
#######################################################
#                                                     #
#                        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   60 (  499),  selected   60 , name one
# Molecule2: number of CA atoms   76 (  627),  selected   60 , 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:    60      15_A - 74_A        2.98     2.98
  LCS_AVERAGE:     78.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      31_A - 71_A        1.99     3.16
  LCS_AVERAGE:     43.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      47_A - 73_A        0.99     3.77
  LONGEST_CONTINUOUS_SEGMENT:    27      48_A - 74_A        0.96     3.84
  LCS_AVERAGE:     24.14

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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    15_A     Y    15_A      9   13   60      4    6   12   15   19   21   32   39   48   55   57   57   59   60   60   60   60   60   60   60 
LCS_GDT     S    16_A     S    16_A     10   13   60     11   17   21   25   34   38   48   51   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     A    17_A     A    17_A     10   13   60      4   19   23   30   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    18_A     N    18_A     10   13   60      5   10   18   28   36   43   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     Q    19_A     Q    19_A     10   13   60      5    9   17   22   29   38   42   49   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     F    20_A     F    20_A     10   13   60      5   13   20   30   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     10   13   60      5   13   23   31   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     K    22_A     K    22_A     10   13   60      4   10   18   27   34   39   46   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     I    23_A     I    23_A     10   13   60      4    9   18   27   34   40   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    24_A     L    24_A     10   13   60     12   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     I    25_A     I    25_A     10   13   60      4    7    9   24   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    26_A     N    26_A      6   13   60      4   21   29   33   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     K    27_A     K    27_A      6   13   60      4    6   21   33   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     D    28_A     D    28_A      6    8   60      4    6    6    6    9   20   24   28   34   52   54   57   59   60   60   60   60   60   60   60 
LCS_GDT     G    29_A     G    29_A      6    8   60      4    6    6    6    9   14   17   29   42   52   56   58   59   60   60   60   60   60   60   60 
LCS_GDT     S    30_A     S    30_A      6    8   60      3    6    6    6    9   14   17   20   34   43   50   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    31_A     N    31_A      6   41   60      3   15   26   32   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     V    32_A     V    32_A     12   41   60      3    4    4   12   13   30   43   50   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     D    33_A     D    33_A     12   41   60     10   15   26   32   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     R    34_A     R    34_A     12   41   60     10   15   26   32   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     K    35_A     K    35_A     12   41   60     10   15   26   32   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     T    36_A     T    36_A     12   41   60     10   15   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     I    37_A     I    37_A     12   41   60     10   17   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     Q    38_A     Q    38_A     12   41   60     10   17   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    39_A     N    39_A     12   41   60     10   15   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     W    40_A     W    40_A     12   41   60     10   17   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     I    41_A     I    41_A     12   41   60     10   17   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    42_A     N    42_A     12   41   60     10   12   26   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     R    43_A     R    43_A     12   41   60      6   11   15   20   29   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     D    44_A     D    44_A     10   41   60      4    5   11   18   26   33   40   48   54   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     Q    45_A     Q    45_A     21   41   60      4    9   17   28   37   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     25   41   60      7   19   25   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    47_A     L    47_A     27   41   60     14   21   27   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    48_A     N    48_A     27   41   60     13   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     D    49_A     D    49_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     W    50_A     W    50_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     V    51_A     V    51_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     I    52_A     I    52_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     V    53_A     V    53_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     Q    54_A     Q    54_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    55_A     L    55_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     E    57_A     E    57_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     E    58_A     E    58_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    60_A     L    60_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     K    61_A     K    61_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     R    62_A     R    62_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     E    63_A     E    63_A     27   41   60     15   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     V    64_A     V    64_A     27   41   60      7   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     I    65_A     I    65_A     27   41   60      9   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    66_A     L    66_A     27   41   60      7   21   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     K    67_A     K    67_A     27   41   60      7   20   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    68_A     N    68_A     27   41   60      7   20   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    69_A     L    69_A     27   41   60      7   20   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    70_A     L    70_A     27   41   60      7   20   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     T    71_A     T    71_A     27   41   60      6   20   29   34   41   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     N    72_A     N    72_A     27   40   60      5   20   29   31   35   42   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     L    73_A     L    73_A     27   40   60      7   20   29   31   35   42   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_GDT     S    74_A     S    74_A     27   40   60      7   20   29   31   37   45   49   52   55   55   57   58   59   60   60   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  48.94  (  24.14   43.73   78.95 )

