
#######################################################
#                                                     #
#                        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   59 (  499),  selected   54 , name one
# Molecule2: number of CA atoms  141 ( 1131),  selected   54 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      28_A - 54_A        3.97    55.85
  LCS_AVERAGE:     13.72

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      29_A - 46_A        1.95    58.43
  LCS_AVERAGE:      8.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      30_A - 40_A        0.66    55.59
  LONGEST_CONTINUOUS_SEGMENT:    11      31_A - 41_A        0.89    56.70
  LONGEST_CONTINUOUS_SEGMENT:    11      63_A - 73_A        0.95    33.93
  LONGEST_CONTINUOUS_SEGMENT:    11      76_A - 86_A        0.78    52.68
  LCS_AVERAGE:      6.19

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   54
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     P    28_A     P    28_A      3    3   22      3    3    3    3   11   14   16   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     P    29_A     P    29_A      3   18   22      3    3    3    8   11   14   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     H    30_A     H    30_A     11   18   22      3    7   11   13   14   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     E    31_A     E    31_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     R    32_A     R    32_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     Y    33_A     Y    33_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     E    34_A     E    34_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     R    35_A     R    35_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     L    36_A     L    36_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     D    37_A     D    37_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     R    38_A     R    38_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     W    39_A     W    39_A     11   18   22      9   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     I    40_A     I    40_A     11   18   22      5   10   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     T    41_A     T    41_A     11   18   22      5    9   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     E    42_A     E    42_A     10   18   22      5    9   11   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     Q    43_A     Q    43_A     10   18   22      5    9   12   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     L    44_A     L    44_A     10   18   22      5    9   10   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     I    45_A     I    45_A     10   18   22      5    9   10   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     Y    46_A     Y    46_A     10   18   22      5    9   10   13   16   17   18   19   19   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     R    52_A     R    52_A      3    4   22      0    3    3    3    3    4    5   10   17   20   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     D    53_A     D    53_A      3    4   22      1    3    3    3    3    4    8   10   12   16   20   21   21   22   22   22   22   22   22   22 
LCS_GDT     E    54_A     E    54_A      3    4   22      0    3    3    3    3    4    4    6    7    9   12   16   21   22   22   22   22   22   22   22 
LCS_GDT     W    55_A     W    55_A      3    3    9      1    3    3    3    3    3    4    6    6    7    7    8    8    9    9   10   11   17   20   21 
LCS_GDT     I    56_A     I    56_A      3    3    9      3    3    3    3    3    4    4    6    6    7    7    8    8    9   16   18   19   19   20   20 
LCS_GDT     D    57_A     D    57_A      3    3   18      3    3    3    3    3    4    4    6    6    7    7    8   17   17   17   18   19   19   20   20 
LCS_GDT     A    58_A     A    58_A      3    3   18      3    3    3    3    3    4    4    6    6    7    7   14   17   17   17   18   19   19   20   20 
LCS_GDT     L    59_A     L    59_A      3    3   19      0    3    3    3    3    4    4    6    6    7   15   15   17   17   17   18   19   19   20   20 
LCS_GDT     A    60_A     A    60_A      3    3   19      0    3    3    3    3    3    4    5   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     E    61_A     E    61_A      3   13   19      0    3    3    3    4    6   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     A    62_A     A    62_A      3   13   19      0    3    3    9   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     A    63_A     A    63_A     11   13   19      3    4   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     G    64_A     G    64_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     I    65_A     I    65_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     F    66_A     F    66_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     K    67_A     K    67_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     E    68_A     E    68_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     A    69_A     A    69_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     L    70_A     L    70_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     E    71_A     E    71_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     R    72_A     R    72_A     11   13   19      9    9   10   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     N    73_A     N    73_A     11   13   19      3    3    3   11   12   12   13   13   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     I    74_A     I    74_A      4   12   19      3    3    4    4    4    8   11   12   14   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     T    75_A     T    75_A      4   12   19      3    3    4    5   10   10   11   12   13   14   15   16   17   18   18   20   20   20   20   21 
LCS_GDT     T    76_A     T    76_A     11   12   19      9   10   10   11   11   11   11   12   13   14   14   16   17   18   18   20   20   20   20   21 
LCS_GDT     P    77_A     P    77_A     11   12   19      9   10   10   11   11   11   11   12   13   14   14   16   17   18   18   20   20   20   20   21 
LCS_GDT     E    78_A     E    78_A     11   12   19      9   10   10   11   11   11   11   12   12   12   14   16   16   16   18   20   20   20   20   21 
LCS_GDT     E    79_A     E    79_A     11   12   18      9   10   10   11   11   11   11   12   12   12   14   16   16   16   16   20   20   20   20   21 
LCS_GDT     F    80_A     F    80_A     11   12   18      9   10   10   11   11   11   11   12   12   12   12   13   15   16   16   17   19   20   20   21 
LCS_GDT     N    81_A     N    81_A     11   12   16      9   10   10   11   11   11   11   12   12   12   12   13   15   16   16   17   19   20   20   20 
LCS_GDT     A    82_A     A    82_A     11   12   15      9   10   10   11   11   11   11   12   12   12   12   13   13   14   15   17   18   20   20   20 
LCS_GDT     F    83_A     F    83_A     11   12   15      9   10   10   11   11   11   11   12   12   12   12   13   13   14   14   16   17   18   20   20 
LCS_GDT     L    84_A     L    84_A     11   12   15      9   10   10   11   11   11   11   12   12   12   12   13   13   14   14   16   17   18   20   20 
LCS_GDT     K    85_A     K    85_A     11   12   15      3   10   10   11   11   11   11   12   12   12   12   13   13   14   14   16   17   18   20   20 
LCS_GDT     E    86_A     E    86_A     11   12   15      3    3    3   11   11   11   11   12   12   12   12   12   13   14   14   16   16   16   17   18 
LCS_AVERAGE  LCS_A:   9.62  (   6.19    8.96   13.72 )

