
#######################################################
#                                                     #
#                        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   47 (  348),  selected   30 , name one
# Molecule2: number of CA atoms  344 ( 2633),  selected   30 , 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:    19      29_A - 47_A        4.81    20.91
  LCS_AVERAGE:      5.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      20_A - 27_A        1.87    16.78
  LONGEST_CONTINUOUS_SEGMENT:     8      24_A - 31_A        1.75    10.52
  LONGEST_CONTINUOUS_SEGMENT:     8      25_A - 32_A        1.74    10.80
  LCS_AVERAGE:      1.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      20_A - 25_A        0.82    20.60
  LCS_AVERAGE:      1.35

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   30
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     G    18_A     G    18_A      3    3   15      0    3    3    3    3    3    5    8   11   11   13   13   13   15   18   19   20   20   21   22 
LCS_GDT     S    19_A     S    19_A      3    5   15      0    3    3    3    5    6    8   10   11   11   13   13   13   14   18   19   20   20   21   22 
LCS_GDT     H    20_A     H    20_A      6    8   15      4    5    6    6    7    8    9    9   11   11   13   13   13   15   18   19   20   20   21   22 
LCS_GDT     M    21_A     M    21_A      6    8   15      4    5    6    6    7    8    9   10   11   11   13   13   14   15   18   19   20   20   21   22 
LCS_GDT     A    22_A     A    22_A      6    8   15      4    5    6    6    7    8    9   10   11   12   13   14   14   15   18   19   20   20   21   22 
LCS_GDT     P    23_A     P    23_A      6    8   15      4    5    6    6    7    8    9   10   11   12   13   14   14   15   18   19   20   20   21   22 
LCS_GDT     I    24_A     I    24_A      6    8   15      3    5    6    6    7    8    9   11   11   12   13   14   14   15   18   19   20   20   21   22 
LCS_GDT     A    25_A     A    25_A      6    8   15      4    5    6    7    7    9   10   11   11   12   13   14   14   15   18   19   20   20   21   22 
LCS_GDT     Q    26_A     Q    26_A      4    8   15      4    4    6    7    7    9   10   11   11   12   13   14   15   16   18   19   20   20   21   22 
LCS_GDT     A    27_A     A    27_A      4    8   18      4    4    6    7    7    9   10   11   11   12   13   14   15   16   19   19   20   20   21   22 
LCS_GDT     V    28_A     V    28_A      4    8   18      4    4    6    7    7    9   10   11   11   12   13   15   17   18   19   19   20   20   21   22 
LCS_GDT     T    29_A     T    29_A      4    8   19      4    4    5    7    7    9   10   11   11   12   13   15   17   18   19   19   20   20   21   22 
LCS_GDT     V    30_A     V    30_A      5    8   19      4    5    6    7    7    9   10   12   12   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     S    31_A     S    31_A      5    8   19      4    5    6    7    7    9   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     L    32_A     L    32_A      5    8   19      3    5    5    6    7    9   10   11   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     N    33_A     N    33_A      5    7   19      3    5    5    5    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     D    34_A     D    34_A      5    7   19      3    5    5    5    7    7    7    8    8    8   11   15   17   18   19   19   20   20   21   22 
LCS_GDT     L    35_A     L    35_A      4    4   19      3    3    4    4    5    6    6    8    8   12   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     K    36_A     K    36_A      4    7   19      3    3    4    5    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     N    37_A     N    37_A      3    7   19      3    3    4    5    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     G    38_A     G    38_A      5    7   19      3    4    5    6    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     T    39_A     T    39_A      5    7   19      2    4    5    6    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     V    40_A     V    40_A      5    7   19      3    4    5    6    7    9   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     S    41_A     S    41_A      5    7   19      3    4    5    6    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     L    42_A     L    42_A      5    7   19      3    4    5    6    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     E    43_A     E    43_A      4    7   19      2    4    5    6    7    8   10   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     A    44_A     A    44_A      4    5   19      3    3    4    5    5    8    9   12   13   14   14   15   17   18   19   19   20   20   21   22 
LCS_GDT     L    45_A     L    45_A      4    4   19      3    3    4    4    4    5    6    6    7   10   13   14   15   17   18   18   19   20   21   22 
LCS_GDT     E    46_A     E    46_A      4    4   19      3    3    4    4    4    5    8   11   13   14   14   15   16   18   19   19   20   20   21   22 
LCS_GDT     E    47_A     E    47_A      4    4   19      3    3    4    4    4    6    6    7    8   10   13   15   16   18   19   19   20   20   21   22 
LCS_AVERAGE  LCS_A:   2.82  (   1.35    1.97    5.16 )

