
#######################################################
#                                                     #
#                        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     2.50
  LCS_AVERAGE:     32.05

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      5   13   23   46   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      6   14   30   52   58   60   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   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   15   34   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   14   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     23   63   63      7   24   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     23   63   63     11   24   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     23   63   63      7   17   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     23   63   63     11   24   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     23   63   63      5   22   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     24   63   63      4   22   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     27   63   63      4   22   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     27   63   63      5   24   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     27   63   63      3    5   23   44   58   60   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      6   24   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     27   63   63      6   24   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     27   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     27   63   63      4   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     27   63   63     11   24   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     27   63   63     11   24   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     27   63   63     11   24   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     27   63   63     11   24   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     27   63   63      6   24   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     27   63   63      6   24   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     27   63   63      5   24   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     27   63   63      6   24   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     27   63   63      7   24   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     27   63   63      6   24   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     27   63   63      5   21   43   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     27   63   63      4   13   37   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     27   63   63      4   21   41   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     27   63   63      7   24   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     27   63   63      6   24   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     27   63   63      6   24   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     27   63   63     11   24   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     27   63   63     11   24   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     27   63   63     11   24   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     27   63   63      5   24   42   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   14   33   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   14   26   39   51   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    4   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   43   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      8   19   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      8   19   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      8   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     11   21   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     13   63   63      4   15   35   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     13   63   63     11   19   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     13   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     13   63   63      5   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     13   63   63      5   18   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     13   63   63      4   13   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     13   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     13   63   63      5    8   20   32   55   60   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   60   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   60   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   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     13   63   63      4   15   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     13   63   63      4   19   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     13   63   63      7   24   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     13   63   63      7   24   43   52   58   60   60   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  77.35  (  32.05  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     24     43     52     58     60     60     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  38.10  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    0.38   0.72   1.08   1.26   1.48   1.61   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   2.42   2.61   2.12   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     2.528     0    0.090   0.142     3.347   71.071   66.857
LGA    H     2_A      H     2_A     1.865     0    0.016   1.156     4.284   75.119   61.095
LGA    I     3_A      I     3_A     0.201     0    0.105   0.910     2.860   90.595   85.238
LGA    D     4_A      D     4_A     1.221     0    0.079   1.055     3.885   83.690   71.786
LGA    C     5_A      C     5_A     2.036     0    0.108   0.249     2.549   70.833   68.889
LGA    D     6_A      D     6_A     1.608     0    0.015   0.572     3.426   77.143   72.202
