      3    6   11   17   26   42   50   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A      9   63   63      3    4   11   14   24   39   48   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A      7   63   63      3    7   26   50   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     12   63   63      3    8   33   53   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     14   63   63      5   24   42   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     14   63   63      4   21   42   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     16   63   63     10   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     16   63   63      4   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     16   63   63      3   19   40   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     16   63   63      3   21   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     16   63   63      3   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     16   63   63      5   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     16   63   63     11   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     16   63   63      6   23   42   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     16   63   63      6   19   42   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     16   63   63      6   16   31   47   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     16   63   63      6   18   36   54   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     16   63   63      4   18   37   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     16   63   63     11   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     16   63   63      5   25   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     16   63   63      4   20   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     16   63   63      4   26   43   55   59   59   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     15   63   63      6    9   16   30   51   56   60   61   62   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  78.81  (  36.43  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     26     43     55     59     59     60     61     62     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  41.27  68.25  87.30  93.65  93.65  95.24  96.83  98.41 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.39   0.71   1.03   1.26   1.41   1.41   1.49   1.58   1.78   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84
GDT RMS_ALL_AT   1.98   2.58   2.01   1.91   1.87   1.87   1.88   1.86   1.85   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84

# Checking swapping
#   possible swapping detected:  D     4_A      D     4_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  D    45_A      D    45_A
#   possible swapping detected:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     1.393     0    0.066   0.105     2.098   72.976   74.667
LGA    H     2_A      H     2_A     1.940     0    0.665   1.142     8.180   63.452   42.524
LGA    I     3_A      I     3_A     1.457     0    0.166   1.531     4.058   77.143   64.702
LGA    D     4_A      D     4_A     1.600     0    0.050   1.275     4.269   75.000   68.452
LGA    C     5_A      C     5_A     1.851     0    0.020   0.156     2.176   72.857   71.508
LGA    D     6_A      D     6_A     1.813     0    0.014   0.652     3.709   77.143   69.286
LGA    K     7_A      K     7_A     0.691     0    0.055   1.259     4.520   92.976   79.206
LGA    E     8_A      E     8_A     0.810     0    0.047   0.693     4.135   88.214   72.804
LGA    C     9_A      C     9_A     1.252     0    0.039   0.075     1.679   81.429   80.000
LGA    N    10_A      N    10_A     0.943     0    0.073   0.648     2.405   88.214   82.738
LGA    R    11_A      R    11_A     1.443     0    0.029   1.210     8.869   81.429   46.970
LGA    R    12_A      R    12_A     1.281     0    0.030   0.821     2.588   81.429   73.896
LGA    C    13_A      C    13_A     1.089     0    0.207   0.240     3.262   88.333   79.365
LGA    S    14_A      S    14_A     0.388     0    0.066   0.656     2.280   90.833   88.016
LGA    K    15_A      K    15_A     1.917     0    0.141   1.017     4.242   77.143   68.148
LGA    A    16_A      A    16_A     0.631     0    0.032   0.035     1.330   88.214   88.667
LGA    S    17_A      S    17_A     1.106     0    0.147   0.657     2.858   81.548   77.460
LGA    A    18_A      A    18_A     1.208     0    0.028   0.031     1.500   83.690   81.524
LGA    H    19_A      H    19_A     1.090     0    0.137   0.403     1.969   81.548   81.571
LGA    D    20_A      D    20_A     0.985     0    0.128   0.909     4.069   90.476   72.619
LGA    R    21_A      R    21_A     0.822     0    0.068   1.055     2.477   92.857   82.597
