
#######################################################
#                                                     #
#                        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        1.88     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:    25      14_A - 38_A        0.98     2.40
  LCS_AVERAGE:     30.74

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     11   63   63      4   14   32   48   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H     2_A     H     2_A     13   63   63      4   12   24   49   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     21   63   63      6   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     4_A     D     4_A     21   63   63      7   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     21   63   63      7   16   35   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     21   63   63      7   12   33   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     21   63   63      7   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     21   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     21   63   63      7   19   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     21   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     21   63   63      4   21   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     21   63   63      4   21   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     23   63   63      4   20   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     25   63   63      5   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     25   63   63      3    5   22   47   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     25   63   63      5   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     25   63   63      5   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     25   63   63      4   11   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     25   63   63      5   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     25   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     25   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     25   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     25   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     25   63   63      6   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     25   63   63      6   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     25   63   63      5   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     25   63   63      6   22   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     25   63   63      6   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     25   63   63      6   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     25   63   63      5   17   40   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     25   63   63      4   14   33   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     25   63   63      5   20   40   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     25   63   63      7   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     25   63   63      6   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     25   63   63      7   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   63   63     10   23   43   52   58   60   60   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   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   63   63      5   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   63   63      5   23   41   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   63   63      3    6   13   31   44   54   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   63   63      3    6   13   23   36   50   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     12   63   63      4    4   13   23   37   50   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   63   63      5   17   41   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   63   63      6   20   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   63   63      6   20   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   63   63      5   17   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   63   63      5   19   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     14   63   63      3   19   42   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   63   63     10   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   63   63      9   19   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   63   63      7   18   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   63   63      7   17   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   63   63      3   14   34   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   63   63      5   15   30   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   63   63      5    7   20   31   54   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   63   63      5   14   29   45   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   63   63      5   14   28   48   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   63   63      5   14   34   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   63   63      5   14   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   63   63      5   20   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   63   63      7   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     12   63   63      7   23   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  76.91  (  30.74  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     10     23     43     52     58     60     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  15.87  36.51  68.25  82.54  92.06  95.24  95.24 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.72   1.09   1.26   1.48   1.59   1.59   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   2.34   2.57   2.10   2.02   1.92   1.91   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

