
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       4_B - 31_B        4.97    14.36
  LCS_AVERAGE:     65.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21       5_B - 25_B        1.90    15.85
  LONGEST_CONTINUOUS_SEGMENT:    21       6_B - 26_B        1.86    15.59
  LCS_AVERAGE:     39.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       7_B - 23_B        0.96    15.88
  LCS_AVERAGE:     28.97

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     2_B     A     2_B      3    4   26      3    3    3    4    4    4    4    8    9    9    9   10   11   11   13   13   14   16   16   19 
LCS_GDT     S     3_B     S     3_B      3    4   27      3    3    4    5    7    9   12   14   16   16   19   19   19   22   24   24   24   25   25   25 
LCS_GDT     Q     4_B     Q     4_B      3   14   28      3    3    6    8   12   14   16   18   22   23   23   23   23   24   25   25   26   26   26   28 
LCS_GDT     R     5_B     R     5_B      3   21   28      3    3    5    7   18   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     L     6_B     L     6_B      6   21   28      3    4    6   10   12   15   17   20   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     F     7_B     F     7_B     17   21   28      8   12   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     V     8_B     V     8_B     17   21   28      5   12   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     L     9_B     L     9_B     17   21   28      8   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     D    10_B     D    10_B     17   21   28      8   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     N    11_B     N    11_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     E    12_B     E    12_B     17   21   28      8   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     R    13_B     R    13_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     Y    14_B     Y    14_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     D    15_B     D    15_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     S    16_B     S    16_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     F    17_B     F    17_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     I    18_B     I    18_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     T    19_B     T    19_B     17   21   28      6   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     Q    20_B     Q    20_B     17   21   28      8   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     L    21_B     L    21_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     E    22_B     E    22_B     17   21   28      9   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     A    23_B     A    23_B     17   21   28      3   14   16   17   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     P    24_B     P    24_B     16   21   28      3    3    8   15   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     V    25_B     V    25_B      3   21   28      3    3    8   16   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     Q    26_B     Q    26_B      3   21   28      3    4   10   16   20   21   21   21   22   23   23   23   23   24   25   25   26   26   27   28 
LCS_GDT     N    27_B     N    27_B     12   19   28      4   11   11   11   12   12   15   16   19   22   22   23   23   24   25   25   26   26   27   28 
LCS_GDT     A    28_B     A    28_B     12   13   28      7   11   11   11   12   12   14   16   17   20   22   23   23   23   25   25   26   26   27   28 
LCS_GDT     E    29_B     E    29_B     12   13   28      9   11   11   11   12   12   14   15   16   18   19   20   22   23   24   25   26   26   27   28 
LCS_GDT     G    30_B     G    30_B     12   13   28      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   25   27   28 
LCS_GDT     R    31_B     R    31_B     12   13   28      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   25   25   26   27   28 
LCS_GDT     E    32_B     E    32_B     12   13   24      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   26   27   28 
LCS_GDT     R    33_B     R    33_B     12   13   24      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     L    34_B     L    34_B     12   13   24      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     M    35_B     M    35_B     12   13   24      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     A    36_B     A    36_B     12   13   24      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     V    37_B     V    37_B     12   13   24      9   11   11   11   12   12   14   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     K    38_B     K    38_B     12   13   24      3    3    4   11   12   12   14   15   16   18   19   20   22   23   23   24   24   24   26   27 
LCS_GDT     P    39_B     P    39_B      4    5   24      3    3    4    4    5    7   10   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     E    40_B     E    40_B      4    5   24      3    3    4    4    5    7   10   14   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     W    41_B     W    41_B      3    5   24      3    3    3    4    5   10   14   15   16   18   19   20   22   23   23   24   24   25   26   27 
LCS_GDT     K    42_B     K    42_B      3    4   24      0    3    3    4    4    4    5    5    5   13   15   19   20   23   23   24   24   24   25   27 
LCS_AVERAGE  LCS_A:  44.68  (  28.97   39.56   65.50 )

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     14     16     17     20     21     21     21     22     23     23     23     23     24     25     25     26     26     27     28 
GDT PERCENT_AT  21.95  34.15  39.02  41.46  48.78  51.22  51.22  51.22  53.66  56.10  56.10  56.10  56.10  58.54  60.98  60.98  63.41  63.41  65.85  68.29
GDT RMS_LOCAL    0.30   0.63   0.87   0.96   1.44   1.69   1.69   1.69   2.00   2.52   2.52   2.52   2.47   2.90   3.40   3.40   4.00   4.21   5.15   4.97
GDT RMS_ALL_AT  19.48  15.89  15.84  15.88  15.34  15.50  15.50  15.50  15.70  16.22  16.22  16.22  15.55  16.07  15.52  15.52  15.06  14.16  13.21  14.36

