
#######################################################
#                                                     #
#                        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   60 (  451),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        2.04     2.04
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    59       1_A - 59_A        1.99     2.04
  LCS_AVERAGE:     97.75

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      26_A - 60_A        0.86     2.49
  LCS_AVERAGE:     46.08

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     D     1_A     D     1_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     20   59   60      9   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     20   59   60      9   39   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     20   59   60      7   27   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     20   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     20   59   60     19   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     20   59   60      7   39   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     20   59   60      8   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     20   59   60     10   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     20   59   60      8   27   37   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     20   59   60      8   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     20   59   60     12   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     20   59   60      7   21   47   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     20   59   60     12   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     20   59   60     10   33   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     20   59   60      7   18   41   52   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A      3   59   60      3    3    6    9   18   24   29   42   55   58   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      3   59   60      3    3    4    5   17   23   34   40   55   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      4   59   60      3    3    6   13   22   31   49   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      4   59   60      3    3    4    4    6   15   28   42   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     35   59   60     19   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     35   59   60     23   37   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     35   59   60     23   34   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     35   59   60     23   34   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     35   59   60     23   37   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     35   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     35   59   60     11   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     35   59   60     19   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     35   59   60     21   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     35   59   60     13   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     35   59   60     12   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     35   59   60     12   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     35   59   60     20   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     35   59   60     17   38   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     35   59   60     13   39   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     35   59   60     23   40   50   54   55   55   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     35   38   60      3    4   16   25   39   53   56   57   58   59   60   60   60   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  81.28  (  46.08   97.75  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     23     40     50     54     55     55     56     57     58     59     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  38.33  66.67  83.33  90.00  91.67  91.67  93.33  95.00  96.67  98.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.63   0.80   0.90   1.00   1.00   1.17   1.46   1.63   1.83   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04
GDT RMS_ALL_AT   2.55   2.38   2.34   2.30   2.23   2.23   2.19   2.11   2.08   2.05   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04

