
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , 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:    61       1_B - 61_B        2.46     2.46
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    54       8_B - 61_B        1.99     2.50
  LCS_AVERAGE:     81.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42      20_B - 61_B        0.98     2.58
  LCS_AVERAGE:     56.25

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B     16   19   61      3   13   15   16   16   17   19   26   35   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     16   19   61     11   14   19   35   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     16   19   61     11   14   15   16   43   49   51   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     16   19   61     11   14   15   16   16   17   19   19   48   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     16   19   61     11   14   15   16   24   50   52   54   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     16   19   61     11   14   23   27   47   49   51   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     16   19   61     11   14   15   16   16   17   51   54   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     16   54   61     11   14   15   16   16   35   52   54   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     16   54   61     11   14   15   22   28   40   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     16   54   61     11   14   15   16   16   45   49   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     16   54   61     11   14   15   16   16   17   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     16   54   61     11   14   25   39   42   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     16   54   61     11   14   15   16   16   23   35   48   57   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     16   54   61      8   14   15   16   16   22   48   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     16   54   61      4   14   15   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     16   54   61      3   11   15   34   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     17   54   61      3    4   17   39   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     23   54   61      3   12   23   39   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     33   54   61      4   15   28   40   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     42   54   61      7   23   36   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     42   54   61      7   23   36   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     42   54   61      7   24   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     42   54   61      7   34   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     42   54   61     10   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     42   54   61     14   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     42   54   61     11   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     42   54   61     14   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     42   54   61     15   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     42   54   61     18   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     42   54   61     12   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     42   54   61     12   35   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     42   54   61     12   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     42   54   61     12   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     42   54   61     12   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     42   54   61     23   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     42   54   61      9   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     42   54   61      9   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     42   54   61      9   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     42   54   61      3   36   40   43   47   50   52   55   58   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  79.40  (  56.25   81.94  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     23     36     40     43     47     50     52     55     58     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  37.70  59.02  65.57  70.49  77.05  81.97  85.25  90.16  95.08 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.59   0.75   1.02   1.34   1.60   1.73   1.93   2.13   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46
GDT RMS_ALL_AT   2.83   2.75   2.65   2.57   2.53   2.48   2.49   2.53   2.49   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46   2.46