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  D    10_B      D    10_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    18.669     0    0.211   0.306    20.274    0.000    0.000
LGA    S     3_B      S     3_B    13.100     0    0.472   0.703    15.346    0.000    0.000
LGA    Q     4_B      Q     4_B     8.829     0    0.362   1.224    10.368    6.548    5.873
LGA    R     5_B      R     5_B     3.717     0    0.075   1.894    11.902   40.714   23.506
LGA    L     6_B      L     6_B     5.521     0    0.063   0.146     9.964   30.476   17.500
LGA    F     7_B      F     7_B     1.790     0    0.176   0.253     3.198   61.190   65.714
LGA    V     8_B      V     8_B     1.993     0    0.103   1.226     4.670   75.000   62.789
LGA    L     9_B      L     9_B     1.226     0    0.142   1.204     3.297   81.429   75.357
LGA    D    10_B      D    10_B     0.854     0    0.039   1.167     3.337   92.976   80.298
LGA    N    11_B      N    11_B     0.444     0    0.123   0.265     0.865   97.619   96.429
LGA    E    12_B      E    12_B     0.584     0    0.061   0.901     3.523   92.857   77.090
LGA    R    13_B      R    13_B     0.722     0    0.036   1.774     9.477   90.476   56.061
LGA    Y    14_B      Y    14_B     0.607     0    0.023   0.170     3.032   95.238   76.627
LGA    D    15_B      D    15_B     0.634     0    0.047   0.391     1.849   92.857   90.655
LGA    S    16_B      S    16_B     1.290     0    0.031   0.173     2.200   83.690   78.730
LGA    F    17_B      F    17_B     1.204     0    0.058   0.269     2.880   85.952   71.126
LGA    I    18_B      I    18_B     1.224     0    0.022   0.857     2.576   85.952   73.452
LGA    T    19_B      T    19_B     1.816     0    0.035   1.211     3.327   75.000   67.415
LGA    Q    20_B      Q    20_B     1.733     0    0.036   0.333     3.718   79.286   66.349
LGA    L    21_B      L    21_B     1.157     0    0.070   1.111     2.764   81.548   75.238
LGA    E    22_B      E    22_B     1.483     0    0.201   0.588     5.319   75.476   60.529
LGA    A    23_B      A    23_B     1.189     0    0.065   0.105     3.595   72.024   67.619
LGA    P    24_B      P    24_B     2.314     0    0.062   0.262     4.054   62.857   57.551
LGA    V    25_B      V    25_B     2.443     0    0.145   1.249     5.511   59.167   50.204
LGA    Q    26_B      Q    26_B     2.814     0    0.298   1.310     6.033   47.619   47.302
LGA    N    27_B      N    27_B     7.221     0    0.408   1.277     8.479   10.833   11.726
LGA    A    28_B      A    28_B     9.366     0    0.090   0.088    12.417    2.143    1.714
LGA    E    29_B      E    29_B    12.123     0    0.047   0.951    14.994    0.000    0.000
LGA    G    30_B      G    30_B    13.261     0    0.126   0.126    15.062    0.000    0.000
LGA    R    31_B      R    31_B    13.093     0    0.033   0.595    16.433    0.000    0.736
LGA    E    32_B      E    32_B    17.789     0    0.067   0.948    21.194    0.000    0.000
LGA    R    33_B      R    33_B    20.428     0    0.039   1.035    22.994    0.000    0.000
LGA    L    34_B      L    34_B    19.806     0    0.022   1.096    22.662    0.000    0.000
LGA    M    35_B      M    35_B    21.892     0    0.118   1.392    26.145    0.000    0.000
LGA    A    36_B      A    36_B    26.719     0    0.174   0.174    30.078    0.000    0.000
LGA    V    37_B      V    37_B    28.536     0    0.572   0.584    30.806    0.000    0.000
LGA    K    38_B      K    38_B    31.705     4    0.222   0.236    33.908    0.000    0.000
LGA    P    39_B      P    39_B    28.037     0    0.553   0.556    29.752    0.000    0.000
LGA    E    40_B      E    40_B    32.303     0    0.451   0.942    34.989    0.000    0.000
LGA    W    41_B      W    41_B    32.827     0    0.171   1.082    36.654    0.000    0.000
LGA    K    42_B      K    42_B    38.498     0    0.467   1.130    43.022    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):    10.955         10.857                 11.002           40.949   35.551

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     21    1.69    46.951    46.957     1.171

LGA_LOCAL      RMSD:   1.693  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.500  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:  10.955  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.633211 * X  +   0.737336 * Y  +  -0.235328 * Z  +  16.600161
  Y_new =   0.537708 * X  +  -0.200392 * Y  +   0.818970 * Z  + -13.523603
  Z_new =   0.556699 * X  +  -0.645119 * Y  +  -0.523363 * Z  +  32.983788 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.704016 -0.590406 -2.252369   [DEG:   40.3372  -33.8278 -129.0512 ]
ZXZ: -2.861785  2.121589  2.429634   [DEG: -163.9682  121.5581  139.2078 ]
 
# END of job
