
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    43       5_B - 47_B        4.40     4.40
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      10_B - 33_B        1.97     5.63
  LCS_AVERAGE:     45.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      15_B - 32_B        0.98     6.72
  LCS_AVERAGE:     29.69

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     14   20   43      9   12   13   16   19   22   24   27   31   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     14   20   43     11   12   13   17   19   22   26   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     14   20   43     11   12   13   17   19   22   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     14   20   43     11   12   13   17   19   22   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     14   22   43     11   12   13   17   20   23   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     14   24   43     11   12   13   17   20   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     14   24   43     11   12   13   17   20   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     14   24   43     11   12   13   19   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     14   24   43     11   12   14   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     14   24   43     11   12   15   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     18   24   43     11   12   13   18   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     18   24   43     10   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     18   24   43     10   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     18   24   43     11   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     18   24   43     11   17   17   20   23   25   27   30   32   33   34   38   40   41   42   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     18   24   43     11   17   17   20   23   25   27   30   32   33   34   38   40   41   42   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     18   24   43     10   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     18   24   43      3   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     18   24   43      3   17   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B      4   24   43      3    4   10   17   23   24   26   29   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B      4   23   43      3    4    4    5    6    9   20   25   27   29   32   34   40   41   42   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B      5   23   43      3   11   17   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B      5   10   43      3    4    5    6    8   10   11   15   21   26   29   30   34   39   42   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B      5   10   43      3    4    5    7    9   10   13   18   20   26   30   34   39   41   42   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B      7   10   43      4    8   13   20   23   25   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B      7   10   43      4    5    7   14   18   22   27   30   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B      7   10   43      4    6   13   17   19   22   24   27   32   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      7   10   43      5    9   13   17   19   22   24   27   29   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      7   10   43      5    6    9   16   19   21   24   27   29   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      7   10   43      5    6    9   16   19   21   24   27   29   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   10   43      5    6    9   13   19   21   21   25   28   33   35   37   40   41   42   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   10   43      5    6    9   16   19   21   24   27   29   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    8   43      3    3    3    4    4    6    8   11   28   33   36   38   40   41   42   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    5   15   22   29   29   31   33   39   40   43   43   43   43 
LCS_AVERAGE  LCS_A:  58.28  (  29.69   45.16  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     11     17     17     20     23     25     27     30     32     33     36     38     40     41     42     42     43     43     43     43 
GDT PERCENT_AT  25.58  39.53  39.53  46.51  53.49  58.14  62.79  69.77  74.42  76.74  83.72  88.37  93.02  95.35  97.67  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.21   0.57   0.57   1.19   1.52   1.88   2.26   2.57   2.76   2.89   3.60   3.72   3.92   4.03   4.19   4.19   4.40   4.40   4.40   4.40
GDT RMS_ALL_AT   9.37   7.08   7.08   6.35   6.09   5.61   5.27   5.28   5.14   5.07   4.45   4.48   4.45   4.43   4.41   4.41   4.40   4.40   4.40   4.40

