
#######################################################
#                                                     #
#                        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:    21      12_A - 32_A        4.83    16.30
  LONGEST_CONTINUOUS_SEGMENT:    21      13_A - 33_A        4.67    16.86
  LCS_AVERAGE:     53.90

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      14_A - 24_A        1.97    17.92
  LONGEST_CONTINUOUS_SEGMENT:    11      15_A - 25_A        1.96    18.33
  LONGEST_CONTINUOUS_SEGMENT:    11      18_A - 28_A        1.72    17.04
  LONGEST_CONTINUOUS_SEGMENT:    11      20_A - 30_A        1.99    17.11
  LCS_AVERAGE:     27.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7      18_A - 24_A        0.75    17.93
  LONGEST_CONTINUOUS_SEGMENT:     7      20_A - 26_A        0.92    16.42
  LONGEST_CONTINUOUS_SEGMENT:     7      26_A - 32_A        0.97    20.14
  LCS_AVERAGE:     16.71

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    7   11      4    4    5    6    6    7    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     R     2_A     R     2_A      5    7   11      4    4    5    6    6    7    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     Q     3_A     Q     3_A      5    7   11      4    4    5    6    6    7    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     S     4_A     S     4_A      5    7   11      4    4    5    6    6    7    8    8    8    9    9    9    9   10   10   11   11   11   11   13 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    4    5    6    6    7    8    8    8    9    9    9   10   10   11   11   12   12   14   14 
LCS_GDT     A     6_A     A     6_A      4    7   11      3    4    4    6    6    7    8    8   10   10   10   10   12   12   12   12   13   13   14   14 
LCS_GDT     T     7_A     T     7_A      4    7   11      3    4    4    4    5    7    8    8   10   10   10   10   12   12   12   12   13   14   15   16 
LCS_GDT     S     8_A     S     8_A      4    6   11      3    4    4    4    5    7    8    8   10   10   10   10   12   12   13   13   13   14   15   16 
LCS_GDT     S     9_A     S     9_A      4    7   11      3    4    4    5    6    6    7    8   10   10   10   10   12   12   13   13   13   14   15   16 
LCS_GDT     F    10_A     F    10_A      4    7   11      3    4    4    5    6    6    7    8   10   10   10   10   12   12   13   13   13   14   15   18 
LCS_GDT     G    11_A     G    11_A      4    7   15      4    4    4    5    6    6    7    8   10   10   10   10   12   14   16   17   17   18   19   20 
LCS_GDT     G    12_A     G    12_A      4    7   21      4    4    4    5    5    6    7    9   10   14   15   15   16   17   19   19   20   20   21   22 
LCS_GDT     L    13_A     L    13_A      4    7   21      4    4    4    5    6    6    8   11   15   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    14_A     G    14_A      4   11   21      4    4    7   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    15_A     G    15_A      3   11   21      3    4    6    9   10   11   12   13   16   16   16   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    16_A     G    16_A      5   11   21      3    4    6    8   10   10   11   13   13   14   15   16   18   18   19   20   20   20   21   22 
LCS_GDT     S    17_A     S    17_A      5   11   21      3    4    6    8   10   11   12   13   14   14   15   17   18   18   19   20   20   20   21   22 
LCS_GDT     V    18_A     V    18_A      7   11   21      5    6    7   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     R    19_A     R    19_A      7   11   21      5    6    7   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     F    20_A     F    20_A      7   11   21      5    6    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    21_A     G    21_A      7   11   21      5    6    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     P    22_A     P    22_A      7   11   21      5    6    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    23_A     G    23_A      7   11   21      4    6    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     V    24_A     V    24_A      7   11   21      4    6    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     A    25_A     A    25_A      7   11   21      4    5    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     F    26_A     F    26_A      7   11   21      5    5    8   10   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     R    27_A     R    27_A      7   11   21      5    5    8    9   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     A    28_A     A    28_A      7   11   21      5    5    6    9   10   12   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     P    29_A     P    29_A      7   11   21      5    5    6    7   10   11   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     S    30_A     S    30_A      7   11   21      5    5    6    7   10   11   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     I    31_A     I    31_A      7    9   21      3    3    6    7    9   11   14   15   16   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     H    32_A     H    32_A      7    9   21      3    5    6    7    9    9   13   13   14   16   17   17   18   18   19   20   20   20   21   22 
LCS_GDT     G    33_A     G    33_A      3    8   21      3    3    3    4    4    7    8    8    9   10   12   12   16   16   19   19   20   20   21   22 
LCS_AVERAGE  LCS_A:  32.81  (  16.71   27.82   53.90 )

