
#######################################################
#                                                     #
#                        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        2.05     2.05
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       2_B - 61_B        1.94     2.06
  LCS_AVERAGE:     98.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      20_B - 60_B        0.93     2.24
  LONGEST_CONTINUOUS_SEGMENT:    41      21_B - 61_B        0.97     2.28
  LCS_AVERAGE:     57.46

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   59   61      3    4    7   11   16   22   29   56   57   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   60   61      3   18   20   22   24   43   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   60   61     10   18   27   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   60   61     15   18   35   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   60   61     15   18   20   24   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   60   61     12   18   20   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   60   61     15   18   31   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   60   61     15   18   20   39   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   60   61     15   18   20   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   60   61     15   18   26   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   60   61     15   18   28   39   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   60   61     15   18   20   39   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   60   61     15   19   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   60   61     15   18   20   32   45   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   60   61     15   18   20   32   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   60   61     15   18   35   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   60   61     15   18   20   35   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   60   61     15   18   20   22   35   51   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     38   60   61      8   18   20   32   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     41   60   61      6   19   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     41   60   61     15   30   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     41   60   61     12   27   34   42   48   54   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     41   60   61     13   33   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     41   60   61     22   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     41   60   61     19   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     41   60   61     18   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     41   60   61     19   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     41   60   61     13   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     41   60   61     21   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     41   60   61     18   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     41   60   61     25   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     41   60   61     12   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     41   60   61     12   34   39   42   48   54   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     41   60   61     11   24   39   42   48   53   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     41   60   61      8   23   32   39   48   52   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     41   60   61      8   23   32   39   48   52   58   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     41   60   61      8   23   31   34   45   52   57   60   60   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  85.26  (  57.46   98.33  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     25     34     39     42     48     54     58     60     60     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  40.98  55.74  63.93  68.85  78.69  88.52  95.08  98.36  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    0.25   0.48   0.78   0.92   1.24   1.62   1.86   1.94   1.94   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05
GDT RMS_ALL_AT   2.35   2.23   2.19   2.21   2.15   2.16   2.07   2.06   2.06   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  D    22_B      D    22_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  F    37_B      F    37_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     5.762     0    0.555   1.104     7.365   16.548   30.833
LGA    Y     2_B      Y     2_B     4.354     0    0.253   1.342     5.358   41.905   45.992
LGA    I     3_B      I     3_B     1.782     0    0.081   0.119     2.907   72.976   67.024
LGA    R     4_B      R     4_B     2.146     0    0.017   0.921     7.225   68.929   43.117
LGA    E     5_B      E     5_B     2.759     0    0.027   1.252     6.562   62.857   44.180
LGA    L     6_B      L     6_B     2.200     0    0.040   0.075     4.775   70.833   55.655
LGA    R     7_B      R     7_B     2.426     0    0.016   0.095     6.233   64.881   42.771
LGA    A     8_B      A     8_B     3.129     0    0.030   0.032     4.176   59.167   54.762
LGA    A     9_B      A     9_B     2.116     0    0.014   0.017     2.903   72.976   69.810
LGA    L    10_B      L    10_B     2.182     0    0.020   0.047     4.524   67.024   53.750
LGA    I    11_B      I    11_B     3.337     0    0.019   0.073     6.109   55.476   41.071
