
#######################################################
#                                                     #
#                        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:    41       5_B - 45_B        4.99     5.79
  LCS_AVERAGE:     93.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      11_B - 34_B        1.95     7.70
  LONGEST_CONTINUOUS_SEGMENT:    24      12_B - 35_B        1.87     7.39
  LCS_AVERAGE:     42.29

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      15_B - 31_B        0.99     7.35
  LONGEST_CONTINUOUS_SEGMENT:    17      16_B - 32_B        0.93     7.98
  LCS_AVERAGE:     27.04

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   21   41      9   12   13   16   18   21   23   26   29   30   32   33   34   35   36   37   38   39   39   41 
LCS_GDT     L     6_B     L     6_B     14   21   41      9   12   13   16   19   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     E     7_B     E     7_B     14   21   41      9   12   13   16   19   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     T     8_B     T     8_B     14   21   41      9   12   13   16   19   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     K     9_B     K     9_B     14   22   41      9   12   13   16   19   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     K    10_B     K    10_B     14   22   41      9   12   13   18   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     A    11_B     A    11_B     14   24   41      9   12   13   16   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     Y    12_B     Y    12_B     14   24   41      9   12   13   18   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     A    13_B     A    13_B     14   24   41      9   12   14   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     A    14_B     A    14_B     15   24   41      9   12   15   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     R    15_B     R    15_B     17   24   41      9   12   14   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     T    16_B     T    16_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     R    17_B     R    17_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     R    18_B     R    18_B     17   24   41      7   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     S    19_B     S    19_B     17   24   41      6   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     N    20_B     N    20_B     17   24   41      7   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     Y    21_B     Y    21_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     A    22_B     A    22_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     A    23_B     A    23_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     S    24_B     S    24_B     17   24   41      7   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     L    25_B     L    25_B     17   24   41      7   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     R    26_B     R    26_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     L    27_B     L    27_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     E    28_B     E    28_B     17   24   41      4   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     G    29_B     G    29_B     17   24   41      4   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     F    30_B     F    30_B     17   24   41      8   15   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     K    31_B     K    31_B     17   24   41      4   13   16   18   21   23   25   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     V    32_B     V    32_B     17   24   41      3    8   16   18   21   22   25   27   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     T    33_B     T    33_B      6   24   41      3    4   10   17   19   22   23   26   28   29   31   32   33   34   36   37   38   39   40   41 
LCS_GDT     F    34_B     F    34_B      3   24   41      3    3   15   18   21   22   25   28   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     A    35_B     A    35_B      4   24   41      3    9   16   19   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     D    36_B     D    36_B      4    6   41      3    4    4    5    6    6    6    8   13   24   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     G    37_B     G    37_B      4    6   41      3    4    4    5    6    6    6    8    9   10   11   19   23   27   29   37   38   39   40   41 
LCS_GDT     E    38_B     E    38_B      4    6   41      3    4    6   10   22   24   27   29   29   30   32   33   34   35   36   37   38   39   40   41 
LCS_GDT     R    39_B     R    39_B      4    5   41      3    4   13   16   19   23   27   29   29   30   31   33   34   35   36   37   38   39   40   41 
LCS_GDT     K    40_B     K    40_B      3    5   41      3    3    4    5    5    5    6   17   20   25   26   31   32   35   36   37   38   39   40   41 
LCS_GDT     M    41_B     M    41_B      3    4   41      3    3    4    7   11   14   19   21   23   27   31   33   34   35   36   37   38   39   40   41 
LCS_GDT     P    42_B     P    42_B      3    4   41      3    3    3    4    4    5    6   19   23   25   31   33   34   35   36   37   38   39   40   41 
LCS_GDT     T    43_B     T    43_B      3    4   41      3    3    3    3    4    5    6    8    8    9   26   28   29   33   35   37   38   39   40   41 
LCS_GDT     R    44_B     R    44_B      3    4   41      3    3    3    4    4    5    6    7    9   10   14   21   25   28   29   32   34   37   40   41 
LCS_GDT     E    45_B     E    45_B      3    4   41      3    3    3    4    4    5    6    7   12   14   19   21   25   27   29   32   34   35   37   38 
LCS_GDT     E    46_B     E    46_B      3    3   37      1    3    3    4    4    5    6    7    9   12   14   22   25   28   29   32   35   37   40   41 
LCS_GDT     V    47_B     V    47_B      3    3   13      0    3    3    3    3    4    6    7    8    9   10   11   12   16   16   20   24   29   30   31 
LCS_AVERAGE  LCS_A:  54.32  (  27.04   42.29   93.62 )

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      9     15     16     19     22     24     27     29     29     30     32     33     34     35     36     37     38     39     40     41 
GDT PERCENT_AT  20.93  34.88  37.21  44.19  51.16  55.81  62.79  67.44  67.44  69.77  74.42  76.74  79.07  81.40  83.72  86.05  88.37  90.70  93.02  95.35
GDT RMS_LOCAL    0.28   0.64   0.72   1.18   1.71   1.98   2.33   2.56   2.54   2.68   3.02   3.13   3.31   3.46   3.64   3.83   4.03   4.24   4.79   4.84
GDT RMS_ALL_AT  11.17   7.29   7.52   6.55   6.18   5.95   6.02   5.95   6.02   6.00   6.15   6.05   5.95   5.95   5.93   5.95   5.95   5.91   5.78   5.80