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  D    30_B      D    30_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     7.841     0    0.636   0.993     9.481   13.690    9.762
LGA    Y     2_B      Y     2_B     3.565     0    0.084   1.461    13.097   54.524   24.762
LGA    I     3_B      I     3_B     3.285     0    0.042   0.624     7.757   56.190   35.952
LGA    R     4_B      R     4_B     5.998     0    0.049   1.000    17.068   27.619   10.519
LGA    E     5_B      E     5_B     5.091     0    0.053   1.269    11.783   39.167   19.418
LGA    L     6_B      L     6_B     3.080     0    0.041   1.009     9.472   59.167   37.321
LGA    R     7_B      R     7_B     4.073     0    0.049   1.250     7.982   50.476   25.758
LGA    A     8_B      A     8_B     4.408     0    0.037   0.044     6.365   45.119   39.524
LGA    A     9_B      A     9_B     4.165     0    0.042   0.045     5.900   46.905   41.810
LGA    L    10_B      L    10_B     4.388     0    0.039   0.127     9.663   43.571   25.060
LGA    I    11_B      I    11_B     3.672     0    0.068   1.205    10.089   55.595   34.405
LGA    L    12_B      L    12_B     3.622     0    0.035   0.193     9.281   53.810   31.369
LGA    L    13_B      L    13_B     4.950     0    0.046   1.162    10.756   37.500   21.369
LGA    A    14_B      A    14_B     4.570     0    0.077   0.094     5.744   40.476   36.667
LGA    L    15_B      L    15_B     2.070     0    0.106   0.115     6.328   72.976   50.952
LGA    K    16_B      K    16_B     2.471     0    0.355   0.768     8.036   67.024   41.376
LGA    K    17_B      K    17_B     2.688     0    0.154   0.730     4.108   59.048   55.026
LGA    Q    18_B      Q    18_B     2.767     0    0.094   0.277     3.307   55.357   54.762
LGA    H    19_B      H    19_B     2.628     0    0.170   0.597     5.224   62.857   51.905
LGA    A    20_B      A    20_B     2.014     0    0.154   0.193     2.353   64.762   66.381
LGA    E    21_B      E    21_B     1.918     0    0.052   0.476     4.458   72.976   61.217
LGA    D    22_B      D    22_B     1.210     0    0.060   1.063     3.146   85.952   79.821
LGA    P    23_B      P    23_B     0.667     0    0.060   0.333     1.560   88.214   86.667
LGA    D    24_B      D    24_B     1.130     0    0.066   0.544     1.684   81.548   80.476
LGA    A    25_B      A    25_B     1.151     0    0.047   0.046     1.188   81.429   81.429
LGA    Q    26_B      Q    26_B     1.035     0    0.044   1.120     4.626   81.429   65.397
LGA    R    27_B      R    27_B     1.343     0    0.030   1.182     8.052   81.429   52.771
LGA    V    28_B      V    28_B     1.356     0    0.028   1.232     3.008   81.429   73.469
LGA    A    29_B      A    29_B     1.108     0    0.036   0.058     1.218   81.429   81.429
LGA    D    30_B      D    30_B     1.156     0    0.040   0.695     2.501   81.429   78.393
LGA    E    31_B      E    31_B     1.393     0    0.036   0.837     4.192   81.429   66.667
LGA    L    32_B      L    32_B     0.998     0    0.046   0.285     1.635   83.690   81.488
LGA    M    33_B      M    33_B     1.058     0    0.033   0.980     4.766   81.429   70.417
LGA    K    34_B      K    34_B     1.055     0    0.036   1.017     5.952   85.952   65.238
LGA    K    35_B      K    35_B     0.794     0    0.043   0.673     3.087   90.476   76.561
LGA    L    36_B      L    36_B     0.910     0    0.033   1.001     4.438   90.476   78.393
LGA    F    37_B      F    37_B     1.075     0    0.044   0.422     2.783   83.690   72.511
LGA    D    38_B      D    38_B     0.895     0    0.046   0.179     0.990   90.476   91.667
LGA    A    39_B      A    39_B     0.685     0    0.025   0.038     0.775   90.476   90.476
LGA    A    40_B      A    40_B     0.886     0    0.091   0.090     1.542   83.810   83.333
LGA    H    41_B      H    41_B     1.494     0    0.095   1.001     3.243   79.286   74.143
LGA    R    42_B      R    42_B     1.340     0    0.125   1.294     7.148   79.286   54.805
LGA    N    43_B      N    43_B     1.445     0    0.036   1.080     5.601   81.429   61.845
LGA    D    44_B      D    44_B     1.037     0    0.090   0.199     1.123   88.333   89.405
LGA    K    45_B      K    45_B     1.270     0    0.067   0.520     4.375   83.690   68.624
LGA    D    46_B      D    46_B     1.115     0    0.026   0.060     1.998   85.952   80.476
LGA    K    47_B      K    47_B     0.573     0    0.018   0.436     1.616   90.476   88.571
LGA    V    48_B      V    48_B     0.547     0    0.046   1.288     3.132   92.857   82.653
LGA    K    49_B      K    49_B     0.793     0    0.033   1.465     8.872   88.214   58.942
LGA    K    50_B      K    50_B     1.145     0    0.028   1.322     6.245   81.429   66.561
LGA    V    51_B      V    51_B     0.947     0    0.041   0.078     1.197   90.476   87.891
LGA    V    52_B      V    52_B     0.436     0    0.039   1.205     2.555   95.238   86.122
LGA    E    53_B      E    53_B     0.865     0    0.033   0.955     3.400   90.476   80.053
LGA    E    54_B      E    54_B     1.289     0    0.034   0.928     3.943   81.429   72.487
LGA    A    55_B      A    55_B     0.939     0    0.037   0.052     0.993   90.476   90.476
LGA    K    56_B      K    56_B     0.445     0    0.048   0.736     1.538   92.857   89.630
LGA    K    57_B      K    57_B     0.775     0    0.030   0.984     5.570   85.952   64.127
LGA    V    58_B      V    58_B     1.542     0    0.105   0.130     2.566   75.000   70.680
LGA    V    59_B      V    59_B     1.536     0    0.073   0.252     1.651   79.286   78.980
LGA    S    60_B      S    60_B     1.426     0    0.192   0.583     2.166   75.119   77.222
LGA    T    61_B      T    61_B     1.392     0    0.055   1.006     3.106   75.119   69.864

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     2.465          2.196                  3.901           73.236   62.713

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     55    1.93    79.918    83.399     2.708

LGA_LOCAL      RMSD:   1.931  Number of atoms:   55  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.525  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.465  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.073838 * X  +  -0.621044 * Y  +  -0.780290 * Z  +  10.095090
  Y_new =  -0.153500 * X  +   0.766024 * Y  +  -0.624215 * Z  +   2.524347
  Z_new =   0.985386 * X  +   0.165865 * Y  +  -0.038769 * Z  +  -2.772362 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.122442 -1.399627  1.800411   [DEG:  -64.3112  -80.1927  103.1560 ]
ZXZ: -0.896068  1.609575  1.404035   [DEG:  -51.3409   92.2218   80.4453 ]
 
# END of job
