
#######################################################
#                                                     #
#                        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        1.87     1.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63       1_A - 63_A        1.87     1.87
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      13_A - 39_A        0.99     2.51
  LCS_AVERAGE:     32.00

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     12   63   63      4   13   23   46   58   59   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      6   14   30   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I     3_A     I     3_A     15   63   63      6   24   44   52   58   59   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   22   44   52   58   59   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   15   36   52   58   59   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   14   33   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     7_A     K     7_A     23   63   63      7   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E     8_A     E     8_A     23   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     23   63   63      7   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    10_A     N    10_A     23   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    11_A     R    11_A     23   63   63      5   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     24   63   63      5   22   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     27   63   63      4   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     27   63   63      3    5   24   44   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     27   63   63      4   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    17_A     S    17_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    18_A     A    18_A     27   63   63      4   10   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    19_A     H    19_A     27   63   63      4   22   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    20_A     D    20_A     27   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     27   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     27   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     27   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     27   63   63      5   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     27   63   63      7   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     27   63   63      5   21   43   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     27   63   63      4   13   36   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     27   63   63      4   21   42   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     27   63   63      7   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    34_A     N    34_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     27   63   63      6   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     27   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     27   63   63      9   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    38_A     P    38_A     27   63   63      6   24   44   52   58   59   60   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   24   41   52   58   59   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   14   32   44   54   60   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    7   15   26   40   52   60   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    5   15   26   42   52   60   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   44   52   58   59   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      8   21   44   52   58   59   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      8   21   44   52   58   59   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   18   44   52   58   59   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      8   21   44   52   58   59   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      9   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   63   63      4   21   38   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     13   63   63      9   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    51_A     A    51_A     13   63   63      9   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    52_A     N    52_A     13   63   63      5   21   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     13   63   63      5   18   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     13   63   63      4   13   34   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     13   63   63      5   15   30   51   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     13   63   63      5    9   20   32   55   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     13   63   63      5   11   30   43   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     13   63   63      5   11   30   50   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    59_A     G    59_A     13   63   63      5   13   33   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    60_A     H    60_A     13   63   63      4   15   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     13   63   63      4   17   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     12   63   63      7   24   44   52   58   59   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   24   44   52   58   59   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.33  (  32.00  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      9     24     44     52     58     59     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  14.29  38.10  69.84  82.54  92.06  93.65  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   0.73   1.11   1.26   1.49   1.54   1.61   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87
GDT RMS_ALL_AT   2.34   2.61   2.09   2.02   1.91   1.90   1.90   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87   1.87

