
#######################################################
#                                                     #
#                        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        2.80     2.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    47      15_B - 61_B        1.93     2.88
  LCS_AVERAGE:     66.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      20_B - 60_B        0.99     2.88
  LONGEST_CONTINUOUS_SEGMENT:    41      21_B - 61_B        0.96     2.88
  LCS_AVERAGE:     54.50

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      7   14   16   16   19   27   33   39   52   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     16   19   61     12   14   16   34   39   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     16   19   61     12   14   16   16   34   44   45   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     16   19   61     12   14   16   16   17   18   19   39   48   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     16   19   61     12   14   16   16   17   45   48   50   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     16   19   61     12   14   16   17   37   45   46   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     16   19   61     12   14   16   16   17   18   43   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     16   19   61     12   14   16   16   19   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     16   19   61     12   14   16   16   17   24   46   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     16   19   61     12   14   16   16   17   32   46   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     16   19   61     12   14   16   16   17   40   42   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     16   19   61     10   14   18   32   41   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     16   19   61     10   14   16   16   17   28   46   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     16   19   61     12   14   16   16   17   18   41   46   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     16   47   61     12   14   16   16   33   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     16   47   61      3    5   16   16   17   33   45   51   54   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B      5   47   61      3    5    6   12   17   18   19   19   49   53   56   60   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B      5   47   61      3    5    6    7   11   17   41   46   48   56   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     40   47   61     12   27   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     41   47   61     12   23   36   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     41   47   61     12   23   29   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     41   47   61     16   27   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     41   47   61     16   29   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     41   47   61     16   29   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     41   47   61     16   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     41   47   61     18   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     41   47   61     12   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     41   47   61     19   31   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     41   47   61     19   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     41   47   61     11   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     41   47   61     14   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     41   47   61     14   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     41   47   61     10   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     41   47   61     10   25   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     41   47   61     10   32   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     41   47   61     10   20   41   43   43   45   48   51   56   59   60   60   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  73.67  (  54.50   66.51  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     19     32     41     43     43     45     48     51     56     59     60     60     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  31.15  52.46  67.21  70.49  70.49  73.77  78.69  83.61  91.80  96.72  98.36  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.65   0.88   1.02   1.02   1.27   1.55   1.80   2.24   2.51   2.65   2.65   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_ALL_AT   3.33   2.97   2.89   2.87   2.87   2.86   2.87   2.86   2.83   2.82   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  D    24_B      D    24_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     6.604     0    0.476   1.277     7.757   20.833   17.798
LGA    Y     2_B      Y     2_B     3.039     0    0.059   1.345    13.010   61.190   26.508
LGA    I     3_B      I     3_B     4.007     0    0.031   1.090    10.460   47.143   27.976
LGA    R     4_B      R     4_B     5.406     0    0.052   0.424    15.925   34.405   13.680
LGA    E     5_B      E     5_B     4.418     0    0.040   0.780     9.696   43.452   23.175
LGA    L     6_B      L     6_B     3.870     0    0.055   1.090     9.734   50.357   28.690
LGA    R     7_B      R     7_B     4.546     0    0.039   1.363    11.413   43.690   20.130
LGA    A     8_B      A     8_B     4.091     0    0.034   0.037     5.973   48.571   43.143
LGA    A     9_B      A     9_B     3.976     0    0.031   0.045     5.908   48.452   43.048
