
#######################################################
#                                                     #
#                        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:    42       6_B - 47_B        4.85     5.46
  LCS_AVERAGE:     97.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      12_B - 32_B        1.99     6.11
  LCS_AVERAGE:     37.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      16_B - 30_B        0.81     7.43
  LCS_AVERAGE:     24.50

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      3    3   41      3    3    4    4    4    4    4    6    7    9   13   13   14   16   18   20   24   25   28   30 
LCS_GDT     L     6_B     L     6_B      3   14   42      3    3    4    4    7   10   16   19   20   20   25   25   25   27   27   29   36   39   40   40 
LCS_GDT     E     7_B     E     7_B     12   18   42     10   11   11   14   16   17   19   24   28   32   33   37   39   39   40   40   40   40   40   41 
LCS_GDT     T     8_B     T     8_B     12   18   42     10   11   11   14   16   19   23   26   29   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     K     9_B     K     9_B     12   18   42     10   11   11   14   16   19   23   26   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     K    10_B     K    10_B     12   18   42     10   11   11   14   16   19   23   26   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     A    11_B     A    11_B     12   18   42     10   11   11   14   16   19   23   26   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     Y    12_B     Y    12_B     12   21   42     10   11   11   14   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     A    13_B     A    13_B     12   21   42     10   11   11   14   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     A    14_B     A    14_B     12   21   42     10   11   11   16   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     R    15_B     R    15_B     12   21   42     10   11   11   14   17   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     T    16_B     T    16_B     15   21   42     10   11   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     R    17_B     R    17_B     15   21   42      6   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     R    18_B     R    18_B     15   21   42      6   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     S    19_B     S    19_B     15   21   42      6   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     N    20_B     N    20_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     Y    21_B     Y    21_B     15   21   42      6   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     A    22_B     A    22_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     A    23_B     A    23_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     S    24_B     S    24_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     L    25_B     L    25_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     R    26_B     R    26_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     L    27_B     L    27_B     15   21   42      6   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     E    28_B     E    28_B     15   21   42      7   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     G    29_B     G    29_B     15   21   42      4   13   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     F    30_B     F    30_B     15   21   42      4   11   15   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     K    31_B     K    31_B     13   21   42      4    8   14   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     V    32_B     V    32_B     11   21   42      4    8   14   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     T    33_B     T    33_B      4   19   42      3    4    4    8   11   15   20   26   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     F    34_B     F    34_B      8   19   42      7    7    9   11   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     A    35_B     A    35_B      8   16   42      7    7    9   14   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     D    36_B     D    36_B      8   10   42      7    7    9   11   12   18   23   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     G    37_B     G    37_B      8   10   42      7    7    9   11   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     E    38_B     E    38_B      8   10   42      7    7   12   17   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     R    39_B     R    39_B      8   10   42      7    7    9   11   18   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     K    40_B     K    40_B      8   10   42      7    7    9   11   14   21   25   29   30   32   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     M    41_B     M    41_B      8   10   42      3    6    9   11   16   21   27   29   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     P    42_B     P    42_B      4    6   42      3    4    4    4   13   17   20   24   28   32   33   36   39   39   40   40   40   40   40   41 
LCS_GDT     T    43_B     T    43_B      4    6   42      3    4    6    9   13   18   21   24   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     R    44_B     R    44_B      4    6   42      3    4    4    4    5   17   19   21   25   30   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     E    45_B     E    45_B      4    6   42      3    4    4    9   13   17   21   24   30   33   35   37   39   39   40   40   40   40   40   41 
LCS_GDT     E    46_B     E    46_B      3    5   42      3    3    3    4    5    6    6    7   15   16   32   33   35   37   40   40   40   40   40   41 
LCS_GDT     V    47_B     V    47_B      3    3   42      3    3    3    3    3    3    4    7    7    8    9   11   16   20   32   33   33   36   39   41 
LCS_AVERAGE  LCS_A:  53.22  (  24.50   37.53   97.62 )

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     10     13     15     17     18     21     27     29     30     33     35     37     39     39     40     40     40     40     40     41 
GDT PERCENT_AT  23.26  30.23  34.88  39.53  41.86  48.84  62.79  67.44  69.77  76.74  81.40  86.05  90.70  90.70  93.02  93.02  93.02  93.02  93.02  95.35
GDT RMS_LOCAL    0.34   0.63   0.81   1.16   1.29   1.76   2.47   2.62   2.73   3.26   3.40   3.61   3.86   3.86   4.06   4.06   4.06   4.06   4.06   4.42
GDT RMS_ALL_AT  11.35   8.02   7.43   7.30   7.25   7.32   6.32   6.40   6.39   5.74   5.82   5.69   5.60   5.60   5.56   5.56   5.56   5.56   5.56   5.58

