
#######################################################
#                                                     #
#                        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        2.47     2.47
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    52      10_B - 61_B        1.95     2.53
  LCS_AVERAGE:     77.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43      19_B - 61_B        0.89     2.53
  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   20   21   21   21   21   26   35   57   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   22   61     19   20   21   28   36   47   48   54   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   22   61     19   20   35   42   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   22   61     19   20   21   21   21   27   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   22   61     19   20   21   21   21   21   48   54   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   22   61     19   20   21   22   34   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   22   61     19   20   30   42   43   45   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   22   61     19   20   21   21   21   27   37   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   22   61     19   20   24   28   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   52   61     19   20   21   29   39   45   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   52   61     19   20   21   21   42   44   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   52   61     19   20   21   21   21   27   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   52   61     19   20   21   21   43   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   52   61     19   20   21   21   28   43   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   52   61     19   20   21   21   21   21   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   52   61     19   20   36   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   52   61     19   20   21   21   32   43   48   50   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   52   61     19   20   21   21   21   21   32   54   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     43   52   61     19   20   21   21   21   44   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     43   52   61     19   28   37   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     43   52   61     27   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     43   52   61     13   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     43   52   61     21   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     43   52   61     13   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     43   52   61     13   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     43   52   61     22   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     43   52   61     28   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     43   52   61     28   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     43   52   61     23   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     43   52   61     28   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     43   52   61     28   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     43   52   61     29   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     43   52   61     22   40   41   43   44   47   48   55   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  79.28  (  59.85   77.99  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     29     40     41     43     44     47     48     55     60     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  47.54  65.57  67.21  70.49  72.13  77.05  78.69  90.16  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.49   0.51   0.71   0.79   1.16   1.25   1.91   2.36   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47
GDT RMS_ALL_AT   2.55   2.54   2.54   2.56   2.56   2.60   2.60   2.52   2.48   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47

