
#######################################################
#                                                     #
#                        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   32 (  293),  selected   25 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   25 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      11_F - 32_F        4.82     7.25
  LCS_AVERAGE:     82.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      20_F - 32_F        1.99    16.14
  LCS_AVERAGE:     39.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      23_F - 32_F        0.62    15.03
  LCS_AVERAGE:     28.31

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   25
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     L     8_D     L     8_F      3    3   17      0    3    3    3    3    5    7    8    8    9   12   13   14   15   17   17   17   19   19   20 
LCS_GDT     Q     9_D     Q     9_F      4    5   17      3    4    4    4    5    5    7    8   10   12   14   14   14   16   17   17   20   22   22   23 
LCS_GDT     K    10_D     K    10_F      4    5   19      3    4    4    4    7    8    9   11   12   13   15   16   18   19   20   22   23   23   23   23 
LCS_GDT     L    11_D     L    11_F      4    5   22      3    4    4    5    5    5    7    9   10   12   15   16   18   19   19   22   23   23   23   23 
LCS_GDT     N    12_D     N    12_F      4    5   22      3    4    4    5    6    8    9   11   13   16   17   18   21   21   21   22   23   23   23   23 
LCS_GDT     S    13_D     S    13_F      6    9   22      4    5    8    9   10   12   12   15   17   18   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     W    14_D     W    14_F      6    9   22      3    4    6    9   11   13   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     D    15_D     D    15_F      7    9   22      4    5    8    9   11   13   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     V    16_D     V    16_F      7    9   22      4    5    8    9   11   13   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     F    17_D     F    17_F      7    9   22      5    5    8    9   11   13   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     G    18_D     G    18_F      7    9   22      5    6    8   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     N    19_D     N    19_F      7    9   22      5    6   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     W    20_D     W    20_F      7   13   22      5    5    8    9   11   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     F    21_D     F    21_F      7   13   22      5    5    8    9   11   12   14   16   17   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     D    22_D     D    22_F      4   13   22      3    6    6   10   11   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     L    23_D     L    23_F     10   13   22      3    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     A    24_D     A    24_F     10   13   22      3    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     S    25_D     S    25_F     10   13   22      7    9   11   12   12   14   14   14   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     W    26_D     W    26_F     10   13   22      7    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     I    27_D     I    27_F     10   13   22      7    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     K    28_D     K    28_F     10   13   22      7    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     Y    29_D     Y    29_F     10   13   22      7    9   11   12   12   14   14   17   18   19   19   20   21   21   21   21   23   23   23   23 
LCS_GDT     I    30_D     I    30_F     10   13   22      7    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     Q    31_D     Q    31_F     10   13   22      7    9   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_GDT     R    32_D     R    32_F     10   13   22      4    8   11   12   12   14   14   17   18   19   19   20   21   21   21   22   23   23   23   23 
LCS_AVERAGE  LCS_A:  50.05  (  28.31   39.23   82.62 )

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      7      9     11     12     12     14     14     17     18     19     19     20     21     21     21     22     23     23     23     23 
GDT PERCENT_AT  26.92  34.62  42.31  46.15  46.15  53.85  53.85  65.38  69.23  73.08  73.08  76.92  80.77  80.77  80.77  84.62  88.46  88.46  88.46  88.46
GDT RMS_LOCAL    0.24   0.56   0.77   1.01   1.01   1.80   1.80   2.78   2.90   3.10   3.10   3.34   3.96   3.96   3.96   5.01   5.14   5.14   5.14   5.14
GDT RMS_ALL_AT  14.95  15.15  14.68  14.18  14.18  14.10  14.10  10.03  10.24   9.95   9.95   9.26   8.31   8.31   8.31   6.61   6.71   6.71   6.71   6.71

# Checking swapping
#   possible swapping detected:  F    17_D      F    17_F
#   possible swapping detected:  D    22_D      D    22_F
#   possible swapping detected:  Y    29_D      Y    29_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    28.904     0    0.323   0.327    33.659    0.000    0.000
LGA    Q     9_D      Q     9_F    22.372     0    0.684   0.593    24.615    0.000    0.000
LGA    K    10_D      K    10_F    20.092     0    0.089   0.928    22.975    0.000    0.000
LGA    L    11_D      L    11_F    19.251     0    0.414   0.367    24.481    0.000    0.000
LGA    N    12_D      N    12_F    13.058     0    0.153   1.009    14.869    0.000    0.000
LGA    S    13_D      S    13_F     7.093     0    0.611   0.794     9.333   17.262   18.651
LGA    W    14_D      W    14_F     3.147     0    0.032   1.648     9.238   54.167   39.388
LGA    D    15_D      D    15_F     2.693     0    0.228   1.210     6.721   55.357   40.119
LGA    V    16_D      V    16_F     2.746     0    0.074   0.101     5.232   71.548   57.007
LGA    F    17_D      F    17_F     2.587     0    0.039   0.168     7.870   59.167   33.853
LGA    G    18_D      G    18_F     2.674     0    0.139   0.139     4.236   56.071   56.071
LGA    N    19_D      N    19_F     2.170     0    0.100   0.938     4.005   62.976   58.631
LGA    W    20_D      W    20_F     3.512     0    0.115   0.272     5.300   39.524   36.735
LGA    F    21_D      F    21_F     5.625     0    0.685   1.292    12.748   33.333   12.597
LGA    D    22_D      D    22_F     1.317     0    0.331   1.348     7.002   75.119   51.607
LGA    L    23_D      L    23_F     1.236     0    0.084   0.893     4.606   81.429   65.417
LGA    A    24_D      A    24_F     3.271     0    0.067   0.105     4.612   52.024   47.905
LGA    S    25_D      S    25_F     4.726     0    0.145   0.710     6.283   38.810   33.968
LGA    W    26_D      W    26_F     2.983     0    0.024   0.209     8.390   59.286   30.578
LGA    I    27_D      I    27_F     1.553     0    0.030   0.063     4.934   83.810   62.143
LGA    K    28_D      K    28_F     2.811     0    0.118   0.579     8.891   64.881   38.466
LGA    Y    29_D      Y    29_F     4.202     0    0.227   1.193     7.058   39.167   26.548
LGA    I    30_D      I    30_F     3.878     0    0.248   1.649     9.162   45.476   32.917
LGA    Q    31_D      Q    31_F     2.654     0    0.091   0.615     7.054   68.929   45.344
LGA    R    32_D      R    32_F     1.723     0    0.468   1.311     9.021   69.286   40.649

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       25     100    100  100.00     223    223  100.00                26
SUMMARY(RMSD_GDC):     6.354          6.110                  8.436           43.370   31.869

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   32   26    4.0     17    2.78    57.692    54.106     0.590

LGA_LOCAL      RMSD:   2.781  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.033  Number of assigned atoms:   25 
Std_ASGN_ATOMS RMSD:   6.354  Standard rmsd on all 25 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.887386 * X  +   0.059685 * Y  +   0.457147 * Z  + -214.115875
  Y_new =   0.155351 * X  +  -0.972304 * Y  +  -0.174615 * Z  + 128.238403
  Z_new =   0.434064 * X  +   0.225969 * Y  +  -0.872082 * Z  + -15.413536 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.173310 -0.448999  2.888054   [DEG:    9.9299  -25.7258  165.4733 ]
ZXZ:  1.205932  2.630236  1.090813   [DEG:   69.0948  150.7014   62.4990 ]
 
# END of job
