
#######################################################
#                                                     #
#                        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   40 (  335),  selected   40 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   40 , 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:    40       3_B - 42_B        2.09     2.09
  LCS_AVERAGE:     97.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39       3_B - 41_B        1.69     2.12
  LCS_AVERAGE:     92.93

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       3_B - 25_B        0.79     2.26
  LCS_AVERAGE:     44.02

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   40
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     S     3_B     S     3_B     23   39   40      7   23   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     Q     4_B     Q     4_B     23   39   40      9   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     R     5_B     R     5_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     L     6_B     L     6_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     F     7_B     F     7_B     23   39   40      5   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     V     8_B     V     8_B     23   39   40      5   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     L     9_B     L     9_B     23   39   40      5   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     D    10_B     D    10_B     23   39   40     11   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     N    11_B     N    11_B     23   39   40     11   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     E    12_B     E    12_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     R    13_B     R    13_B     23   39   40     11   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     Y    14_B     Y    14_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     D    15_B     D    15_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     S    16_B     S    16_B     23   39   40     11   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     F    17_B     F    17_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     I    18_B     I    18_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     T    19_B     T    19_B     23   39   40     10   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     Q    20_B     Q    20_B     23   39   40      8   24   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     L    21_B     L    21_B     23   39   40     11   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     E    22_B     E    22_B     23   39   40     10   25   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     A    23_B     A    23_B     23   39   40     11   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     P    24_B     P    24_B     23   39   40     10   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     V    25_B     V    25_B     23   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     Q    26_B     Q    26_B      4   39   40      3    4    5    6   10   15   15   18   28   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     N    27_B     N    27_B      4   39   40      3    4    5    5    9   15   15   34   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     A    28_B     A    28_B     13   39   40      3    6    8   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     E    29_B     E    29_B     13   39   40      3   12   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     G    30_B     G    30_B     13   39   40      9   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     R    31_B     R    31_B     13   39   40      9   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     E    32_B     E    32_B     13   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     R    33_B     R    33_B     13   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     L    34_B     L    34_B     13   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     M    35_B     M    35_B     13   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     A    36_B     A    36_B     13   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     V    37_B     V    37_B     13   39   40      5   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     K    38_B     K    38_B     13   39   40     14   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     P    39_B     P    39_B     13   39   40      3   30   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     E    40_B     E    40_B     13   39   40      3   23   35   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     W    41_B     W    41_B     13   39   40      3    9   34   36   37   37   37   37   37   39   39   40   40   40   40   40   40   40   40   40 
LCS_GDT     K    42_B     K    42_B      3    3   40      0    3    3    6    7    8   12   14   34   38   39   40   40   40   40   40   40   40   40   40 
LCS_AVERAGE  LCS_A:  78.17  (  44.02   92.93   97.56 )

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     14     30     35     36     37     37     37     37     37     39     39     40     40     40     40     40     40     40     40     40 
GDT PERCENT_AT  34.15  73.17  85.37  87.80  90.24  90.24  90.24  90.24  90.24  95.12  95.12  97.56  97.56  97.56  97.56  97.56  97.56  97.56  97.56  97.56
GDT RMS_LOCAL    0.38   0.70   0.83   0.89   0.95   0.95   0.95   0.95   0.95   1.69   1.69   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09
GDT RMS_ALL_AT   2.24   2.20   2.19   2.16   2.16   2.16   2.16   2.16   2.16   2.12   2.12   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.09