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      5      6      8     10     10     12     14     15     16     16     17     17     18     18     19     20     20     20     21     22 
GDT PERCENT_AT  15.15  18.18  24.24  30.30  30.30  36.36  42.42  45.45  48.48  48.48  51.52  51.52  54.55  54.55  57.58  60.61  60.61  60.61  63.64  66.67
GDT RMS_LOCAL    0.28   0.53   1.11   1.33   1.33   1.86   2.52   2.67   2.89   2.89   3.30   3.25   3.53   3.53   3.91   4.18   4.18   4.18   4.67   5.18
GDT RMS_ALL_AT  18.60  18.71  16.32  17.16  17.16  16.94  16.86  16.93  17.02  17.02  16.43  17.25  16.55  16.55  16.99  16.94  16.94  16.94  16.86  16.28

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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    27.670     0    0.033   0.831    29.382    0.000    0.000
LGA    R     2_A      R     2_A    29.627     0    0.125   1.053    33.897    0.000    0.000
LGA    Q     3_A      Q     3_A    29.678     0    0.154   0.661    31.078    0.000    0.000
LGA    S     4_A      S     4_A    30.551     0    0.184   0.678    32.091    0.000    0.000
LGA    S     5_A      S     5_A    31.962     0    0.556   0.591    34.244    0.000    0.000
LGA    A     6_A      A     6_A    31.722     0    0.202   0.232    31.722    0.000    0.000
LGA    T     7_A      T     7_A    31.118     0    0.198   0.281    34.098    0.000    0.000
LGA    S     8_A      S     8_A    28.431     0    0.399   0.707    29.358    0.000    0.000
LGA    S     9_A      S     9_A    27.456     0    0.487   0.776    29.340    0.000    0.000
LGA    F    10_A      F    10_A    20.901     0    0.519   1.056    23.273    0.000    0.000
LGA    G    11_A      G    11_A    18.541     0    0.372   0.372    19.749    0.000    0.000
LGA    G    12_A      G    12_A    13.051     0    0.034   0.034    15.312    0.000    0.000
LGA    L    13_A      L    13_A     7.105     0    0.098   0.182    12.423   20.000   10.595
LGA    G    14_A      G    14_A     3.277     0    0.560   0.560     4.367   43.452   43.452
LGA    G    15_A      G    15_A     5.637     0    0.234   0.234     7.571   18.333   18.333
LGA    G    16_A      G    16_A     8.480     0    0.607   0.607     8.480    9.762    9.762
LGA    S    17_A      S    17_A     7.573     0    0.074   0.665    11.424   11.548    8.175
LGA    V    18_A      V    18_A     3.321     0    0.202   0.934     4.743   45.357   50.612
LGA    R    19_A      R    19_A     2.917     0    0.203   0.769     8.470   53.571   35.368
LGA    F    20_A      F    20_A     1.659     0    0.121   0.291     2.824   77.143   68.658
LGA    G    21_A      G    21_A     1.442     0    0.110   0.110     2.236   72.976   72.976
LGA    P    22_A      P    22_A     1.360     0    0.608   0.805     4.321   66.190   76.599
LGA    G    23_A      G    23_A     1.636     0    0.617   0.617     2.039   75.119   75.119
LGA    V    24_A      V    24_A     0.327     0    0.097   0.968     1.616   83.929   82.925
LGA    A    25_A      A    25_A     2.765     0    0.010   0.047     3.629   59.286   56.095
LGA    F    26_A      F    26_A     3.179     0    0.157   1.313     4.280   51.786   55.758
LGA    R    27_A      R    27_A     3.304     0    0.017   0.951     6.918   57.381   35.498
LGA    A    28_A      A    28_A     2.108     0    0.034   0.035     2.770   66.786   64.857
LGA    P    29_A      P    29_A     2.954     0    0.033   0.342     3.971   62.976   56.531
LGA    S    30_A      S    30_A     3.392     0    0.082   0.643     5.415   42.381   37.857
LGA    I    31_A      I    31_A     3.714     0    0.619   0.478     7.038   38.333   34.583
LGA    H    32_A      H    32_A     7.011     0    0.063   1.429     9.775    9.881    6.857
LGA    G    33_A      G    33_A    11.333     0    0.548   0.548    12.605    0.357    0.357

# 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):    12.821         12.720                 13.037           29.289   27.302

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     15    2.67    38.636    36.714     0.542

LGA_LOCAL      RMSD:   2.669  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.934  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  12.821  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.602920 * X  +  -0.784991 * Y  +   0.142397 * Z  + -42.512871
  Y_new =  -0.797288 * X  +  -0.586454 * Y  +   0.142841 * Z  +  35.262959
  Z_new =  -0.028620 * X  +  -0.199653 * Y  +  -0.979449 * Z  + -81.393639 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.923331  0.028624 -2.940505   [DEG:  -52.9030    1.6400 -168.4785 ]
ZXZ:  2.357752  2.938505 -2.999215   [DEG:  135.0892  168.3640 -171.8424 ]
 
# END of job
