
#######################################################
#                                                     #
#                        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        2.38     2.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    53       9_B - 61_B        1.98     2.40
  LCS_AVERAGE:     80.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43      19_B - 61_B        0.87     2.42
  LCS_AVERAGE:     59.85

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     21   22   61      8   15   20   21   21   21   30   55   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   22   61     17   19   25   28   37   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   22   61     17   20   35   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   22   61     17   19   20   21   27   45   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   22   61     17   19   20   21   21   21   48   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   22   61     17   19   20   23   34   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   22   61     17   19   30   43   44   45   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   22   61     17   19   20   21   27   39   48   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   53   61     17   19   20   28   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   53   61     17   19   20   28   39   45   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   53   61     17   19   20   21   44   45   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   53   61     17   19   20   21   21   39   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   53   61     17   19   20   21   34   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   53   61     17   19   20   21   30   44   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   53   61     15   19   20   21   21   21   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   53   61     11   19   25   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   53   61     17   19   20   21   32   43   48   50   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   53   61     17   19   20   21   21   21   36   56   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     43   53   61     17   19   20   21   21   45   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     43   53   61     17   27   37   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     43   53   61     18   39   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     43   53   61     13   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     43   53   61     15   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     43   53   61     12   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     43   53   61     17   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     43   53   61     29   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     43   53   61     28   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     43   53   61     29   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     43   53   61     17   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     43   53   61     31   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     43   53   61     25   40   41   43   44   46   49   58   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  80.02  (  59.85   80.22  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     31     40     41     43     44     46     49     58     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  50.82  65.57  67.21  70.49  72.13  75.41  80.33  95.08 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.44   0.49   0.73   0.83   1.11   1.41   2.13   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38
GDT RMS_ALL_AT   2.45   2.43   2.44   2.46   2.45   2.48   2.52   2.39   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38