# 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     2.542     0    0.101   0.149     3.347   71.071   66.857
LGA    H     2_A      H     2_A     1.852     0    0.018   1.143     4.238   75.119   61.714
LGA    I     3_A      I     3_A     0.193     0    0.061   0.912     2.884   90.595   85.238
LGA    D     4_A      D     4_A     1.252     0    0.070   1.065     3.943   83.690   71.786
LGA    C     5_A      C     5_A     2.014     0    0.086   0.238     2.519   70.833   67.540
LGA    D     6_A      D     6_A     1.619     0    0.018   0.562     3.457   79.405   73.333
LGA    K     7_A      K     7_A     0.426     0    0.086   0.533     2.540   92.857   84.974
LGA    E     8_A      E     8_A     1.087     0    0.061   0.425     1.585   81.548   84.497
LGA    C     9_A      C     9_A     1.458     0    0.080   0.092     1.787   81.429   78.571
LGA    N    10_A      N    10_A     0.736     0    0.117   0.330     1.507   88.214   84.881
LGA    R    11_A      R    11_A     1.490     0    0.032   1.475     5.783   79.286   62.771
LGA    R    12_A      R    12_A     1.422     0    0.023   1.422     6.575   81.429   63.030
LGA    C    13_A      C    13_A     1.139     0    0.248   0.266     3.015   81.548   76.270
LGA    S    14_A      S    14_A     0.985     0    0.076   0.667     3.165   79.643   76.508
LGA    K    15_A      K    15_A     2.958     0    0.147   1.011     4.350   59.048   55.926
LGA    A    16_A      A    16_A     1.817     0    0.055   0.063     2.149   70.833   72.952
LGA    S    17_A      S    17_A     2.154     0    0.028   0.690     4.054   66.786   61.508
LGA    A    18_A      A    18_A     2.196     0    0.043   0.049     2.355   64.762   64.762
LGA    H    19_A      H    19_A     1.880     0    0.203   1.163     3.358   66.905   65.810
LGA    D    20_A      D    20_A     1.576     0    0.198   0.228     2.293   75.000   70.893
LGA    R    21_A      R    21_A     1.769     0    0.069   0.964     4.933   77.143   56.753
LGA    C    22_A      C    22_A     1.207     0    0.080   0.123     1.532   79.286   81.508
LGA    L    23_A      L    23_A     1.069     0    0.062   0.164     1.841   85.952   81.548
LGA    K    24_A      K    24_A     2.313     0    0.088   0.430     5.298   66.786   53.016
LGA    Y    25_A      Y    25_A     2.200     0    0.020   0.718     3.332   64.762   62.976
LGA    C    26_A      C    26_A     1.678     0    0.096   0.197     1.899   72.857   74.286
LGA    G    27_A      G    27_A     1.760     0    0.195   0.195     2.764   68.929   68.929
LGA    I    28_A      I    28_A     1.729     0    0.102   0.722     4.572   72.857   64.643
LGA    C    29_A      C    29_A     1.637     0    0.046   0.673     1.665   75.000   75.714
LGA    C    30_A      C    30_A     1.483     0    0.035   0.054     2.024   79.286   75.794
LGA    E    31_A      E    31_A     1.507     0    0.042   0.708     4.100   77.143   64.974
LGA    K    32_A      K    32_A     1.211     0    0.051   1.052     6.304   81.429   60.688
LGA    C    33_A      C    33_A     0.853     0    0.601   0.525     3.561   74.286   72.619
LGA    N    34_A      N    34_A     1.026     0    0.226   0.383     3.078   86.071   74.702
LGA    C    35_A      C    35_A     1.039     0    0.027   0.376     1.744   88.214   83.095
LGA    V    36_A      V    36_A     0.585     0    0.146   0.173     1.547   90.476   87.959
LGA    P    37_A      P    37_A     0.332     0    0.057   0.311     0.731   95.238   95.918
LGA    P    38_A      P    38_A     1.355     0    0.055   0.108     1.519   81.429   82.789
LGA    G    39_A      G    39_A     2.115     0    0.118   0.118     3.087   61.190   61.190
LGA    T    40_A      T    40_A     4.416     0    0.560   0.558     5.490   36.190   32.653
LGA    Y    41_A      Y    41_A     4.540     0    0.120   1.256     5.102   34.286   32.024
LGA    G    42_A      G    42_A     4.258     0    0.600   0.600     5.356   35.952   35.952
LGA    N    43_A      N    43_A     1.121     0    0.289   0.340     1.818   79.286   81.488
LGA    E    44_A      E    44_A     0.348     0    0.128   0.688     2.947  100.000   81.799
LGA    D    45_A      D    45_A     0.996     0    0.100   1.091     5.708   85.952   66.667
LGA    S    46_A      S    46_A     1.353     0    0.156   0.165     1.816   79.286   80.000
LGA    C    47_A      C    47_A     0.750     0    0.084   0.344     1.667   92.857   87.619
LGA    P    48_A      P    48_A     0.460     0    0.068   0.337     1.295   92.976   93.265
LGA    C    49_A      C    49_A     1.810     0    0.037   0.237     3.156   72.976   67.778
LGA    Y    50_A      Y    50_A     0.932     0    0.108   0.361     2.554   88.214   82.500
LGA    A    51_A      A    51_A     0.970     0    0.129   0.131     1.472   85.952   86.857
LGA    N    52_A      N    52_A     1.191     0    0.081   0.155     2.388   85.952   78.393
LGA    L    53_A      L    53_A     1.096     0    0.081   0.613     2.229   81.429   80.476
LGA    K    54_A      K    54_A     1.447     0    0.100   1.254     4.983   81.429   68.836
LGA    N    55_A      N    55_A     1.993     0    0.051   0.122     2.818   67.143   70.060
LGA    S    56_A      S    56_A     3.918     0    0.167   0.677     6.444   42.024   36.111
LGA    K    57_A      K    57_A     2.899     0    0.170   0.565     5.310   57.143   49.894
LGA    G    58_A      G    58_A     2.622     0    0.138   0.138     2.622   60.952   60.952
LGA    G    59_A      G    59_A     1.556     0    0.018   0.018     1.874   79.405   79.405
LGA    H    60_A      H    60_A     1.307     0    0.172   1.039     5.913   83.690   59.381
LGA    K    61_A      K    61_A     1.357     0    0.040   0.747     1.824   77.143   81.587
LGA    C    62_A      C    62_A     1.844     0    0.047   0.082     2.265   75.000   71.587
LGA    P    63_A      P    63_A     1.806     0    0.322   0.462     2.305   70.833   70.544

# 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):     1.867          1.897                  2.367           75.625   70.552

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.87    80.159    90.455     3.203

LGA_LOCAL      RMSD:   1.867  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.867  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.867  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.649358 * X  +  -0.138916 * Y  +   0.747687 * Z  + -11.189173
  Y_new =  -0.192625 * X  +  -0.921068 * Y  +  -0.338423 * Z  +   0.713620
  Z_new =   0.735683 * X  +  -0.363781 * Y  +   0.571344 * Z  +  -6.284967 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.853222 -0.826674 -0.566976   [DEG: -163.4776  -47.3649  -32.4853 ]
ZXZ:  1.145761  0.962653  2.030018   [DEG:   65.6473   55.1560  116.3115 ]
 
# END of job