LGA    L    12_B      L    12_B     2.838     0    0.016   1.092     8.259   62.976   41.310
LGA    L    13_B      L    13_B     1.859     0    0.075   1.400     7.691   75.000   48.988
LGA    A    14_B      A    14_B     3.364     0    0.018   0.023     4.566   52.024   47.905
LGA    L    15_B      L    15_B     3.690     0    0.029   0.249     7.135   50.119   35.060
LGA    K    16_B      K    16_B     1.868     0    0.047   0.151     6.796   77.143   52.328
LGA    K    17_B      K    17_B     2.414     0    0.011   0.588     6.292   65.119   46.878
LGA    Q    18_B      Q    18_B     4.051     0    0.033   1.429     9.771   41.905   25.608
LGA    H    19_B      H    19_B     3.372     0    0.134   0.810     7.732   51.905   30.810
LGA    A    20_B      A    20_B     2.159     0    0.294   0.330     3.351   72.976   68.381
LGA    E    21_B      E    21_B     1.219     0    0.376   0.597     1.858   77.143   80.582
LGA    D    22_B      D    22_B     3.035     0    0.539   1.121     8.279   63.095   36.310
LGA    P    23_B      P    23_B     1.671     0    0.095   0.344     1.813   77.143   75.306
LGA    D    24_B      D    24_B     0.729     0    0.022   0.487     1.486   88.214   88.214
LGA    A    25_B      A    25_B     1.480     0    0.044   0.042     1.965   81.429   79.714
LGA    Q    26_B      Q    26_B     1.380     0    0.020   1.274     6.139   81.429   57.302
LGA    R    27_B      R    27_B     0.753     0    0.021   1.135     4.806   90.476   76.190
LGA    V    28_B      V    28_B     1.069     0    0.009   0.039     1.687   83.690   81.497
LGA    A    29_B      A    29_B     1.289     0    0.020   0.033     1.586   81.429   79.714
LGA    D    30_B      D    30_B     0.992     0    0.013   0.713     1.348   90.476   87.083
LGA    E    31_B      E    31_B     0.711     0    0.027   0.885     3.859   90.476   71.746
LGA    L    32_B      L    32_B     0.822     0    0.007   1.048     2.747   90.476   82.976
LGA    M    33_B      M    33_B     0.752     0    0.014   0.736     2.994   90.476   81.012
LGA    K    34_B      K    34_B     0.639     0    0.052   1.413     8.046   90.476   64.180
LGA    K    35_B      K    35_B     0.354     0    0.003   0.272     0.778  100.000   98.942
LGA    L    36_B      L    36_B     0.511     0    0.016   1.398     3.754   92.857   76.548
LGA    F    37_B      F    37_B     0.970     0    0.020   0.136     2.225   90.476   77.836
LGA    D    38_B      D    38_B     0.572     0    0.035   0.173     0.666   90.476   92.857
LGA    A    39_B      A    39_B     0.581     0    0.013   0.021     0.746   90.476   90.476
LGA    A    40_B      A    40_B     0.832     0    0.078   0.083     1.331   85.952   86.857
LGA    H    41_B      H    41_B     0.962     0    0.037   1.407     4.273   88.214   69.667
LGA    R    42_B      R    42_B     0.893     0    0.017   1.001     2.687   85.952   81.818
LGA    N    43_B      N    43_B     1.143     0    0.073   0.806     3.511   85.952   74.762
LGA    D    44_B      D    44_B     0.787     0    0.018   0.169     1.049   90.476   89.345
LGA    K    45_B      K    45_B     0.840     0    0.034   0.998     8.217   90.476   62.381
LGA    D    46_B      D    46_B     0.722     0    0.019   0.045     0.799   90.476   90.476
LGA    K    47_B      K    47_B     0.428     0    0.016   0.915     5.157   97.619   78.254
LGA    V    48_B      V    48_B     0.526     0    0.014   0.063     0.763   95.238   93.197
LGA    K    49_B      K    49_B     0.454     0    0.008   0.631     2.408   97.619   85.079
LGA    K    50_B      K    50_B     0.449     0    0.007   0.372     1.900  100.000   93.810
LGA    V    51_B      V    51_B     0.330     0    0.039   0.046     0.775  100.000   95.918
LGA    V    52_B      V    52_B     0.355     0    0.026   0.083     0.679   97.619   95.918
LGA    E    53_B      E    53_B     0.390     0    0.016   0.851     2.803  100.000   87.249
LGA    E    54_B      E    54_B     0.454     0    0.005   0.926     4.121   95.238   77.460
LGA    A    55_B      A    55_B     0.880     0    0.012   0.021     1.258   85.952   86.857
LGA    K    56_B      K    56_B     1.175     0    0.007   0.712     2.290   83.690   79.630
LGA    K    57_B      K    57_B     1.202     0    0.011   0.588     2.083   77.143   78.836
LGA    V    58_B      V    58_B     2.192     0    0.115   0.184     3.194   61.190   60.612
LGA    V    59_B      V    59_B     2.827     0    0.066   0.136     3.133   57.262   55.170
LGA    S    60_B      S    60_B     2.934     0    0.058   0.605     3.693   51.905   60.476
LGA    T    61_B      T    61_B     3.755     0    0.169   1.110     4.445   41.905   40.748

# 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):     2.054          1.955                  2.941           77.104   68.020

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   61    4.0     60    1.94    80.738    88.662     2.939

LGA_LOCAL      RMSD:   1.942  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.062  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.054  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.227972 * X  +  -0.937145 * Y  +   0.264174 * Z  +  14.805794
  Y_new =  -0.298145 * X  +  -0.191097 * Y  +  -0.935196 * Z  + -10.030064
  Z_new =   0.926897 * X  +  -0.291961 * Y  +  -0.235840 * Z  +   7.135367 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.223598 -1.186059 -2.250264   [DEG: -127.4028  -67.9562 -128.9306 ]
ZXZ:  0.275307  1.808880  1.875946   [DEG:   15.7739  103.6412  107.4838 ]
 
# END of job
