
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , 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:    41       2_B - 42_B        1.51     1.51
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       2_B - 42_B        1.51     1.51
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38       2_B - 39_B        0.95     1.54
  LCS_AVERAGE:     88.52

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B     38   41   41      3    4   12   16   37   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S     3_B     S     3_B     38   41   41      4   28   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q     4_B     Q     4_B     38   41   41      5   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R     5_B     R     5_B     38   41   41      5   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     6_B     L     6_B     38   41   41      5   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F     7_B     F     7_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V     8_B     V     8_B     38   41   41      5   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L     9_B     L     9_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    10_B     D    10_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    11_B     N    11_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    12_B     E    12_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    13_B     R    13_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Y    14_B     Y    14_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     D    15_B     D    15_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     S    16_B     S    16_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     F    17_B     F    17_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     I    18_B     I    18_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     T    19_B     T    19_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    20_B     Q    20_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    21_B     L    21_B     38   41   41     15   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    22_B     E    22_B     38   41   41     16   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    23_B     A    23_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    24_B     P    24_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    25_B     V    25_B     38   41   41      3   31   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     Q    26_B     Q    26_B     38   41   41      4   17   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     N    27_B     N    27_B     38   41   41     11   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    28_B     A    28_B     38   41   41     11   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    29_B     E    29_B     38   41   41     11   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     G    30_B     G    30_B     38   41   41     16   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    31_B     R    31_B     38   41   41     17   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    32_B     E    32_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     R    33_B     R    33_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     L    34_B     L    34_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     M    35_B     M    35_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     A    36_B     A    36_B     38   41   41     18   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     V    37_B     V    37_B     38   41   41     11   32   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    38_B     K    38_B     38   41   41     11   30   35   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     P    39_B     P    39_B     38   41   41      4   13   19   37   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     E    40_B     E    40_B     21   41   41      4    6   15   17   27   38   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     W    41_B     W    41_B     20   41   41      4   13   18   32   38   39   40   40   40   41   41   41   41   41   41   41   41   41   41   41 
LCS_GDT     K    42_B     K    42_B      3   41   41      3    3    3    3    4    4    6   16   17   41   41   41   41   41   41   41   41   41   41   41 
LCS_AVERAGE  LCS_A:  96.17  (  88.52  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     18     32     35     37     38     39     40     40     40     41     41     41     41     41     41     41     41     41     41     41 
GDT PERCENT_AT  43.90  78.05  85.37  90.24  92.68  95.12  97.56  97.56  97.56 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.57   0.67   0.83   0.95   1.06   1.23   1.23   1.23   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51
GDT RMS_ALL_AT   1.57   1.56   1.56   1.53   1.52   1.52   1.53   1.53   1.53   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51   1.51

