
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , 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:    24       5_A - 28_A        4.92     9.30
  LONGEST_CONTINUOUS_SEGMENT:    24       6_A - 29_A        4.93     9.22
  LCS_AVERAGE:     65.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       1_A - 9_A         1.86    14.75
  LONGEST_CONTINUOUS_SEGMENT:     9      13_A - 21_A        1.97    10.45
  LCS_AVERAGE:     24.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      18_A - 23_A        0.94    15.02
  LCS_AVERAGE:     13.77

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      5    9   12      4    4    5    6    8    9    9   12   13   14   15   16   16   17   18   20   21   22   25   27 
LCS_GDT     R     2_A     R     2_A      5    9   12      4    4    5    6    8    9    9   12   13   14   14   16   16   17   18   20   20   22   25   27 
LCS_GDT     Q     3_A     Q     3_A      5    9   12      4    4    5    6    8    9    9   12   13   14   15   16   16   17   19   21   23   25   26   27 
LCS_GDT     S     4_A     S     4_A      5    9   21      4    4    5    6    8    9    9   12   13   14   15   16   17   17   19   21   23   25   26   27 
LCS_GDT     S     5_A     S     5_A      5    9   24      3    4    5    6    8    9   10   12   13   14   15   19   21   23   25   25   25   25   27   27 
LCS_GDT     A     6_A     A     6_A      5    9   24      3    4    5    5    8    9    9   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     T     7_A     T     7_A      5    9   24      3    4    5    6    8    9   10   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     S     8_A     S     8_A      5    9   24      3    4    5    6    8    9   10   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     S     9_A     S     9_A      3    9   24      3    3    4    5    7    9   10   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     F    10_A     F    10_A      3    6   24      3    3    5    6    8   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     G    11_A     G    11_A      3    6   24      3    3    4    5    6    8    9   11   14   16   17   19   22   24   25   25   25   25   26   27 
LCS_GDT     G    12_A     G    12_A      3    6   24      3    3    4    6    8   10   12   13   15   16   18   19   22   24   25   25   25   25   26   27 
LCS_GDT     L    13_A     L    13_A      5    9   24      3    4    5    6    7    9   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     G    14_A     G    14_A      5    9   24      3    4    5    6    7   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     G    15_A     G    15_A      5    9   24      3    4    5    6    8   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     G    16_A     G    16_A      5    9   24      3    4    5    6    8   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     S    17_A     S    17_A      5    9   24      3    4    6    6    7   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     V    18_A     V    18_A      6    9   24      3    5    6    7    8   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     R    19_A     R    19_A      6    9   24      3    5    6    7    7    9   12   13   15   16   17   19   22   24   25   25   25   25   27   27 
LCS_GDT     F    20_A     F    20_A      6    9   24      3    5    6    7    8   10   12   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     G    21_A     G    21_A      6    9   24      3    5    6    7    8   10   12   13   15   16   17   19   22   24   25   25   25   25   27   27 
LCS_GDT     P    22_A     P    22_A      6    8   24      3    5    6    7    8   10   12   13   14   16   17   19   22   24   25   25   25   25   27   27 
LCS_GDT     G    23_A     G    23_A      6    8   24      3    5    6    7    7    9   11   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     V    24_A     V    24_A      5    8   24      3    3    6    7    7    9   10   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     A    25_A     A    25_A      3    8   24      3    3    4    5    7    9   11   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     F    26_A     F    26_A      3    7   24      3    3    4    6    7    8   11   13   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     R    27_A     R    27_A      4    7   24      3    4    5    6    6    9   10   11   15   17   18   19   22   24   25   25   25   25   27   27 
LCS_GDT     A    28_A     A    28_A      4    7   24      3    4    5    5    7    9   10   11   12   13   15   19   20   24   25   25   25   25   27   27 
LCS_GDT     P    29_A     P    29_A      4    7   24      3    4    5    5    7    9   10   11   12   13   16   19   21   24   25   25   25   25   27   27 
LCS_GDT     S    30_A     S    30_A      4    7   15      3    4    5    5    7    9   10   11   12   13   15   16   17   18   19   24   24   25   27   27 
LCS_GDT     I    31_A     I    31_A      4    7   15      3    4    5    5    7    9   10   11   12   13   15   16   17   18   18   22   23   25   27   27 
LCS_GDT     H    32_A     H    32_A      3    7   15      3    3    4    5    7    9   10   11   12   13   15   16   17   18   18   22   23   23   27   27 
LCS_GDT     G    33_A     G    33_A      3    7   15      3    3    4    4    5    8   10   11   12   13   15   16   17   18   18   22   24   25   27   27 
LCS_AVERAGE  LCS_A:  34.74  (  13.77   24.61   65.84 )