LGA    C    22_A      C    22_A     0.537     0    0.105   0.173     0.829   92.857   93.651
LGA    L    23_A      L    23_A     0.755     0    0.133   0.220     1.778   92.857   86.071
LGA    K    24_A      K    24_A     1.805     0    0.100   0.940     3.241   72.857   72.328
LGA    Y    25_A      Y    25_A     1.863     0    0.008   0.739     2.847   70.833   72.421
LGA    C    26_A      C    26_A     1.598     0    0.073   0.184     1.909   72.857   74.286
LGA    G    27_A      G    27_A     1.699     0    0.179   0.179     2.691   68.929   68.929
LGA    I    28_A      I    28_A     1.413     0    0.040   0.685     3.630   81.429   73.452
LGA    C    29_A      C    29_A     1.551     0    0.093   0.172     2.111   77.143   74.365
LGA    C    30_A      C    30_A     1.782     0    0.029   0.052     2.267   72.857   71.508
LGA    E    31_A      E    31_A     2.009     0    0.021   0.630     3.579   70.833   60.952
LGA    K    32_A      K    32_A     1.364     0    0.053   0.863     5.314   81.429   69.101
LGA    C    33_A      C    33_A     0.853     0    0.609   0.528     3.542   74.286   72.619
LGA    N    34_A      N    34_A     1.018     0    0.219   0.322     3.652   90.595   73.214
LGA    C    35_A      C    35_A     1.005     0    0.053   0.882     1.606   88.214   83.095
LGA    V    36_A      V    36_A     0.738     0    0.205   0.243     1.578   90.476   86.667
LGA    P    37_A      P    37_A     0.613     0    0.011   0.114     1.202   95.238   91.905
LGA    P    38_A      P    38_A     0.640     0    0.030   0.103     0.788   92.857   91.837
LGA    G    39_A      G    39_A     1.116     0    0.144   0.144     2.673   73.452   73.452
LGA    T    40_A      T    40_A     4.435     0    0.602   0.541     6.425   34.405   34.082
LGA    Y    41_A      Y    41_A     5.655     0    0.205   1.120    10.812   27.619   12.302
LGA    G    42_A      G    42_A     5.770     0    0.481   0.481     6.112   22.857   22.857
LGA    N    43_A      N    43_A     3.042     0    0.375   0.325     3.640   51.905   58.393
LGA    E    44_A      E    44_A     2.365     0    0.563   1.092     4.333   57.857   55.132
LGA    D    45_A      D    45_A     0.833     0    0.412   0.801     4.498   79.524   67.083
LGA    S    46_A      S    46_A     1.063     0    0.255   0.409     1.844   83.690   81.508
LGA    C    47_A      C    47_A     0.723     0    0.145   0.452     2.515   90.595   83.492
LGA    P    48_A      P    48_A     1.154     0    0.014   0.106     1.571   85.952   82.789
LGA    C    49_A      C    49_A     1.515     0    0.074   0.238     3.291   75.238   69.286
LGA    Y    50_A      Y    50_A     1.148     0    0.044   1.220     8.657   83.690   53.016
LGA    A    51_A      A    51_A     1.099     0    0.174   0.187     1.976   79.286   81.524
LGA    N    52_A      N    52_A     0.885     0    0.203   0.194     2.058   95.238   83.095
LGA    L    53_A      L    53_A     0.559     0    0.081   0.946     2.465   90.476   85.000
LGA    K    54_A      K    54_A     0.940     0    0.062   1.272     4.558   88.214   77.302
LGA    N    55_A      N    55_A     1.261     0    0.051   0.868     5.143   77.381   63.810
LGA    S    56_A      S    56_A     2.852     0    0.131   0.663     5.092   55.595   49.762
LGA    K    57_A      K    57_A     2.186     0    0.184   0.566     5.214   64.762   56.402
LGA    G    58_A      G    58_A     1.898     0    0.615   0.615     3.956   65.476   65.476
LGA    G    59_A      G    59_A     0.600     0    0.288   0.288     3.002   78.095   78.095
LGA    H    60_A      H    60_A     0.980     0    0.125   1.435     6.963   90.476   59.143
LGA    K    61_A      K    61_A     1.590     0    0.032   0.776     2.134   75.000   78.730
LGA    C    62_A      C    62_A     1.963     0    0.451   0.907     3.377   63.214   64.048
LGA    P    63_A      P    63_A     3.872     0    0.356   0.347     6.299   53.810   40.748

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     1.845          1.905                  2.711           77.099   70.471

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     61    1.58    81.349    90.783     3.623

LGA_LOCAL      RMSD:   1.584  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.861  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.845  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.112673 * X  +  -0.926139 * Y  +   0.359960 * Z  +   4.927181
  Y_new =  -0.125132 * X  +   0.346158 * Y  +   0.929794 * Z  +   2.201718
  Z_new =  -0.985721 * X  +  -0.149805 * Y  +  -0.076887 * Z  +  -1.281085 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.837743  1.401606 -2.044986   [DEG:  -47.9991   80.3061 -117.1690 ]
ZXZ:  2.772221  1.647759 -1.721618   [DEG:  158.8366   94.4097  -98.6414 ]
 
# END of job