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     15     21     29     34     41     45     49     52     55     55     57     58     59     60     60     60     60     60     60     60 
GDT PERCENT_AT  19.74  27.63  38.16  44.74  53.95  59.21  64.47  68.42  72.37  72.37  75.00  76.32  77.63  78.95  78.95  78.95  78.95  78.95  78.95  78.95
GDT RMS_LOCAL    0.25   0.51   0.97   1.44   1.70   1.83   2.00   2.18   2.38   2.38   2.57   2.76   2.86   2.98   2.98   2.98   2.98   2.98   2.98   2.98
GDT RMS_ALL_AT   3.75   3.65   3.87   3.22   3.09   3.09   3.08   3.03   3.01   3.01   3.02   2.99   2.98   2.98   2.98   2.98   2.98   2.98   2.98   2.98

# Checking swapping
#   possible swapping detected:  D    28_A      D    28_A
#   possible swapping detected:  D    44_A      D    44_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y    15_A      Y    15_A     6.769     0    0.018   1.444    16.493   17.381    6.746
LGA    S    16_A      S    16_A     4.856     0    0.027   0.070     5.631   31.786   29.921
LGA    A    17_A      A    17_A     2.718     0    0.037   0.039     3.336   55.357   57.238
LGA    N    18_A      N    18_A     3.805     0    0.076   0.785     4.829   41.905   40.357
LGA    Q    19_A      Q    19_A     5.008     0    0.027   0.926     8.652   31.548   21.217
LGA    F    20_A      F    20_A     2.806     0    0.063   1.047     5.143   57.500   48.442
LGA    A    21_A      A    21_A     2.528     0    0.217   0.283     2.855   59.048   58.667
LGA    K    22_A      K    22_A     4.445     0    0.147   0.938     9.823   35.952   23.545
LGA    I    23_A      I    23_A     3.753     0    0.133   1.396     8.492   48.452   35.417
LGA    L    24_A      L    24_A     1.233     0    0.141   1.129     5.922   86.190   65.060
LGA    I    25_A      I    25_A     2.738     0    0.610   0.712     8.424   75.357   45.357
LGA    N    26_A      N    26_A     2.373     0    0.646   0.574     7.696   73.095   45.655
LGA    K    27_A      K    27_A     2.340     0    0.115   0.365     9.941   49.167   31.534
LGA    D    28_A      D    28_A     7.411     0    0.035   0.845     9.669   10.952    6.786
LGA    G    29_A      G    29_A     7.245     0    0.069   0.069     8.843    9.286    9.286
LGA    S    30_A      S    30_A     7.243     0    0.600   0.739     8.844   17.738   13.095
LGA    N    31_A      N    31_A     2.250     0    0.467   1.165     3.969   57.500   61.190
LGA    V    32_A      V    32_A     4.561     0    0.595   0.950     8.732   37.381   23.878
LGA    D    33_A      D    33_A     2.376     0    0.282   0.762     5.307   68.810   53.393
LGA    R    34_A      R    34_A     2.517     0    0.032   1.242     8.213   60.952   43.203
LGA    K    35_A      K    35_A     2.622     0    0.097   0.926     8.700   62.976   39.683
LGA    T    36_A      T    36_A     1.822     0    0.020   0.265     2.890   75.119   73.129
LGA    I    37_A      I    37_A     1.076     0    0.033   0.152     1.821   83.690   80.417
LGA    Q    38_A      Q    38_A     1.587     0    0.014   0.167     2.133   75.000   72.011
LGA    N    39_A      N    39_A     1.697     0    0.032   0.981     1.967   75.000   75.000
LGA    W    40_A      W    40_A     0.873     0    0.028   0.074     1.167   85.952   87.891
LGA    I    41_A      I    41_A     0.589     0    0.102   1.125     3.305   90.476   77.083
LGA    N    42_A      N    42_A     2.030     0    0.142   0.193     3.009   64.881   61.071
LGA    R    43_A      R    43_A     3.147     0    0.039   1.160    14.824   59.167   25.411
LGA    D    44_A      D    44_A     5.337     0    0.412   1.321     9.689   32.262   18.155
LGA    Q    45_A      Q    45_A     3.198     0    0.045   1.010     5.855   50.119   44.021