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_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
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     5.376     0    0.654   0.677    10.055   39.167   26.905
LGA    L     6_B      L     6_B     3.434     0    0.045   1.393     4.569   52.262   48.869
LGA    E     7_B      E     7_B     3.354     0    0.073   0.641     4.840   55.476   49.841
LGA    T     8_B      T     8_B     3.239     0    0.050   0.999     5.063   55.476   49.796
LGA    K     9_B      K     9_B     2.281     0    0.052   1.116     3.702   71.190   67.090
LGA    K    10_B      K    10_B     0.307     0    0.029   0.833     4.526   90.595   68.783
LGA    A    11_B      A    11_B     1.596     0    0.037   0.040     2.404   81.548   78.190
LGA    Y    12_B      Y    12_B     0.919     0    0.031   0.219     4.901   85.952   60.754
LGA    A    13_B      A    13_B     2.461     0    0.035   0.044     3.268   63.333   62.095
LGA    A    14_B      A    14_B     3.073     0    0.073   0.069     4.006   50.476   50.381
LGA    R    15_B      R    15_B     2.058     0    0.098   1.322     7.684   62.857   51.039
LGA    T    16_B      T    16_B     2.425     0    0.152   1.238     3.624   62.857   57.551
LGA    R    17_B      R    17_B     3.052     0    0.048   1.398    11.712   55.357   29.221
LGA    R    18_B      R    18_B     2.577     0    0.037   1.219     6.479   60.952   42.814
LGA    S    19_B      S    19_B     1.747     0    0.073   0.069     2.162   72.976   74.365
LGA    N    20_B      N    20_B     2.103     0    0.093   0.367     2.585   68.810   66.845
LGA    Y    21_B      Y    21_B     2.204     0    0.049   0.967     9.298   68.810   37.857
LGA    A    22_B      A    22_B     1.207     0    0.031   0.036     1.443   85.952   85.048
LGA    A    23_B      A    23_B     1.133     0    0.035   0.039     1.801   83.929   81.714
LGA    S    24_B      S    24_B     2.252     0    0.066   0.613     2.873   68.810   66.190
LGA    L    25_B      L    25_B     1.310     0    0.044   1.423     5.155   88.333   74.940
LGA    R    26_B      R    26_B     1.609     0    0.045   0.780     7.217   73.333   44.502
LGA    L    27_B      L    27_B     2.638     0    0.082   0.883     5.206   57.619   54.464
LGA    E    28_B      E    28_B     2.097     0    0.151   1.067     3.343   62.857   65.873
LGA    G    29_B      G    29_B     2.771     0    0.073   0.073     3.252   57.262   57.262
LGA    F    30_B      F    30_B     2.476     0    0.054   1.383     5.360   57.738   51.082
LGA    K    31_B      K    31_B     4.863     0    0.045   0.846     5.612   29.048   36.561
LGA    V    32_B      V    32_B     6.412     0    0.073   0.845     6.993   16.310   19.320
LGA    T    33_B      T    33_B     8.603     0    0.187   1.174    12.686    6.786    3.946
LGA    F    34_B      F    34_B     6.693     0    0.560   1.261     8.927   26.190   14.502
LGA    A    35_B      A    35_B     3.208     0    0.605   0.596     5.041   44.048   45.238
LGA    D    36_B      D    36_B     5.632     0    0.410   1.467     9.601   22.024   14.881
LGA    G    37_B      G    37_B     8.164     0    0.554   0.554     8.164   10.476   10.476
LGA    E    38_B      E    38_B     2.482     0    0.125   1.068     7.191   52.500   38.942
LGA    R    39_B      R    39_B     4.146     0    0.543   1.417     7.851   34.167   26.494
LGA    K    40_B      K    40_B     7.827     0    0.565   1.316    17.140   10.357    4.656
LGA    M    41_B      M    41_B     6.511     0    0.623   1.693     8.369   15.238   14.821
LGA    P    42_B      P    42_B     6.920     0    0.541   0.894     7.876   16.548   13.333
LGA    T    43_B      T    43_B     8.957     0    0.556   0.963    12.941    2.500    1.429
LGA    R    44_B      R    44_B    11.526     0    0.385   0.774    14.744    0.000    0.000
LGA    E    45_B      E    45_B    14.602     0    0.319   1.185    16.964    0.000    0.000
LGA    E    46_B      E    46_B    12.270     0    0.548   1.016    15.049    0.000    0.159
LGA    V    47_B      V    47_B    17.723     0    0.355   1.333    19.258    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):     5.735          5.704                  6.486           46.980   40.657

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     29    2.56    58.140    55.351     1.088

LGA_LOCAL      RMSD:   2.564  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.946  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   5.735  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.197010 * X  +  -0.544565 * Y  +  -0.815252 * Z  +  87.394348
  Y_new =  -0.877550 * X  +   0.272823 * Y  +  -0.394302 * Z  + -22.127253
  Z_new =   0.437142 * X  +   0.793106 * Y  +  -0.424134 * Z  + -42.049034 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.349958 -0.452419  2.061877   [DEG:  -77.3469  -25.9217  118.1368 ]
ZXZ: -1.120309  2.008802  0.503747   [DEG:  -64.1890  115.0959   28.8626 ]
 
# END of job