# Checking swapping
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    53_B      E    53_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     5.446     0    0.462   1.300     8.192   27.976   18.036
LGA    Y     2_B      Y     2_B     4.728     0    0.069   0.195    10.752   42.143   18.810
LGA    I     3_B      I     3_B     2.407     0    0.069   0.065     6.143   68.810   47.917
LGA    R     4_B      R     4_B     3.760     0    0.038   0.545    13.148   50.357   21.602
LGA    E     5_B      E     5_B     4.583     0    0.047   0.935    11.237   43.690   22.116
LGA    L     6_B      L     6_B     3.756     0    0.043   1.175     8.059   50.119   31.964
LGA    R     7_B      R     7_B     3.456     0    0.026   0.192    12.476   55.476   24.242
LGA    A     8_B      A     8_B     4.035     0    0.048   0.052     5.923   48.571   43.143
LGA    A     9_B      A     9_B     3.770     0    0.020   0.029     5.530   51.905   45.810
LGA    L    10_B      L    10_B     3.938     0    0.019   0.050     8.851   48.452   29.107
LGA    I    11_B      I    11_B     4.113     0    0.014   0.048     8.443   46.905   29.226
LGA    L    12_B      L    12_B     3.411     0    0.041   0.058     8.207   59.167   36.012
LGA    L    13_B      L    13_B     3.770     0    0.012   0.080     8.965   50.357   29.821
LGA    A    14_B      A    14_B     4.829     0    0.034   0.038     6.484   37.500   33.429
LGA    L    15_B      L    15_B     4.119     0    0.077   1.379    10.475   50.357   28.512
LGA    K    16_B      K    16_B     2.787     0    0.035   0.701    13.661   62.976   33.545
LGA    K    17_B      K    17_B     4.890     0    0.047   0.680    13.855   34.762   17.090
LGA    Q    18_B      Q    18_B     5.694     0    0.040   0.872    12.978   27.857   13.651
LGA    H    19_B      H    19_B     3.469     0    0.259   0.532     9.983   52.024   26.714
LGA    A    20_B      A    20_B     2.850     0    0.647   0.605     5.109   69.048   60.476
LGA    E    21_B      E    21_B     1.344     0    0.138   0.789     4.703   81.786   66.455
LGA    D    22_B      D    22_B     1.361     0    0.077   0.281     3.312   85.952   71.607
LGA    P    23_B      P    23_B     0.638     0    0.077   0.079     1.470   90.476   86.599
LGA    D    24_B      D    24_B     1.190     0    0.078   0.211     2.355   81.429   76.131
LGA    A    25_B      A    25_B     1.094     0    0.030   0.033     1.145   85.952   85.048
LGA    Q    26_B      Q    26_B     0.468     0    0.052   0.996     4.290   97.619   81.376
LGA    R    27_B      R    27_B     0.416     0    0.019   0.164     0.713  100.000   95.671
LGA    V    28_B      V    28_B     0.692     0    0.015   0.031     0.874   90.476   90.476
LGA    A    29_B      A    29_B     0.656     0    0.019   0.019     0.663   90.476   90.476
LGA    D    30_B      D    30_B     0.428     0    0.035   0.635     2.382   97.619   88.690
LGA    E    31_B      E    31_B     0.336     0    0.025   0.176     0.660  100.000   97.884
LGA    L    32_B      L    32_B     0.399     0    0.019   0.103     0.572  100.000   98.810
LGA    M    33_B      M    33_B     0.404     0    0.024   1.017     2.241  100.000   88.869
LGA    K    34_B      K    34_B     0.326     0    0.032   0.870     5.453  100.000   75.503
LGA    K    35_B      K    35_B     0.172     0    0.020   0.268     0.738  100.000   97.884
LGA    L    36_B      L    36_B     0.187     0    0.014   1.361     3.035  100.000   83.095
LGA    F    37_B      F    37_B     0.567     0    0.023   0.106     1.412   95.238   88.095
LGA    D    38_B      D    38_B     0.482     0    0.011   0.889     3.861   97.619   79.286
LGA    A    39_B      A    39_B     0.442     0    0.030   0.034     0.581   95.238   96.190
LGA    A    40_B      A    40_B     0.478     0    0.092   0.107     0.963   92.857   94.286
LGA    H    41_B      H    41_B     0.701     0    0.078   0.943     2.491   88.214   78.381
LGA    R    42_B      R    42_B     0.889     0    0.028   0.776     2.737   90.476   82.684
LGA    N    43_B      N    43_B     0.797     0    0.066   0.268     1.062   90.476   89.345
LGA    D    44_B      D    44_B     0.706     0    0.049   0.121     0.771   92.857   91.667
LGA    K    45_B      K    45_B     0.865     0    0.021   0.230     2.104   90.476   80.794
LGA    D    46_B      D    46_B     0.784     0    0.023   0.160     1.720   90.476   86.012
LGA    K    47_B      K    47_B     0.106     0    0.035   0.205     1.810  100.000   91.852
LGA    V    48_B      V    48_B     0.359     0    0.015   0.048     0.773  100.000   95.918
LGA    K    49_B      K    49_B     0.452     0    0.025   0.964     6.161  100.000   70.688
LGA    K    50_B      K    50_B     0.515     0    0.036   0.336     1.945   97.619   91.693
LGA    V    51_B      V    51_B     0.506     0    0.021   0.041     0.795   95.238   93.197
LGA    V    52_B      V    52_B     0.348     0    0.021   0.106     0.699  100.000   97.279
LGA    E    53_B      E    53_B     0.206     0    0.023   0.923     3.614  100.000   83.175
LGA    E    54_B      E    54_B     0.509     0    0.050   0.330     1.746   97.619   90.741
LGA    A    55_B      A    55_B     0.549     0    0.027   0.027     0.691   92.857   92.381
LGA    K    56_B      K    56_B     0.275     0    0.022   0.432     1.702  100.000   93.810
LGA    K    57_B      K    57_B     0.168     0    0.021   0.047     1.175  100.000   94.762
LGA    V    58_B      V    58_B     0.717     0    0.145   0.247     1.805   90.595   85.442
LGA    V    59_B      V    59_B     0.861     0    0.043   0.118     0.967   90.476   90.476
LGA    S    60_B      S    60_B     0.572     0    0.193   0.706     2.327   90.476   87.778
LGA    T    61_B      T    61_B     0.619     0    0.028   0.054     0.834   90.476   90.476

# 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):     2.375          2.070                  3.939           79.500   68.889

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     58    2.13    82.787    83.098     2.599

LGA_LOCAL      RMSD:   2.131  Number of atoms:   58  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.394  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.375  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.336269 * X  +  -0.413932 * Y  +   0.845922 * Z  +  -0.040760
  Y_new =   0.937679 * X  +  -0.230751 * Y  +   0.259831 * Z  + -12.366789
  Z_new =   0.087645 * X  +   0.880576 * Y  +   0.465730 * Z  +   1.479464 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.915128 -0.087758  1.084303   [DEG:  109.7288   -5.0281   62.1260 ]
ZXZ:  1.868807  1.086337  0.099205   [DEG:  107.0747   62.2425    5.6840 ]
 
# END of job