LGA    K     7_A      K     7_A     0.420     0    0.087   0.539     2.580   92.857   84.974
LGA    E     8_A      E     8_A     1.059     0    0.062   0.417     1.571   81.548   84.497
LGA    C     9_A      C     9_A     1.461     0    0.078   0.108     1.739   81.429   78.571
LGA    N    10_A      N    10_A     0.749     0    0.101   0.316     1.516   88.214   84.881
LGA    R    11_A      R    11_A     1.503     0    0.044   1.493     5.869   75.000   60.606
LGA    R    12_A      R    12_A     1.431     0    0.041   1.419     6.546   81.429   63.030
LGA    C    13_A      C    13_A     1.144     0    0.204   0.239     2.993   83.690   78.889
LGA    S    14_A      S    14_A     1.044     0    0.068   0.647     3.184   77.381   75.000
LGA    K    15_A      K    15_A     2.942     0    0.128   1.010     4.379   59.048   55.926
LGA    A    16_A      A    16_A     1.806     0    0.056   0.071     2.153   70.833   72.952
LGA    S    17_A      S    17_A     2.144     0    0.038   0.689     4.101   66.786   61.508
LGA    A    18_A      A    18_A     2.215     0    0.068   0.064     2.347   64.762   64.762
LGA    H    19_A      H    19_A     1.900     0    0.179   1.163     3.422   68.929   65.810
LGA    D    20_A      D    20_A     1.561     0    0.172   0.207     2.374   77.143   71.964
LGA    R    21_A      R    21_A     1.727     0    0.075   0.982     4.981   77.143   56.753
LGA    C    22_A      C    22_A     1.219     0    0.120   0.161     1.538   79.286   81.508
LGA    L    23_A      L    23_A     1.087     0    0.089   0.194     1.846   85.952   81.548
LGA    K    24_A      K    24_A     2.273     0    0.083   0.440     5.303   66.786   53.016
LGA    Y    25_A      Y    25_A     2.209     0    0.016   0.725     3.348   64.762   62.976
LGA    C    26_A      C    26_A     1.668     0    0.072   0.186     1.903   72.857   74.286
LGA    G    27_A      G    27_A     1.756     0    0.191   0.191     2.709   68.929   68.929
LGA    I    28_A      I    28_A     1.695     0    0.077   0.720     4.548   72.857   64.643
LGA    C    29_A      C    29_A     1.615     0    0.055   0.684     1.689   75.000   75.714
LGA    C    30_A      C    30_A     1.482     0    0.040   0.057     2.047   79.286   75.794
LGA    E    31_A      E    31_A     1.517     0    0.047   0.706     4.069   77.143   64.974
LGA    K    32_A      K    32_A     1.234     0    0.052   1.041     6.315   81.429   60.688
LGA    C    33_A      C    33_A     0.844     0    0.588   0.523     3.571   74.286   72.619
LGA    N    34_A      N    34_A     1.018     0    0.244   0.391     3.067   86.071   74.702
LGA    C    35_A      C    35_A     1.057     0    0.037   0.369     1.714   88.214   84.524
LGA    V    36_A      V    36_A     0.609     0    0.169   0.178     1.542   90.476   87.959
LGA    P    37_A      P    37_A     0.334     0    0.053   0.322     0.791   95.238   95.918
LGA    P    38_A      P    38_A     1.334     0    0.063   0.103     1.492   81.429   84.014
LGA    G    39_A      G    39_A     2.077     0    0.130   0.130     2.933   62.976   62.976
LGA    T    40_A      T    40_A     4.409     0    0.542   0.547     5.440   36.190   33.469
LGA    Y    41_A      Y    41_A     4.573     0    0.119   1.255     5.120   34.286   32.024
LGA    G    42_A      G    42_A     4.304     0    0.590   0.590     5.419   34.524   34.524
LGA    N    43_A      N    43_A     1.135     0    0.296   0.341     1.808   77.143   80.417
LGA    E    44_A      E    44_A     0.327     0    0.145   0.713     2.991  100.000   81.799
LGA    D    45_A      D    45_A     0.977     0    0.093   1.094     5.671   88.214   67.024
LGA    S    46_A      S    46_A     1.335     0    0.123   0.154     1.686   79.286   80.000
LGA    C    47_A      C    47_A     0.725     0    0.059   0.337     1.646   92.857   87.619
LGA    P    48_A      P    48_A     0.428     0    0.051   0.334     1.335   92.976   93.265
LGA    C    49_A      C    49_A     1.822     0    0.033   0.228     3.116   72.976   67.778
LGA    Y    50_A      Y    50_A     0.924     0    0.075   0.349     2.766   88.214   81.825
LGA    A    51_A      A    51_A     0.951     0    0.149   0.162     1.519   83.810   85.143
LGA    N    52_A      N    52_A     1.198     0    0.099   0.165     2.401   85.952   78.393
LGA    L    53_A      L    53_A     1.088     0    0.081   0.607     2.241   81.429   80.476
LGA    K    54_A      K    54_A     1.395     0    0.087   1.238     4.959   81.429   69.735
LGA    N    55_A      N    55_A     1.971     0    0.041   0.133     2.794   67.143   70.060
LGA    S    56_A      S    56_A     3.914     0    0.169   0.674     6.505   40.714   34.603
LGA    K    57_A      K    57_A     2.929     0    0.161   0.565     5.316   55.357   49.101
LGA    G    58_A      G    58_A     2.653     0    0.135   0.135     2.653   60.952   60.952
LGA    G    59_A      G    59_A     1.582     0    0.020   0.020     1.891   79.405   79.405
LGA    H    60_A      H    60_A     1.352     0    0.163   1.029     5.901   83.690   59.381
LGA    K    61_A      K    61_A     1.334     0    0.057   0.740     1.819   77.143   81.587
LGA    C    62_A      C    62_A     1.816     0    0.041   0.056     2.215   75.000   71.587
LGA    P    63_A      P    63_A     1.889     0    0.188   0.306     2.177   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):     1.869          1.895                  2.369           75.510   70.535

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    1.87    80.159    90.434     3.200

LGA_LOCAL      RMSD:   1.869  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.869  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   1.869  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.649677 * X  +  -0.139659 * Y  +   0.747272 * Z  + -11.187643
  Y_new =  -0.191960 * X  +  -0.920989 * Y  +  -0.339014 * Z  +   0.711060
  Z_new =   0.735575 * X  +  -0.363696 * Y  +   0.571536 * Z  +  -6.283364 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.854297 -0.826516 -0.566718   [DEG: -163.5392  -47.3559  -32.4706 ]
ZXZ:  1.144895  0.962419  2.029984   [DEG:   65.5977   55.1426  116.3095 ]
 
# END of job