# Checking swapping
#   possible swapping detected:  E     8_A      E     8_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  E    44_A      E    44_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     2.474     0    0.084   0.125     3.546   77.381   70.571
LGA    H     2_A      H     2_A     2.156     0    0.018   0.798     6.414   70.952   46.810
LGA    I     3_A      I     3_A     0.340     0    0.086   0.903     2.914   90.595   86.369
LGA    D     4_A      D     4_A     1.358     0    0.054   1.065     3.949   79.405   69.643
LGA    C     5_A      C     5_A     2.030     0    0.081   0.251     2.502   70.833   68.889
LGA    D     6_A      D     6_A     1.648     0    0.020   0.530     3.500   79.405   73.333
LGA    K     7_A      K     7_A     0.368     0    0.087   0.542     2.347   92.857   85.820
LGA    E     8_A      E     8_A     1.100     0    0.061   0.390     1.618   81.548   84.497
LGA    C     9_A      C     9_A     1.461     0    0.078   0.089     1.753   81.429   78.571
LGA    N    10_A      N    10_A     0.781     0    0.123   0.280     1.410   85.952   83.690
LGA    R    11_A      R    11_A     1.524     0    0.030   1.473     5.864   75.000   60.606
LGA    R    12_A      R    12_A     1.471     0    0.018   1.483     6.624   81.429   62.251
LGA    C    13_A      C    13_A     1.166     0    0.253   0.269     3.014   81.548   76.270
LGA    S    14_A      S    14_A     1.055     0    0.069   0.671     3.259   75.476   73.730
LGA    K    15_A      K    15_A     3.101     0    0.152   1.019     4.504   57.262   52.169
LGA    A    16_A      A    16_A     1.903     0    0.053   0.062     2.278   70.833   72.952
LGA    S    17_A      S    17_A     2.190     0    0.032   0.691     4.060   64.762   60.159
LGA    A    18_A      A    18_A     2.117     0    0.069   0.074     2.269   64.762   64.762
LGA    H    19_A      H    19_A     1.820     0    0.199   1.185     3.609   68.929   65.238
LGA    D    20_A      D    20_A     1.429     0    0.194   0.216     2.123   81.429   77.202
LGA    R    21_A      R    21_A     1.643     0    0.077   1.287     8.309   77.143   50.087
LGA    C    22_A      C    22_A     1.150     0    0.082   0.129     1.454   83.690   84.444
LGA    L    23_A      L    23_A     1.022     0    0.065   0.166     1.894   85.952   81.548
LGA    K    24_A      K    24_A     2.252     0    0.091   0.424     5.017   66.786   54.339
LGA    Y    25_A      Y    25_A     2.177     0    0.023   0.654     3.174   64.762   62.976
LGA    C    26_A      C    26_A     1.705     0    0.105   0.202     1.926   72.857   74.286
LGA    G    27_A      G    27_A     1.790     0    0.169   0.169     2.705   66.905   66.905
LGA    I    28_A      I    28_A     1.777     0    0.105   0.704     4.594   72.857   64.643
LGA    C    29_A      C    29_A     1.682     0    0.053   0.698     1.687   75.000   75.714
LGA    C    30_A      C    30_A     1.570     0    0.053   0.074     2.139   77.143   74.365
LGA    E    31_A      E    31_A     1.635     0    0.037   0.410     3.678   75.000   63.810
LGA    K    32_A      K    32_A     1.264     0    0.063   1.119     6.906   81.429   60.794
LGA    C    33_A      C    33_A     0.880     0    0.605   0.524     3.641   74.286   73.889
LGA    N    34_A      N    34_A     1.028     0    0.217   0.435     3.191   86.071   74.702
LGA    C    35_A      C    35_A     1.061     0    0.020   0.390     1.721   85.952   81.587
LGA    V    36_A      V    36_A     0.574     0    0.145   0.164     1.521   90.476   87.959
LGA    P    37_A      P    37_A     0.347     0    0.070   0.319     0.664   95.238   95.918
LGA    P    38_A      P    38_A     1.403     0    0.045   0.097     1.648   81.429   80.204
LGA    G    39_A      G    39_A     2.137     0    0.152   0.152     2.887   62.976   62.976
LGA    T    40_A      T    40_A     4.551     0    0.577   0.537     5.763   34.762   31.156
LGA    Y    41_A      Y    41_A     4.713     0    0.150   1.036     6.971   32.857   25.675
LGA    G    42_A      G    42_A     4.456     0    0.588   0.588     5.565   31.786   31.786
LGA    N    43_A      N    43_A     1.238     0    0.304   0.331     1.995   77.143   80.417
LGA    E    44_A      E    44_A     0.369     0    0.128   0.633     2.951  100.000   81.799
LGA    D    45_A      D    45_A     0.981     0    0.094   1.065     5.735   88.214   67.024
LGA    S    46_A      S    46_A     1.284     0    0.125   0.229     1.640   79.286   80.000
LGA    C    47_A      C    47_A     0.734     0    0.081   0.333     1.639   92.857   87.619
LGA    P    48_A      P    48_A     0.466     0    0.082   0.337     1.188   92.976   93.265
LGA    C    49_A      C    49_A     1.641     0    0.047   0.233     2.940   75.119   70.397
LGA    Y    50_A      Y    50_A     0.744     0    0.119   0.299     2.217   90.476   83.889
LGA    A    51_A      A    51_A     0.848     0    0.141   0.143     1.312   88.214   88.667
LGA    N    52_A      N    52_A     1.038     0    0.090   0.106     2.088   88.214   80.595
LGA    L    53_A      L    53_A     1.094     0    0.081   0.728     2.305   79.286   79.405
LGA    K    54_A      K    54_A     1.449     0    0.103   1.274     5.024   81.429   69.153
LGA    N    55_A      N    55_A     1.930     0    0.050   0.096     2.755   67.143   70.060
LGA    S    56_A      S    56_A     3.874     0    0.151   0.677     6.498   42.024   36.111
LGA    K    57_A      K    57_A     2.744     0    0.180   0.550     4.911   57.143   52.804
LGA    G    58_A      G    58_A     2.556     0    0.144   0.144     2.556   60.952   60.952
LGA    G    59_A      G    59_A     1.538     0    0.023   0.023     1.824   79.405   79.405
LGA    H    60_A      H    60_A     1.397     0    0.175   1.012     5.965   81.429   58.476
LGA    K    61_A      K    61_A     1.292     0    0.035   0.752     1.824   81.429   83.492
LGA    C    62_A      C    62_A     1.670     0    0.044   0.078     2.145   77.143   74.365
LGA    P    63_A      P    63_A     1.555     0    0.331   0.487     2.006   70.833   71.701

# 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):     1.878          1.901                  2.478           75.522   70.205

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.88    79.762    90.309     3.184

LGA_LOCAL      RMSD:   1.878  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.878  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.878  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.693322 * X  +  -0.188021 * Y  +  -0.695667 * Z  + -15.444896
  Y_new =  -0.720625 * X  +   0.178311 * Y  +   0.670003 * Z  +   0.555881
  Z_new =  -0.001930 * X  +   0.965843 * Y  +  -0.259120 * Z  + -13.125772 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.336887  0.001930  1.832907   [DEG: -133.8938    0.1106  105.0179 ]
ZXZ: -2.337405  1.832907 -0.001998   [DEG: -133.9234  105.0178   -0.1145 ]
 
# END of job