# 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     6.537     0    0.682   1.507     8.738   18.929   12.500
LGA    Y     2_B      Y     2_B     5.527     0    0.077   0.177    11.461   32.024   13.333
LGA    I     3_B      I     3_B     2.102     0    0.062   0.065     5.653   68.929   50.595
LGA    R     4_B      R     4_B     3.915     0    0.045   0.592    13.329   48.690   20.216
LGA    E     5_B      E     5_B     5.121     0    0.052   0.933    11.886   37.500   18.466
LGA    L     6_B      L     6_B     3.897     0    0.038   0.137     8.355   50.119   31.190
LGA    R     7_B      R     7_B     3.194     0    0.024   0.691    12.105   57.500   24.848
LGA    A     8_B      A     8_B     4.178     0    0.055   0.057     6.173   48.571   42.286
LGA    A     9_B      A     9_B     3.983     0    0.014   0.024     5.765   50.119   44.381
LGA    L    10_B      L    10_B     3.905     0    0.019   0.033     8.786   48.452   29.524
LGA    I    11_B      I    11_B     4.203     0    0.010   0.048     8.533   46.905   28.631
LGA    L    12_B      L    12_B     3.453     0    0.051   0.059     8.220   57.262   35.060
LGA    L    13_B      L    13_B     3.712     0    0.010   1.405    10.477   50.357   28.631
LGA    A    14_B      A    14_B     5.054     0    0.046   0.049     6.747   36.190   31.619
LGA    L    15_B      L    15_B     4.353     0    0.079   1.369    10.553   46.905   26.548
LGA    K    16_B      K    16_B     2.541     0    0.049   0.539    13.365   64.881   34.550
LGA    K    17_B      K    17_B     5.024     0    0.039   0.779    11.379   33.452   17.037
LGA    Q    18_B      Q    18_B     6.048     0    0.026   1.334    12.535   25.357   12.910
LGA    H    19_B      H    19_B     3.706     0    0.252   0.527    10.152   50.357   26.000
LGA    A    20_B      A    20_B     2.562     0    0.641   0.600     4.853   73.333   64.952
LGA    E    21_B      E    21_B     0.973     0    0.159   0.251     1.878   86.071   79.683
LGA    D    22_B      D    22_B     1.495     0    0.077   0.336     3.350   83.690   69.583
LGA    P    23_B      P    23_B     0.852     0    0.082   0.325     1.410   88.214   85.306
LGA    D    24_B      D    24_B     1.359     0    0.082   0.182     2.464   81.429   76.131
LGA    A    25_B      A    25_B     1.205     0    0.027   0.028     1.251   85.952   85.048
LGA    Q    26_B      Q    26_B     0.523     0    0.055   1.010     4.373   90.476   77.407
LGA    R    27_B      R    27_B     0.511     0    0.024   0.208     0.825   92.857   91.342
LGA    V    28_B      V    28_B     0.768     0    0.014   0.028     0.954   90.476   90.476
LGA    A    29_B      A    29_B     0.676     0    0.022   0.023     0.698   90.476   90.476
LGA    D    30_B      D    30_B     0.328     0    0.046   0.640     2.564  100.000   90.000
LGA    E    31_B      E    31_B     0.282     0    0.023   0.166     0.858  100.000   96.825
LGA    L    32_B      L    32_B     0.473     0    0.025   0.080     0.673  100.000   96.429
LGA    M    33_B      M    33_B     0.496     0    0.033   0.875     2.717  100.000   91.071
LGA    K    34_B      K    34_B     0.269     0    0.060   0.872     5.487  100.000   75.503
LGA    K    35_B      K    35_B     0.088     0    0.024   0.249     0.802  100.000   96.825
LGA    L    36_B      L    36_B     0.168     0    0.017   1.365     3.310  100.000   83.988
LGA    F    37_B      F    37_B     0.421     0    0.014   0.156     1.165  100.000   92.338
LGA    D    38_B      D    38_B     0.381     0    0.025   0.204     1.073   97.619   94.107
LGA    A    39_B      A    39_B     0.269     0    0.034   0.041     0.347  100.000  100.000
LGA    A    40_B      A    40_B     0.267     0    0.106   0.123     0.766   97.619   98.095
LGA    H    41_B      H    41_B     0.567     0    0.070   0.910     2.872   92.857   81.286
LGA    R    42_B      R    42_B     0.959     0    0.019   0.825     3.058   88.214   80.390
LGA    N    43_B      N    43_B     0.682     0    0.065   0.203     1.266   95.238   89.464
LGA    D    44_B      D    44_B     0.407     0    0.039   0.123     0.642  100.000   98.810
LGA    K    45_B      K    45_B     0.405     0    0.022   0.298     2.087  100.000   88.889
LGA    D    46_B      D    46_B     0.504     0    0.024   0.168     1.390   97.619   92.917
LGA    K    47_B      K    47_B     0.284     0    0.030   0.207     1.784  100.000   91.852
LGA    V    48_B      V    48_B     0.334     0    0.020   0.061     0.659  100.000   98.639
LGA    K    49_B      K    49_B     0.187     0    0.035   0.961     5.894  100.000   73.545
LGA    K    50_B      K    50_B     0.602     0    0.037   0.326     1.775   92.857   89.577
LGA    V    51_B      V    51_B     0.768     0    0.021   0.035     1.042   90.476   89.184
LGA    V    52_B      V    52_B     0.418     0    0.017   0.095     0.611  100.000   97.279
LGA    E    53_B      E    53_B     0.171     0    0.020   0.929     3.636  100.000   84.233
LGA    E    54_B      E    54_B     0.707     0    0.060   0.361     2.182   90.476   86.667
LGA    A    55_B      A    55_B     0.744     0    0.023   0.023     0.853   90.476   90.476
LGA    K    56_B      K    56_B     0.282     0    0.036   0.420     1.512  100.000   94.868
LGA    K    57_B      K    57_B     0.222     0    0.020   0.051     1.156  100.000   95.820
LGA    V    58_B      V    58_B     0.850     0    0.156   0.241     1.838   88.214   84.082
LGA    V    59_B      V    59_B     0.960     0    0.049   0.111     1.007   90.476   87.891
LGA    S    60_B      S    60_B     0.769     0    0.186   0.228     0.946   90.476   90.476
LGA    T    61_B      T    61_B     0.858     0    0.034   0.083     0.948   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):     2.470          2.173                  3.991           79.157   69.356

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     55    1.91    81.557    82.210     2.736

LGA_LOCAL      RMSD:   1.910  Number of atoms:   55  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.520  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.470  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.641647 * X  +   0.434658 * Y  +   0.631950 * Z  +   1.985522
  Y_new =   0.257830 * X  +   0.898211 * Y  +  -0.356007 * Z  +  -9.464958
  Z_new =  -0.722366 * X  +  -0.065495 * Y  +  -0.688402 * Z  +   0.245427 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.759515  0.807218 -3.046737   [DEG:  158.1085   46.2502 -174.5652 ]
ZXZ:  1.057764  2.330081 -1.661217   [DEG:   60.6054  133.5038  -95.1807 ]
 
# END of job