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      9     10     12     13     16     17     18     19     19     20     20     21     21     22     22     22     22     22     22     22 
GDT PERCENT_AT   6.38   7.09   8.51   9.22  11.35  12.06  12.77  13.48  13.48  14.18  14.18  14.89  14.89  15.60  15.60  15.60  15.60  15.60  15.60  15.60
GDT RMS_LOCAL    0.27   0.36   0.92   1.07   1.60   1.73   1.95   2.21   2.21   2.59   2.59   3.29   3.29   3.97   3.97   3.97   3.97   3.97   3.97   3.97
GDT RMS_ALL_AT  35.13  53.49  57.08  57.57  58.88  58.39  58.43  58.75  58.75  58.30  58.30  57.20  57.20  55.85  55.85  55.85  55.85  55.85  55.85  55.85

# Checking swapping
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    33_A      Y    33_A
#   possible swapping detected:  E    34_A      E    34_A
#   possible swapping detected:  Y    46_A      Y    46_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  E    68_A      E    68_A
#   possible swapping detected:  E    78_A      E    78_A
#   possible swapping detected:  E    79_A      E    79_A
#   possible swapping detected:  F    80_A      F    80_A
#   possible swapping detected:  F    83_A      F    83_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P    28_A      P    28_A     4.384     0    0.612   0.628     5.027   40.833   41.156
LGA    P    29_A      P    29_A     3.359     0    0.639   0.780     5.767   42.976   38.980
LGA    H    30_A      H    30_A     3.661     0    0.586   1.190    10.849   59.405   28.000
LGA    E    31_A      E    31_A     1.508     0    0.167   1.138     6.691   70.833   49.418
LGA    R    32_A      R    32_A     2.757     0    0.016   1.207     7.015   64.881   50.693
LGA    Y    33_A      Y    33_A     2.179     0    0.010   1.392    13.433   70.952   32.698
LGA    E    34_A      E    34_A     1.215     0    0.000   1.044     5.605   81.548   57.937
LGA    R    35_A      R    35_A     1.214     0    0.000   1.337     8.715   88.214   53.853
LGA    L    36_A      L    36_A     0.835     0    0.000   0.992     2.502   88.214   81.786
LGA    D    37_A      D    37_A     2.356     0    0.123   0.284     5.171   67.024   51.607
LGA    R    38_A      R    38_A     2.829     0    0.095   1.032     7.217   55.595   43.939
LGA    W    39_A      W    39_A     1.367     0    0.069   1.189     7.720   79.286   47.721
LGA    I    40_A      I    40_A     1.182     0    0.146   0.630     3.644   83.690   75.655
LGA    T    41_A      T    41_A     1.299     0    0.117   1.164     2.750   85.952   78.095
LGA    E    42_A      E    42_A     0.359     0    0.107   0.136     2.186   95.238   83.915
LGA    Q    43_A      Q    43_A     0.541     0    0.000   1.299     4.544   92.857   73.386
LGA    L    44_A      L    44_A     1.629     0    0.159   0.306     3.668   72.976   62.560
LGA    I    45_A      I    45_A     2.092     0    0.000   0.252     2.571   64.881   68.869
LGA    Y    46_A      Y    46_A     2.157     0    0.331   1.211     8.262   68.810   46.111
LGA    R    52_A      R    52_A     7.474     0    0.527   1.204    10.358    4.643   30.736
LGA    D    53_A      D    53_A    12.514     0    0.688   1.134    15.464    0.000    0.000
LGA    E    54_A      E    54_A    15.809     0    0.598   0.706    19.353    0.000    0.000
LGA    W    55_A      W    55_A    20.778     0    0.610   0.572    24.082    0.000    0.000
LGA    I    56_A      I    56_A    25.833     0    0.598   0.713    29.617    0.000    0.000
LGA    D    57_A      D    57_A    30.653     0    0.601   0.806    33.301    0.000    0.000
LGA    A    58_A      A    58_A    32.701     0    0.620   0.590    36.194    0.000    0.000