# Checking swapping
#   possible swapping detected:  E    12_B      E    12_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    32_B      E    32_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B     3.051     0    0.369   0.490     4.989   43.929   46.571
LGA    S     3_B      S     3_B     1.943     0    0.220   0.557     2.305   77.143   74.365
LGA    Q     4_B      Q     4_B     1.132     0    0.010   0.301     1.749   81.429   80.476
LGA    R     5_B      R     5_B     0.898     0    0.093   0.901     5.103   88.214   69.004
LGA    L     6_B      L     6_B     0.704     0    0.068   0.117     1.546   88.214   84.881
LGA    F     7_B      F     7_B     0.558     0    0.038   0.130     0.837   90.476   96.537
LGA    V     8_B      V     8_B     0.759     0    0.054   1.144     2.466   90.476   83.129
LGA    L     9_B      L     9_B     0.462     0    0.020   0.148     0.921   92.857   91.667
LGA    D    10_B      D    10_B     0.452     0    0.040   0.473     1.428   97.619   91.786
LGA    N    11_B      N    11_B     0.218     0    0.079   0.880     2.429   97.619   88.810
LGA    E    12_B      E    12_B     0.625     0    0.023   0.978     4.599   92.857   77.566
LGA    R    13_B      R    13_B     0.798     0    0.041   1.053     3.381   90.476   76.017
LGA    Y    14_B      Y    14_B     0.368     0    0.055   0.115     0.799  100.000   96.825
LGA    D    15_B      D    15_B     0.196     0    0.025   0.456     1.127  100.000   94.167
LGA    S    16_B      S    16_B     0.451     0    0.023   0.788     2.611   97.619   89.683
LGA    F    17_B      F    17_B     0.390     0    0.021   0.212     0.761  100.000   95.671
LGA    I    18_B      I    18_B     0.280     0    0.031   0.116     0.373  100.000  100.000
LGA    T    19_B      T    19_B     0.311     0    0.013   0.230     1.146  100.000   97.347
LGA    Q    20_B      Q    20_B     0.539     0    0.029   0.841     2.367   97.619   88.889
LGA    L    21_B      L    21_B     0.666     0    0.019   1.308     2.886   90.476   83.095
LGA    E    22_B      E    22_B     0.591     0    0.027   0.747     1.948   92.857   83.704
LGA    A    23_B      A    23_B     0.601     0    0.084   0.099     0.736   92.857   92.381
LGA    P    24_B      P    24_B     0.484     0    0.021   0.319     1.365   92.857   91.905
LGA    V    25_B      V    25_B     1.197     0    0.142   1.257     3.545   83.690   77.279
LGA    Q    26_B      Q    26_B     1.593     0    0.606   1.163     4.851   64.048   59.101
LGA    N    27_B      N    27_B     0.965     0    0.124   0.111     1.389   90.476   87.083
LGA    A    28_B      A    28_B     1.015     0    0.107   0.118     1.096   85.952   85.048
LGA    E    29_B      E    29_B     0.988     0    0.051   0.523     1.986   90.595   84.603
LGA    G    30_B      G    30_B     0.702     0    0.094   0.094     0.825   90.476   90.476
LGA    R    31_B      R    31_B     0.492     0    0.050   1.083     5.807   97.619   70.649
LGA    E    32_B      E    32_B     0.285     0    0.099   0.759     3.051  100.000   87.513
LGA    R    33_B      R    33_B     0.514     0    0.050   1.300     4.684   95.238   77.792
LGA    L    34_B      L    34_B     0.588     0    0.017   0.073     0.944   92.857   91.667
LGA    M    35_B      M    35_B     0.302     0    0.038   0.523     1.915   97.619   95.417
LGA    A    36_B      A    36_B     0.310     0    0.016   0.027     0.610   97.619   98.095
LGA    V    37_B      V    37_B     0.686     0    0.042   0.069     0.945   90.476   90.476
LGA    K    38_B      K    38_B     1.137     4    0.098   0.114     2.793   75.476   40.741
LGA    P    39_B      P    39_B     2.335     0    0.087   0.368     2.542   67.024   69.728
LGA    E    40_B      E    40_B     3.918     0    0.374   0.490     9.104   50.119   27.143
LGA    W    41_B      W    41_B     2.929     0    0.590   0.913     4.757   45.476   46.599
LGA    K    42_B      K    42_B     6.022     0    0.549   1.020    12.979   22.857   10.529

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     1.510          1.561                  2.385           86.176   79.620

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     40    1.23    91.463    95.325     3.017

LGA_LOCAL      RMSD:   1.226  Number of atoms:   40  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.533  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   1.510  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.424134 * X  +  -0.716540 * Y  +  -0.553788 * Z  +  24.930557
  Y_new =  -0.799783 * X  +  -0.583229 * Y  +   0.142097 * Z  +  -8.056068
  Z_new =  -0.424804 * X  +   0.382642 * Y  +  -0.820443 * Z  +  31.136515 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.083195  0.438745  2.705197   [DEG:  -62.0625   25.1382  154.9964 ]
ZXZ: -1.821969  2.532982 -0.837567   [DEG: -104.3911  145.1292  -47.9890 ]
 
# END of job