# Checking swapping
#   possible swapping detected:  D     8_A      D     8_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     1.189     0    0.497   1.327     7.191   81.548   54.643
LGA    D     2_A      D     2_A     0.881     0    0.061   0.198     1.061   85.952   90.595
LGA    K     3_A      K     3_A     1.043     0    0.024   0.575     1.360   83.690   82.434
LGA    A     4_A      A     4_A     1.105     0    0.061   0.062     1.261   83.690   83.238
LGA    A     5_A      A     5_A     1.070     0    0.059   0.069     1.104   81.429   81.429
LGA    C     6_A      C     6_A     1.238     0    0.014   0.254     2.445   81.429   78.651
LGA    A     7_A      A     7_A     0.869     0    0.031   0.034     0.979   90.476   90.476
LGA    D     8_A      D     8_A     0.753     0    0.096   0.819     3.905   90.476   75.357
LGA    G     9_A      G     9_A     1.508     0    0.037   0.037     1.508   79.286   79.286
LGA    I    10_A      I    10_A     0.549     0    0.027   0.150     1.522   95.238   89.524
LGA    A    11_A      A    11_A     0.619     0    0.011   0.014     1.237   90.595   90.571
LGA    A    12_A      A    12_A     1.392     0    0.026   0.024     1.704   79.286   78.000
LGA    V    13_A      V    13_A     1.083     0    0.038   0.064     1.515   83.690   84.082
LGA    K    14_A      K    14_A     1.188     0    0.009   0.822     2.184   79.405   76.772
LGA    A    15_A      A    15_A     1.977     0    0.029   0.035     2.139   72.857   71.238
LGA    R    16_A      R    16_A     1.453     0    0.039   1.497     8.512   83.810   54.848
LGA    V    17_A      V    17_A     0.671     0    0.035   0.840     1.950   85.952   84.082
LGA    E    18_A      E    18_A     1.583     0    0.049   0.873     4.733   79.286   62.751
LGA    K    19_A      K    19_A     0.911     0    0.103   1.024     3.379   90.595   80.370
LGA    L    20_A      L    20_A     0.773     0    0.041   0.175     2.401   81.667   76.310
LGA    A    21_A      A    21_A     2.528     0    0.703   0.635     3.837   55.833   60.952
LGA    P    22_A      P    22_A     7.893     0    0.419   0.693    10.610    8.571    5.918
LGA    E    23_A      E    23_A     7.057     0    0.670   1.205    11.137   20.476    9.947
LGA    A    24_A      A    24_A     6.447     0    0.261   0.280     8.185   17.262   14.762
LGA    V    25_A      V    25_A     5.809     0    0.078   0.166    10.709   31.429   19.048
LGA    P    26_A      P    26_A     1.649     0    0.634   0.603     4.523   75.000   59.796
LGA    Q    27_A      Q    27_A     1.356     0    0.046   1.384     4.915   81.429   66.190
LGA    K    28_A      K    28_A     1.171     0    0.025   0.879     3.616   81.429   70.899
LGA    L    29_A      L    29_A     0.833     0    0.042   1.080     2.690   90.476   83.095
LGA    K    30_A      K    30_A     1.207     0    0.049   0.129     3.194   83.690   71.587
LGA    R    31_A      R    31_A     0.906     0    0.039   1.842     6.881   88.214   64.329
LGA    A    32_A      A    32_A     0.681     0    0.026   0.035     0.681   90.476   92.381
LGA    L    33_A      L    33_A     0.731     0    0.062   0.088     0.999   90.476   90.476
LGA    K    34_A      K    34_A     0.717     0    0.033   0.683     2.976   92.857   85.820
LGA    I    35_A      I    35_A     0.510     0    0.028   0.078     0.790   95.238   92.857
LGA    A    36_A      A    36_A     0.128     0    0.016   0.016     0.264  100.000  100.000
LGA    E    37_A      E    37_A     0.300     0    0.056   0.168     1.017  100.000   95.820
LGA    R    38_A      R    38_A     0.202     0    0.056   0.998     2.639  100.000   91.169
LGA    E    39_A      E    39_A     0.354     0    0.023   1.121     5.061   97.619   76.772
LGA    Q    40_A      Q    40_A     0.662     0    0.018   0.247     2.015   92.857   83.757
LGA    G    41_A      G    41_A     0.620     0    0.080   0.080     0.789   92.857   92.857
LGA    E    42_A      E    42_A     0.331     0    0.045   0.128     1.987   95.238   85.714
LGA    G    43_A      G    43_A     1.089     0    0.030   0.030     1.325   83.690   83.690
LGA    E    44_A      E    44_A     1.304     0    0.058   0.943     3.998   81.429   72.646
LGA    F    45_A      F    45_A     1.646     0    0.047   0.325     2.109   75.000   72.900
LGA    D    46_A      D    46_A     1.839     0    0.070   1.064     3.189   75.000   70.060
LGA    E    47_A      E    47_A     1.352     0    0.024   0.497     3.373   79.286   72.328
LGA    C    48_A      C    48_A     0.667     0    0.065   0.103     1.156   90.476   88.968
LGA    L    49_A      L    49_A     0.693     0    0.081   1.399     3.075   90.476   79.048
LGA    E    50_A      E    50_A     0.396     0    0.031   0.570     3.404  100.000   80.794
LGA    A    51_A      A    51_A     0.436     0    0.032   0.032     0.669   95.238   96.190
LGA    L    52_A      L    52_A     0.818     0    0.037   1.442     3.286   90.476   77.917
LGA    D    53_A      D    53_A     1.085     0    0.030   0.831     4.301   85.952   69.464
LGA    D    54_A      D    54_A     0.718     0    0.036   0.205     1.086   92.857   90.536
LGA    A    55_A      A    55_A     0.447     0    0.035   0.045     0.611   95.238   96.190
LGA    K    56_A      K    56_A     0.724     0    0.151   0.981     3.813   88.214   75.026
LGA    R    57_A      R    57_A     0.841     0    0.028   1.018     4.235   88.214   78.355
LGA    A    58_A      A    58_A     0.503     0    0.086   0.093     0.956   92.857   94.286
LGA    L    59_A      L    59_A     0.560     0    0.580   1.283     2.944   86.190   78.631
LGA    P    60_A      P    60_A     4.319     0    0.119   0.189     8.183   43.452   30.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     2.036          1.921                  2.719           81.597   74.764

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   60   60    4.0     57    1.46    87.917    92.924     3.657

LGA_LOCAL      RMSD:   1.459  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.110  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   2.036  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.584993 * X  +  -0.084111 * Y  +  -0.806665 * Z  +   3.257798
  Y_new =  -0.752970 * X  +  -0.425898 * Y  +  -0.501644 * Z  +  14.119267
  Z_new =  -0.301364 * X  +   0.900853 * Y  +  -0.312480 * Z  +  13.846806 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.910292  0.306122  1.904681   [DEG:  -52.1559   17.5395  109.1302 ]
ZXZ: -1.014448  1.888599 -0.322828   [DEG:  -58.1236  108.2088  -18.4967 ]
 
# END of job