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B    21.142     0    0.648   0.963    22.598    0.000    0.000
LGA    L     6_B      L     6_B    17.544     0    0.581   1.356    19.238    0.000    0.000
LGA    E     7_B      E     7_B    11.411     0    0.644   1.237    13.478    0.357    0.317
LGA    T     8_B      T     8_B     9.308     0    0.092   0.162    10.357    3.333    2.313
LGA    K     9_B      K     9_B     8.005     0    0.048   1.598    13.166    7.024    4.021
LGA    K    10_B      K    10_B     7.893     0    0.053   0.695    11.775   11.667    5.344
LGA    A    11_B      A    11_B     6.980     0    0.037   0.046     8.015   19.048   16.190
LGA    Y    12_B      Y    12_B     3.831     0    0.032   1.157     8.346   48.095   30.992
LGA    A    13_B      A    13_B     3.354     0    0.037   0.043     4.718   59.881   54.190
LGA    A    14_B      A    14_B     3.525     0    0.084   0.083     5.187   48.333   43.905
LGA    R    15_B      R    15_B     3.560     0    0.073   0.837     8.279   48.452   31.299
LGA    T    16_B      T    16_B     1.871     0    0.175   1.217     4.544   72.976   64.694
LGA    R    17_B      R    17_B     0.767     0    0.049   1.157     3.160   90.476   83.593
LGA    R    18_B      R    18_B     1.735     0    0.041   1.090     9.921   70.952   42.771
LGA    S    19_B      S    19_B     3.318     0    0.032   0.545     5.406   51.786   45.079
LGA    N    20_B      N    20_B     2.957     0    0.071   0.559     6.749   60.952   44.345
LGA    Y    21_B      Y    21_B     1.068     0    0.049   0.145     4.231   81.548   65.159
LGA    A    22_B      A    22_B     2.271     0    0.030   0.045     3.173   64.881   61.905
LGA    A    23_B      A    23_B     3.223     0    0.041   0.047     4.052   55.357   51.714
LGA    S    24_B      S    24_B     2.114     0    0.095   0.695     2.482   68.810   70.238
LGA    L    25_B      L    25_B     1.594     0    0.025   1.020     6.249   75.000   56.667
LGA    R    26_B      R    26_B     2.416     0    0.054   1.219     5.871   64.762   46.147
LGA    L    27_B      L    27_B     2.034     0    0.087   1.109     5.387   68.810   60.179
LGA    E    28_B      E    28_B     1.407     0    0.162   0.847     4.664   75.119   68.466
LGA    G    29_B      G    29_B     1.875     0    0.088   0.088     1.973   75.000   75.000
LGA    F    30_B      F    30_B     1.416     0    0.062   0.311     3.564   79.286   69.048
LGA    K    31_B      K    31_B     1.304     0    0.294   0.929     5.691   73.214   63.122
LGA    V    32_B      V    32_B     1.205     0    0.113   0.858     4.198   67.738   60.408
LGA    T    33_B      T    33_B     5.102     0    0.591   0.591     8.896   37.619   25.782
LGA    F    34_B      F    34_B     3.483     0    0.445   1.294    12.541   51.905   23.203
LGA    A    35_B      A    35_B     2.149     0    0.044   0.046     2.649   60.952   61.714
LGA    D    36_B      D    36_B     4.019     0    0.042   0.182     6.606   45.119   32.321
LGA    G    37_B      G    37_B     2.782     0    0.167   0.167     3.138   59.167   59.167
LGA    E    38_B      E    38_B     0.947     0    0.502   0.944     1.900   83.690   83.492
LGA    R    39_B      R    39_B     3.068     0    0.096   1.316     8.803   51.786   34.199
LGA    K    40_B      K    40_B     3.894     0    0.618   1.463    10.936   36.310   23.280
LGA    M    41_B      M    41_B     3.316     0    0.280   0.745    10.307   51.786   31.131
LGA    P    42_B      P    42_B     6.115     0    0.652   0.709     8.747   26.548   18.163
LGA    T    43_B      T    43_B     4.997     0    0.113   1.124     5.519   25.119   27.075
LGA    R    44_B      R    44_B     6.374     0    0.581   0.837    11.772   13.690    7.879
LGA    E    45_B      E    45_B     5.422     0    0.505   1.494     6.297   21.667   32.328
LGA    E    46_B      E    46_B     9.490     0    0.582   1.499    13.837    2.143    0.952
LGA    V    47_B      V    47_B    12.831     0    0.466   1.129    14.195    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):     5.399          5.267                  6.083           46.752   39.018

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     29    2.62    57.558    54.283     1.066

LGA_LOCAL      RMSD:   2.622  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.396  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   5.399  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.726462 * X  +  -0.685515 * Y  +  -0.048184 * Z  +   6.472380
  Y_new =  -0.423604 * X  +  -0.501912 * Y  +   0.754085 * Z  + -16.176195
  Z_new =  -0.541121 * X  +  -0.527403 * Y  +  -0.655007 * Z  +   2.600573 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.527905  0.571769 -2.463697   [DEG:  -30.2467   32.7600 -141.1594 ]
ZXZ: -3.077782  2.284988 -2.343358   [DEG: -176.3439  130.9202 -134.2645 ]
 
# END of job