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B
#   possible swapping detected:  E    40_B      E    40_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     3_B      S     3_B     1.298     0    0.374   0.356     2.463   81.786   83.175
LGA    Q     4_B      Q     4_B     0.880     0    0.017   0.927     3.231   90.476   77.407
LGA    R     5_B      R     5_B     0.715     0    0.039   1.160     3.901   90.476   77.316
LGA    L     6_B      L     6_B     0.937     0    0.031   0.071     2.110   90.476   81.726
LGA    F     7_B      F     7_B     0.843     0    0.028   0.045     1.266   90.476   87.186
LGA    V     8_B      V     8_B     0.868     0    0.038   1.167     2.743   88.214   79.660
LGA    L     9_B      L     9_B     0.717     0    0.052   0.144     1.538   90.476   86.012
LGA    D    10_B      D    10_B     0.935     0    0.066   0.625     1.812   90.476   86.012
LGA    N    11_B      N    11_B     0.863     0    0.133   0.949     3.211   90.476   76.012
LGA    E    12_B      E    12_B     0.628     0    0.016   0.428     1.931   92.857   88.571
LGA    R    13_B      R    13_B     0.580     0    0.042   1.042     5.021   92.857   73.853
LGA    Y    14_B      Y    14_B     0.394     0    0.021   0.152     0.824  100.000   93.651
LGA    D    15_B      D    15_B     0.505     0    0.060   0.448     1.480   90.476   89.345
LGA    S    16_B      S    16_B     0.660     0    0.108   0.620     2.479   90.595   86.270
LGA    F    17_B      F    17_B     0.366     0    0.035   0.294     0.908  100.000   95.671
LGA    I    18_B      I    18_B     0.149     0    0.024   0.100     0.549  100.000   98.810
LGA    T    19_B      T    19_B     0.895     0    0.083   0.258     2.418   92.857   85.578
LGA    Q    20_B      Q    20_B     1.222     0    0.030   1.161     2.966   85.952   80.847
LGA    L    21_B      L    21_B     0.851     0    0.019   1.327     2.788   90.476   83.155
LGA    E    22_B      E    22_B     1.008     0    0.456   0.787     3.045   78.214   81.005
LGA    A    23_B      A    23_B     0.890     0    0.095   0.119     1.427   88.214   86.857
LGA    P    24_B      P    24_B     0.908     0    0.301   0.510     2.713   77.619   74.694
LGA    V    25_B      V    25_B     0.868     0    0.659   0.681     3.432   74.405   68.231
LGA    Q    26_B      Q    26_B     6.636     0    0.682   0.713    15.003   18.810    8.519
LGA    N    27_B      N    27_B     6.423     0    0.238   0.823    13.081   21.786   11.250
LGA    A    28_B      A    28_B     2.244     0    0.648   0.600     3.709   66.786   62.095
LGA    E    29_B      E    29_B     1.342     0    0.582   0.918     3.487   71.429   72.328
LGA    G    30_B      G    30_B     0.982     0    0.120   0.120     1.280   88.214   88.214
LGA    R    31_B      R    31_B     0.854     0    0.034   1.084     6.015   90.476   66.710
LGA    E    32_B      E    32_B     0.455     0    0.084   1.098     6.169   95.238   72.222
LGA    R    33_B      R    33_B     0.258     0    0.074   0.645     1.891   97.619   89.091
LGA    L    34_B      L    34_B     0.368     0    0.052   0.089     0.813   95.238   97.619
LGA    M    35_B      M    35_B     0.916     0    0.057   1.078     3.307   90.476   80.952
LGA    A    36_B      A    36_B     0.572     0    0.102   0.104     0.878   92.857   92.381
LGA    V    37_B      V    37_B     1.000     0    0.015   0.067     2.049   90.476   81.769
LGA    K    38_B      K    38_B     0.275     4    0.087   0.104     0.798   95.238   52.381
LGA    P    39_B      P    39_B     0.907     0    0.043   0.056     1.049   90.595   91.905
LGA    E    40_B      E    40_B     1.520     0    0.323   1.099     8.025   81.548   47.407
LGA    W    41_B      W    41_B     1.925     0    0.537   0.599     7.856   58.690   43.741
LGA    K    42_B      K    42_B     8.242     0    0.611   1.205    14.248    6.905    3.069

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       40     160    160  100.00     331    331  100.00                41
SUMMARY(RMSD_GDC):     2.086          2.140                  3.344           80.737   72.749

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   40   41    4.0     37    0.95    87.195    90.594     3.514

LGA_LOCAL      RMSD:   0.953  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.161  Number of assigned atoms:   40 
Std_ASGN_ATOMS RMSD:   2.086  Standard rmsd on all 40 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.837715 * X  +   0.443729 * Y  +   0.318337 * Z  +  17.106014
  Y_new =   0.355610 * X  +   0.000837 * Y  +   0.934634 * Z  + -63.217720
  Z_new =   0.414458 * X  +   0.896161 * Y  +  -0.158496 * Z  +  58.194241 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.740145 -0.427347  1.745847   [DEG:  156.9988  -24.4852  100.0297 ]
ZXZ:  2.813316  1.729964  0.433185   [DEG:  161.1911   99.1196   24.8197 ]
 
# END of job