LGA    L    59_A      L    59_A    38.538     0    0.614   1.231    41.567    0.000    0.000
LGA    A    60_A      A    60_A    43.150     0    0.588   0.583    46.390    0.000    0.000
LGA    E    61_A      E    61_A    47.706     0    0.642   1.095    50.651    0.000    0.000
LGA    A    62_A      A    62_A    52.241     0    0.629   0.567    55.388    0.000    0.000
LGA    A    63_A      A    63_A    57.387     0    0.603   0.598    61.026    0.000    0.000
LGA    G    64_A      G    64_A    63.492     0    0.081   0.081    67.428    0.000    0.000
LGA    I    65_A      I    65_A    65.152     0    0.073   0.118    69.050    0.000    0.000
LGA    F    66_A      F    66_A    66.925     0    0.000   1.248    71.307    0.000    0.000
LGA    K    67_A      K    67_A    70.752     0    0.000   0.816    75.440    0.000    0.000
LGA    E    68_A      E    68_A    75.072     0    0.033   0.940    78.893    0.000    0.000
LGA    A    69_A      A    69_A    76.365     0    0.093   0.069    80.361    0.000    0.000
LGA    L    70_A      L    70_A    78.628     0    0.000   1.371    83.180    0.000    0.000
LGA    E    71_A      E    71_A    83.328     0    0.184   0.238    87.525    0.000    0.000
LGA    R    72_A      R    72_A    86.582     0    0.617   0.752    88.410    0.000    0.000
LGA    N    73_A      N    73_A    88.886     0    0.354   0.757    89.747    0.000    0.000
LGA    I    74_A      I    74_A    87.675     0    0.572   0.642    89.595    0.000    0.000
LGA    T    75_A      T    75_A    91.454     0    0.178   1.207    94.734    0.000    0.000
LGA    T    76_A      T    76_A    91.177     0    0.603   0.730    92.890    0.000    0.000
LGA    P    77_A      P    77_A    88.105     0    0.053   0.102    89.170    0.000    0.000
LGA    E    78_A      E    78_A    90.784     0    0.089   1.150    93.389    0.000    0.000
LGA    E    79_A      E    79_A    94.663     0    0.155   0.896    99.229    0.000    0.000
LGA    F    80_A      F    80_A    92.132     0    0.000   1.427    92.666    0.000    0.000
LGA    N    81_A      N    81_A    90.956     0    0.000   0.088    93.138    0.000    0.000
LGA    A    82_A      A    82_A    96.527     0    0.000   0.051    98.232    0.000    0.000
LGA    F    83_A      F    83_A    97.009     0    0.144   1.449    97.009    0.000    0.000
LGA    L    84_A      L    84_A    93.381     0    0.117   0.147    94.530    0.000    0.000
LGA    K    85_A      K    85_A    96.846     0    0.418   0.882    99.202    0.000    0.000
LGA    E    86_A      E    86_A   101.944     0    0.620   1.220   104.392    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       54     216    216  100.00     463    463  100.00               141
SUMMARY(RMSD_GDC):    25.914         25.750                 26.660            9.779    7.781

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   59  141    4.0     19    2.21    11.348    11.254     0.822

LGA_LOCAL      RMSD:   2.210  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  58.748  Number of assigned atoms:   54 
Std_ASGN_ATOMS RMSD:  25.914  Standard rmsd on all 54 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.277456 * X  +   0.204345 * Y  +  -0.938755 * Z  + 261.515686
  Y_new =   0.298118 * X  +   0.910574 * Y  +   0.286322 * Z  + -1111.632080
  Z_new =   0.913315 * X  +  -0.359301 * Y  +   0.191726 * Z  + -637.663696 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.821280 -1.151351 -1.080626   [DEG:   47.0559  -65.9675  -61.9153 ]
ZXZ: -1.866835  1.377876  1.945603   [DEG: -106.9618   78.9465  111.4748 ]
 
# END of job