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      4      5      6      7      8     10     12     13     15     17     18     19     22     24     25     25     25     25     27     27 
GDT PERCENT_AT  12.12  15.15  18.18  21.21  24.24  30.30  36.36  39.39  45.45  51.52  54.55  57.58  66.67  72.73  75.76  75.76  75.76  75.76  81.82  81.82
GDT RMS_LOCAL    0.11   0.62   0.94   1.17   1.70   2.22   2.51   2.69   3.37   3.68   3.84   4.08   4.57   4.93   5.05   5.05   5.05   5.05   6.54   5.89
GDT RMS_ALL_AT  14.38  16.00  15.02  15.98  15.03  10.22  10.22  10.15   9.68   9.54   9.54   9.56   9.68   9.22   9.14   9.14   9.14   9.14   8.83   8.95

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  F    26_A      F    26_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    19.778     0    0.295   1.505    22.249    0.000    0.000
LGA    R     2_A      R     2_A    18.656     0    0.075   0.878    27.368    0.000    0.000
LGA    Q     3_A      Q     3_A    14.391     0    0.040   1.205    15.536    0.000    0.582
LGA    S     4_A      S     4_A    14.180     0    0.652   0.825    17.708    0.000    0.000
LGA    S     5_A      S     5_A    11.408     0    0.562   0.865    12.169    0.000    0.000
LGA    A     6_A      A     6_A     7.604     0    0.103   0.117    10.168    3.214    6.000
LGA    T     7_A      T     7_A     8.894     0    0.161   1.049    11.616    7.024    4.014
LGA    S     8_A      S     8_A     6.593     0    0.539   0.843     8.732   13.810   11.905
LGA    S     9_A      S     9_A     4.108     0    0.676   0.882     5.298   52.619   45.635
LGA    F    10_A      F    10_A     2.628     0    0.699   1.216    10.791   45.238   23.939
LGA    G    11_A      G    11_A     5.375     0    0.176   0.176     5.375   42.857   42.857
LGA    G    12_A      G    12_A     2.564     0    0.262   0.262     3.973   54.167   54.167
LGA    L    13_A      L    13_A     3.419     0    0.037   0.137     9.982   57.500   32.798
LGA    G    14_A      G    14_A     2.095     0    0.198   0.198     2.915   71.190   71.190
LGA    G    15_A      G    15_A     2.502     0    0.662   0.662     3.224   61.190   61.190
LGA    G    16_A      G    16_A     2.202     0    0.329   0.329     2.264   66.786   66.786
LGA    S    17_A      S    17_A     3.162     0    0.147   0.292     7.867   63.333   46.984
LGA    V    18_A      V    18_A     1.634     0    0.157   1.164     5.620   75.119   55.034
LGA    R    19_A      R    19_A     3.213     0    0.176   1.222    15.669   55.833   22.944
LGA    F    20_A      F    20_A     1.921     0    0.082   1.329    11.768   75.476   32.597
LGA    G    21_A      G    21_A     1.354     0    0.064   0.064     3.060   71.429   71.429
LGA    P    22_A      P    22_A     2.868     0    0.111   0.449     6.019   49.762   54.014
LGA    G    23_A      G    23_A     6.227     0    0.619   0.619     9.844   16.429   16.429
LGA    V    24_A      V    24_A    10.562     0    0.618   1.156    13.533    0.714    0.408
LGA    A    25_A      A    25_A    13.207     0    0.165   0.213    13.898    0.000    0.000
LGA    F    26_A      F    26_A    13.148     0    0.235   1.248    14.607    0.000    0.000
LGA    R    27_A      R    27_A    12.443     0    0.657   0.638    18.073    0.714    0.260
LGA    A    28_A      A    28_A     9.328     0    0.121   0.146    12.221    0.357    0.286
LGA    P    29_A      P    29_A     9.520     0    0.665   0.727    12.687    0.833    6.463
LGA    S    30_A      S    30_A    14.581     0    0.573   0.549    18.371    0.000    0.000
LGA    I    31_A      I    31_A    15.421     0    0.566   1.618    16.485    0.000    0.000
LGA    H    32_A      H    32_A    16.586     0    0.094   0.814    18.919    0.000    0.000
LGA    G    33_A      G    33_A    16.115     0    0.292   0.292    18.508    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):     8.447          8.375                  9.568           26.836   22.058

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     13    2.69    37.879    35.392     0.465

LGA_LOCAL      RMSD:   2.693  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.145  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   8.447  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.337860 * X  +   0.365364 * Y  +   0.867387 * Z  + -67.495323
  Y_new =  -0.703470 * X  +  -0.710279 * Y  +   0.025175 * Z  +  83.164803
  Z_new =   0.625284 * X  +  -0.601675 * Y  +   0.496997 * Z  + -49.053337 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.018540 -0.675496 -0.880388   [DEG: -115.6538  -38.7031  -50.4425 ]
ZXZ:  1.599812  1.050661  2.336955   [DEG:   91.6625   60.1985  133.8977 ]
 
# END of job
