
#######################################################
#                                                     #
#                        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   64 (  513),  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        1.95     1.95
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.95     1.95
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40      19_B - 58_B        0.96     2.04
  LONGEST_CONTINUOUS_SEGMENT:    40      20_B - 59_B        0.90     2.09
  LONGEST_CONTINUOUS_SEGMENT:    40      21_B - 60_B        0.97     2.10
  LCS_AVERAGE:     56.33

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   61   61      3    7   12   18   29   39   47   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   61   61      8   18   20   22   30   50   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   61   61      8   18   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   61   61      8   18   37   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   61   61      7   18   20   30   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   61   61      9   18   26   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   61   61     10   23   37   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   61   61     10   18   32   42   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   61   61     10   18   22   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   61   61     10   18   31   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   61   61     10   18   26   41   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   61   61     10   18   20   32   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   61   61     12   22   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   61   61     10   18   20   35   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   61   61     10   18   20   35   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   61   61     10   18   37   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   61   61     10   18   20   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   61   61     10   18   20   35   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     40   61   61      7   16   30   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     40   61   61      4   17   37   44   51   55   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     40   61   61     12   35   39   45   51   55   57   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     40   61   61     19   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     40   61   61     12   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     40   61   61     17   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     40   61   61     16   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     40   61   61     20   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     40   61   61     18   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     40   61   61     22   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     40   61   61     23   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     40   61   61     20   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     40   61   61     24   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     40   61   61     20   35   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     40   61   61      9   32   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     40   61   61      6   32   39   45   51   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     40   61   61      5   26   34   43   49   54   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     40   61   61      5   17   30   39   49   53   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     40   61   61      5   17   25   33   47   53   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     38   61   61      5    9   25   30   38   52   58   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  85.44  (  56.33  100.00  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     24     35     39     45     51     55     58     60     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  39.34  57.38  63.93  73.77  83.61  90.16  95.08  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.61   0.77   1.04   1.32   1.56   1.84   1.85   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95
GDT RMS_ALL_AT   2.21   2.07   2.07   2.04   2.05   2.07   1.96   1.96   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  F    37_B      F    37_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     5.363     0    0.025   0.902     7.064   22.262   34.464
LGA    Y     2_B      Y     2_B     4.151     0    0.187   1.357     5.122   43.571   44.206
LGA    I     3_B      I     3_B     1.652     0    0.031   0.035     2.847   75.119   68.095
LGA    R     4_B      R     4_B     1.965     0    0.016   0.415     7.413   72.976   45.455
LGA    E     5_B      E     5_B     2.682     0    0.021   1.267     5.922   62.857   44.550
LGA    L     6_B      L     6_B     1.950     0    0.025   0.069     4.482   77.143   62.024
LGA    R     7_B      R     7_B     2.249     0    0.022   0.079     5.655   67.024   45.801
LGA    A     8_B      A     8_B     3.040     0    0.030   0.032     4.000   59.167   56.000
LGA    A     9_B      A     9_B     1.913     0    0.016   0.018     2.616   77.143   73.143
LGA    L    10_B      L    10_B     2.011     0    0.035   0.054     4.281   68.929   57.143