LGA    D    46_A      D    46_A     1.706     0    0.027   0.196     2.126   70.833   69.821
LGA    L    47_A      L    47_A     1.702     0    0.037   1.061     3.662   72.857   68.155
LGA    N    48_A      N    48_A     1.877     0    0.047   0.737     2.164   75.000   75.060
LGA    D    49_A      D    49_A     1.444     0    0.019   0.563     3.646   79.286   70.357
LGA    W    50_A      W    50_A     1.327     0    0.025   1.201     6.557   81.429   55.544
LGA    V    51_A      V    51_A     1.356     0    0.023   1.164     3.768   81.429   76.054
LGA    I    52_A      I    52_A     1.637     0    0.049   0.136     2.188   72.857   70.833
LGA    V    53_A      V    53_A     1.482     0    0.030   0.290     1.763   79.286   77.755
LGA    Q    54_A      Q    54_A     1.237     0    0.043   1.435     6.459   81.429   63.862
LGA    L    55_A      L    55_A     1.454     0    0.028   0.165     1.784   77.143   78.214
LGA    K    56_A      K    56_A     2.000     0    0.019   0.896     5.525   70.833   58.095
LGA    E    57_A      E    57_A     1.662     0    0.012   1.097     6.393   77.143   58.466
LGA    E    58_A      E    58_A     1.213     0    0.032   0.249     1.520   79.286   84.497
LGA    L    59_A      L    59_A     1.766     0    0.017   0.091     2.281   72.857   68.810
LGA    L    60_A      L    60_A     1.751     0    0.051   0.125     1.834   72.857   72.857
LGA    K    61_A      K    61_A     1.402     0    0.053   0.554     1.926   81.429   81.481
LGA    R    62_A      R    62_A     1.412     0    0.015   1.496     8.264   81.429   52.381
LGA    E    63_A      E    63_A     1.518     0    0.025   0.557     4.155   77.143   64.762
LGA    V    64_A      V    64_A     1.345     0    0.016   0.056     1.654   81.429   78.980
LGA    I    65_A      I    65_A     1.198     0    0.015   0.117     1.472   81.429   81.429
LGA    L    66_A      L    66_A     1.713     0    0.042   1.256     3.640   75.000   73.631
LGA    K    67_A      K    67_A     1.228     0    0.101   0.857     3.631   81.429   81.270
LGA    N    68_A      N    68_A     1.422     0    0.015   0.926     4.433   75.119   64.048
LGA    L    69_A      L    69_A     2.142     0    0.039   1.411     5.219   64.881   58.155
LGA    L    70_A      L    70_A     1.889     0    0.062   0.158     2.196   70.833   72.917
LGA    T    71_A      T    71_A     2.243     0    0.082   1.195     4.070   62.976   57.687
LGA    N    72_A      N    72_A     3.427     0    0.057   0.081     4.228   46.905   46.786
LGA    L    73_A      L    73_A     3.301     0    0.280   1.346     5.705   43.690   40.060
LGA    S    74_A      S    74_A     2.896     0    0.129   0.681     4.811   45.714   59.286

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     499    499  100.00                76
SUMMARY(RMSD_GDC):     2.976          2.938                  4.079           49.920   43.883

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   60   76    4.0     52    2.18    54.934    55.519     2.280

LGA_LOCAL      RMSD:   2.181  Number of atoms:   52  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.031  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   2.976  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.171515 * X  +  -0.440674 * Y  +   0.881129 * Z  +   4.991117
  Y_new =   0.667143 * X  +   0.710057 * Y  +   0.225255 * Z  + -28.504726
  Z_new =  -0.724916 * X  +   0.549204 * Y  +   0.415778 * Z  +   7.392854 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.319157  0.810913  0.922795   [DEG:   75.5821   46.4619   52.8723 ]
ZXZ:  1.821079  1.141998 -0.922442   [DEG:  104.3401   65.4317  -52.8520 ]
 
# END of job