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  D    36_B      D    36_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     6.168     0    0.631   0.938    10.134   25.238   17.063
LGA    L     6_B      L     6_B     4.519     0    0.049   1.217     5.439   37.738   38.810
LGA    E     7_B      E     7_B     3.895     0    0.037   0.840     6.870   46.905   33.810
LGA    T     8_B      T     8_B     3.488     0    0.041   1.213     6.598   53.810   43.333
LGA    K     9_B      K     9_B     2.579     0    0.015   0.163     5.284   67.143   49.471
LGA    K    10_B      K    10_B     1.008     0    0.014   0.940     4.643   83.810   72.328
LGA    A    11_B      A    11_B     1.834     0    0.011   0.011     2.610   77.143   73.143
LGA    Y    12_B      Y    12_B     0.356     0    0.014   1.230     9.160   88.452   52.103
LGA    A    13_B      A    13_B     1.594     0    0.012   0.013     2.648   73.333   73.238
LGA    A    14_B      A    14_B     2.383     0    0.076   0.082     3.983   57.738   59.143
LGA    R    15_B      R    15_B     3.243     0    0.050   1.199     5.303   46.905   53.506
LGA    T    16_B      T    16_B     3.875     0    0.200   1.073     6.033   45.000   41.633
LGA    R    17_B      R    17_B     3.065     0    0.043   0.790     7.489   53.571   33.074
LGA    R    18_B      R    18_B     2.756     0    0.009   1.153     4.881   57.143   46.320
LGA    S    19_B      S    19_B     3.247     0    0.046   0.719     3.893   53.571   51.270
LGA    N    20_B      N    20_B     2.820     0    0.015   0.321     3.726   60.952   55.536
LGA    Y    21_B      Y    21_B     1.297     0    0.059   0.316     2.005   81.548   82.381
LGA    A    22_B      A    22_B     1.344     0    0.007   0.014     1.935   83.690   81.524
LGA    A    23_B      A    23_B     1.365     0    0.026   0.027     1.941   81.429   79.714
LGA    S    24_B      S    24_B     1.530     0    0.067   0.724     1.788   77.143   77.143
LGA    L    25_B      L    25_B     0.694     0    0.053   0.085     1.235   88.214   91.726
LGA    R    26_B      R    26_B     1.059     0    0.037   0.977     6.169   81.548   55.455
LGA    L    27_B      L    27_B     1.968     0    0.057   0.231     2.798   66.905   65.833
LGA    E    28_B      E    28_B     2.047     0    0.152   1.020     4.724   66.786   59.048
LGA    G    29_B      G    29_B     2.573     0    0.072   0.072     2.798   60.952   60.952
LGA    F    30_B      F    30_B     2.111     0    0.102   1.375     7.699   62.857   45.584
LGA    K    31_B      K    31_B     2.484     0    0.578   0.901     8.496   61.071   38.042
LGA    V    32_B      V    32_B     2.729     0    0.195   0.265     3.759   51.905   57.415
LGA    T    33_B      T    33_B     4.395     0    0.088   0.160     5.249   33.214   34.966
LGA    F    34_B      F    34_B     7.201     0    0.233   1.458    14.619   18.690    6.926
LGA    A    35_B      A    35_B     2.740     0    0.639   0.626     4.834   55.357   50.571
LGA    D    36_B      D    36_B     7.525     0    0.492   1.184    13.140   15.000    7.560
LGA    G    37_B      G    37_B     6.399     0    0.081   0.081     6.886   26.190   26.190
LGA    E    38_B      E    38_B     2.577     0    0.280   1.260     8.846   63.333   36.085
LGA    R    39_B      R    39_B     3.642     0    0.120   1.254    10.500   50.357   22.078
LGA    K    40_B      K    40_B     5.355     0    0.347   1.491     6.325   25.119   25.873
LGA    M    41_B      M    41_B     6.611     0    0.010   0.249     7.299   12.619   16.548
LGA    P    42_B      P    42_B     8.853     0    0.020   0.073     9.504    3.571    2.993
LGA    T    43_B      T    43_B    10.244     0    0.064   0.053    11.397    0.119    0.068
LGA    R    44_B      R    44_B    11.692     0    0.597   1.442    17.288    0.000    0.000
LGA    E    45_B      E    45_B    12.020     0    0.452   1.389    13.619    0.000    0.000
LGA    E    46_B      E    46_B     8.371     0    0.610   1.424    12.065    1.548    4.497
LGA    V    47_B      V    47_B    13.701     0    0.416   1.356    16.335    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     4.403          4.330                  5.477           48.782   42.394

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     30    2.57    63.372    60.178     1.125

LGA_LOCAL      RMSD:   2.567  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.281  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.403  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.076649 * X  +  -0.424549 * Y  +  -0.902155 * Z  +  24.608971
  Y_new =   0.777161 * X  +  -0.592270 * Y  +   0.212690 * Z  + -58.740776
  Z_new =  -0.624617 * X  +  -0.684817 * Y  +   0.375339 * Z  +  23.865208 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.669105  0.674641 -1.069423   [DEG:   95.6327   38.6541  -61.2734 ]
ZXZ: -1.802326  1.186034 -2.402137   [DEG: -103.2657   67.9547 -137.6323 ]
 
# END of job