LGA    L    10_B      L    10_B     5.063     0    0.039   0.181    10.154   34.524   19.524
LGA    I    11_B      I    11_B     4.237     0    0.031   0.636     9.826   48.571   29.167
LGA    L    12_B      L    12_B     3.188     0    0.051   1.438     9.805   59.167   35.060
LGA    L    13_B      L    13_B     4.849     0    0.095   1.005     8.567   34.762   21.250
LGA    A    14_B      A    14_B     5.784     0    0.038   0.055     7.193   29.048   25.238
LGA    L    15_B      L    15_B     3.091     0    0.452   0.412     7.839   63.571   40.357
LGA    K    16_B      K    16_B     4.221     0    0.039   1.035    12.783   37.976   18.307
LGA    K    17_B      K    17_B     7.767     0    0.030   0.931    15.693   10.357    4.762
LGA    Q    18_B      Q    18_B     7.629     0    0.088   0.286    14.171   12.857    6.243
LGA    H    19_B      H    19_B     1.964     0    0.432   1.189     7.751   63.095   46.190
LGA    A    20_B      A    20_B     2.555     0    0.079   0.103     2.728   59.048   60.190
LGA    E    21_B      E    21_B     3.219     0    0.063   1.164     3.927   55.357   53.492
LGA    D    22_B      D    22_B     1.467     0    0.110   0.859     3.116   77.262   72.262
LGA    P    23_B      P    23_B     1.297     0    0.051   0.351     2.454   83.690   79.116
LGA    D    24_B      D    24_B     0.383     0    0.074   0.909     4.343   92.857   73.274
LGA    A    25_B      A    25_B     1.000     0    0.043   0.047     1.274   85.952   85.048
LGA    Q    26_B      Q    26_B     0.857     0    0.044   0.802     2.540   90.476   85.767
LGA    R    27_B      R    27_B     0.499     0    0.032   0.748     4.223   92.857   72.727
LGA    V    28_B      V    28_B     0.883     0    0.028   0.949     3.039   90.476   82.109
LGA    A    29_B      A    29_B     0.806     0    0.034   0.061     0.942   90.476   90.476
LGA    D    30_B      D    30_B     0.538     0    0.042   0.778     3.180   90.476   80.000
LGA    E    31_B      E    31_B     0.929     0    0.053   0.826     4.075   88.214   75.979
LGA    L    32_B      L    32_B     0.975     0    0.024   0.871     3.175   90.476   83.155
LGA    M    33_B      M    33_B     0.563     0    0.038   0.846     2.700   90.476   79.881
LGA    K    34_B      K    34_B     0.773     0    0.045   0.972     4.883   90.476   73.651
LGA    K    35_B      K    35_B     1.160     0    0.046   1.079     2.758   88.214   76.190
LGA    L    36_B      L    36_B     0.487     0    0.033   0.104     0.750   97.619   95.238
LGA    F    37_B      F    37_B     0.729     0    0.032   0.261     1.048   90.476   90.519
LGA    D    38_B      D    38_B     1.016     0    0.039   1.082     4.663   85.952   71.369
LGA    A    39_B      A    39_B     0.558     0    0.026   0.035     0.738   90.476   90.476
LGA    A    40_B      A    40_B     0.653     0    0.099   0.100     1.285   85.952   86.857
LGA    H    41_B      H    41_B     1.390     0    0.119   1.073     4.060   79.286   70.429
LGA    R    42_B      R    42_B     0.737     0    0.159   1.669     5.335   90.476   72.035
LGA    N    43_B      N    43_B     0.918     0    0.048   0.740     2.104   90.476   82.798
LGA    D    44_B      D    44_B     0.710     0    0.118   0.360     1.135   92.857   90.536
LGA    K    45_B      K    45_B     1.379     0    0.087   1.033     7.007   81.429   57.778
LGA    D    46_B      D    46_B     1.461     0    0.028   0.535     2.577   81.429   74.167
LGA    K    47_B      K    47_B     0.874     0    0.022   1.026     3.632   90.476   82.222
LGA    V    48_B      V    48_B     0.551     0    0.042   1.280     2.810   90.476   82.313
LGA    K    49_B      K    49_B     1.131     0    0.028   1.248     7.288   83.690   55.661
LGA    K    50_B      K    50_B     1.421     0    0.031   1.618     8.914   81.429   54.762
LGA    V    51_B      V    51_B     0.978     0    0.030   0.059     1.209   88.214   86.599
LGA    V    52_B      V    52_B     0.589     0    0.037   1.249     2.705   90.476   80.952
LGA    E    53_B      E    53_B     1.031     0    0.025   0.889     4.618   88.214   70.053
LGA    E    54_B      E    54_B     1.099     0    0.029   0.801     2.245   85.952   80.635
LGA    A    55_B      A    55_B     0.531     0    0.046   0.059     0.692   95.238   94.286
LGA    K    56_B      K    56_B     0.537     0    0.057   0.520     2.387   97.619   85.873
LGA    K    57_B      K    57_B     0.340     0    0.039   1.164     7.248  100.000   65.767
LGA    V    58_B      V    58_B     0.837     0    0.084   1.140     3.864   88.333   75.442
LGA    V    59_B      V    59_B     1.201     0    0.070   0.229     1.973   83.690   80.272
LGA    S    60_B      S    60_B     0.837     0    0.222   0.230     1.280   88.214   87.460
LGA    T    61_B      T    61_B     1.143     0    0.035   1.010     3.354   77.381   71.156

# 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):     2.798          2.507                  4.438           72.863   61.463

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     51    1.80    76.639    77.069     2.678

LGA_LOCAL      RMSD:   1.804  Number of atoms:   51  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.858  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   2.798  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.337024 * X  +  -0.614995 * Y  +  -0.712878 * Z  +   8.954077
  Y_new =   0.026765 * X  +   0.763129 * Y  +  -0.645692 * Z  +   2.528272
  Z_new =   0.941115 * X  +   0.198534 * Y  +   0.273653 * Z  +  -7.798500 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.079249 -1.225915  0.627632   [DEG:    4.5406  -70.2397   35.9607 ]
ZXZ: -0.834812  1.293607  1.362889   [DEG:  -47.8312   74.1182   78.0878 ]
 
# END of job