LGA    I    11_B      I    11_B     3.465     0    0.015   0.126     6.591   53.571   38.333
LGA    L    12_B      L    12_B     3.004     0    0.015   1.139     8.385   61.190   39.524
LGA    L    13_B      L    13_B     1.678     0    0.091   1.399     7.563   79.286   52.500
LGA    A    14_B      A    14_B     3.128     0    0.034   0.035     4.375   55.476   51.810
LGA    L    15_B      L    15_B     3.625     0    0.021   0.195     7.248   53.690   36.369
LGA    K    16_B      K    16_B     2.021     0    0.054   0.178     6.508   72.976   50.952
LGA    K    17_B      K    17_B     2.014     0    0.019   1.134     2.844   68.929   65.079
LGA    Q    18_B      Q    18_B     3.092     0    0.021   1.430     8.918   59.167   36.508
LGA    H    19_B      H    19_B     2.508     0    0.151   0.437     6.864   59.167   40.048
LGA    A    20_B      A    20_B     2.560     0    0.403   0.451     3.647   64.881   60.571
LGA    E    21_B      E    21_B     1.603     0    0.053   0.488     1.928   77.143   81.534
LGA    D    22_B      D    22_B     1.119     0    0.018   0.275     1.425   83.690   87.083
LGA    P    23_B      P    23_B     1.105     0    0.066   0.341     1.321   85.952   84.014
LGA    D    24_B      D    24_B     0.711     0    0.026   0.973     5.133   88.214   72.083
LGA    A    25_B      A    25_B     1.365     0    0.030   0.029     1.781   81.429   79.714
LGA    Q    26_B      Q    26_B     1.386     0    0.041   0.406     2.765   81.429   71.376
LGA    R    27_B      R    27_B     0.708     0    0.055   0.248     2.096   90.476   82.511
LGA    V    28_B      V    28_B     1.155     0    0.016   0.036     1.761   83.690   81.497
LGA    A    29_B      A    29_B     1.481     0    0.023   0.039     1.731   81.429   79.714
LGA    D    30_B      D    30_B     1.037     0    0.017   0.705     1.687   85.952   83.750
LGA    E    31_B      E    31_B     0.764     0    0.021   0.121     0.962   90.476   90.476
LGA    L    32_B      L    32_B     1.006     0    0.061   1.378     5.067   88.214   67.321
LGA    M    33_B      M    33_B     0.937     0    0.046   0.804     3.299   90.476   78.095
LGA    K    34_B      K    34_B     0.707     0    0.062   1.417     8.280   90.476   63.651
LGA    K    35_B      K    35_B     0.316     0    0.011   0.606     2.309  100.000   93.069
LGA    L    36_B      L    36_B     0.368     0    0.009   0.978     3.955   95.238   83.810
LGA    F    37_B      F    37_B     1.044     0    0.026   0.247     2.902   88.214   73.463
LGA    D    38_B      D    38_B     0.658     0    0.012   0.157     0.849   90.476   90.476
LGA    A    39_B      A    39_B     0.494     0    0.045   0.047     1.173   92.976   94.381
LGA    A    40_B      A    40_B     0.966     0    0.146   0.149     1.322   83.690   85.048
LGA    H    41_B      H    41_B     1.038     0    0.045   1.412     4.507   85.952   66.000
LGA    R    42_B      R    42_B     0.778     0    0.016   0.818     2.986   85.952   81.775
LGA    N    43_B      N    43_B     1.203     0    0.093   0.796     3.342   81.429   72.262
LGA    D    44_B      D    44_B     0.874     0    0.018   0.106     0.952   90.476   90.476
LGA    K    45_B      K    45_B     0.951     0    0.009   0.315     2.857   90.476   79.947
LGA    D    46_B      D    46_B     0.804     0    0.020   0.918     4.358   92.857   72.143
LGA    K    47_B      K    47_B     0.363     0    0.011   0.277     1.680   97.619   93.862
LGA    V    48_B      V    48_B     0.417     0    0.017   0.084     0.858  100.000   97.279
LGA    K    49_B      K    49_B     0.380     0    0.044   1.039     7.005  100.000   70.423
LGA    K    50_B      K    50_B     0.394     0    0.016   0.195     1.023  100.000   94.762
LGA    V    51_B      V    51_B     0.380     0    0.036   0.047     0.766  100.000   95.918
LGA    V    52_B      V    52_B     0.256     0    0.031   0.088     0.453  100.000  100.000
LGA    E    53_B      E    53_B     0.281     0    0.020   0.372     1.519  100.000   91.799
LGA    E    54_B      E    54_B     0.537     0    0.048   0.568     3.218   92.857   84.074
LGA    A    55_B      A    55_B     0.942     0    0.013   0.015     1.339   85.952   86.857
LGA    K    56_B      K    56_B     1.229     0    0.018   0.381     1.906   81.548   80.529
LGA    K    57_B      K    57_B     1.310     0    0.023   0.057     1.938   77.143   86.667
LGA    V    58_B      V    58_B     2.333     0    0.113   0.185     3.306   61.190   60.612
LGA    V    59_B      V    59_B     2.879     0    0.067   0.139     3.377   55.476   55.170
LGA    S    60_B      S    60_B     3.469     0    0.240   0.258     4.216   45.119   46.746
LGA    T    61_B      T    61_B     3.833     0    0.016   0.077     4.460   40.238   42.517

# 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):     1.954          1.876                  2.702           78.171   70.090

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   61    4.0     60    1.85    82.377    90.056     3.075

LGA_LOCAL      RMSD:   1.851  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.960  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.954  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.277018 * X  +  -0.930926 * Y  +   0.237989 * Z  +  14.873763
  Y_new =  -0.336888 * X  +  -0.137861 * Y  +  -0.931397 * Z  + -10.358711
  Z_new =   0.899871 * X  +  -0.338189 * Y  +  -0.275428 * Z  +   5.107261 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.258977 -1.119473 -2.254269   [DEG: -129.4299  -64.1411 -129.1601 ]
ZXZ:  0.250166  1.849831  1.930285   [DEG:   14.3334  105.9875  110.5972 ]
 
# END of job