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      4      5      6      7      7      9     10     12     13     14     14     15     17     18     19     19     20     20     21     22 
GDT PERCENT_AT   1.16   1.45   1.74   2.03   2.03   2.62   2.91   3.49   3.78   4.07   4.07   4.36   4.94   5.23   5.52   5.52   5.81   5.81   6.10   6.40
GDT RMS_LOCAL    0.11   0.40   0.82   1.32   1.27   2.00   2.26   2.82   3.01   3.24   3.24   3.55   4.56   4.52   4.83   4.83   5.29   5.13   5.68   5.97
GDT RMS_ALL_AT  11.30  19.82  20.60  10.44  18.96  11.57  23.35  21.77  23.24  22.09  22.09  21.93  18.84  20.55  19.27  19.27  17.78  19.54  16.30  16.46

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    18_A      G    18_A    49.482     0    0.260   0.260    49.546    0.000    0.000
LGA    S    19_A      S    19_A    50.169     0    0.692   0.585    52.381    0.000    0.000
LGA    H    20_A      H    20_A    45.962     0    0.718   1.175    47.354    0.000    0.000
LGA    M    21_A      M    21_A    39.851     0    0.099   0.647    41.779    0.000    0.000
LGA    A    22_A      A    22_A    38.905     0    0.038   0.049    39.131    0.000    0.000
LGA    P    23_A      P    23_A    35.476     0    0.044   0.127    38.857    0.000    0.000
LGA    I    24_A      I    24_A    30.010     0    0.105   1.181    31.803    0.000    0.000
LGA    A    25_A      A    25_A    25.457     0    0.091   0.102    26.995    0.000    0.000
LGA    Q    26_A      Q    26_A    19.676     0    0.126   1.212    21.898    0.000    0.000
LGA    A    27_A      A    27_A    15.909     0    0.087   0.130    16.972    0.000    0.000
LGA    V    28_A      V    28_A    11.566     0    0.623   1.321    13.333    1.905    1.088
LGA    T    29_A      T    29_A     9.238     0    0.020   0.081    13.117    2.500    1.429
LGA    V    30_A      V    30_A     4.066     0    0.086   1.240     5.392   40.952   42.993
LGA    S    31_A      S    31_A     2.884     0    0.210   0.552     4.114   53.571   48.095
LGA    L    32_A      L    32_A     6.431     0    0.097   1.136    13.160   22.976   11.845
LGA    N    33_A      N    33_A     2.232     0    0.612   1.230     5.441   53.690   46.548
LGA    D    34_A      D    34_A     7.383     0    0.037   1.124    12.417   12.738    6.488
LGA    L    35_A      L    35_A     6.738     0    0.623   1.208    12.138   23.810   12.798
LGA    K    36_A      K    36_A     2.517     0    0.067   0.728     6.644   50.357   41.746
LGA    N    37_A      N    37_A     2.664     0    0.659   0.561     6.052   47.619   40.060
LGA    G    38_A      G    38_A     3.556     0    0.599   0.599     3.556   59.524   59.524
LGA    T    39_A      T    39_A     0.344     0    0.640   0.614     3.103   88.333   75.034
LGA    V    40_A      V    40_A     3.353     0    0.171   1.149     5.196   55.476   47.891
LGA    S    41_A      S    41_A     2.876     0    0.127   0.532     3.530   57.262   56.190
LGA    L    42_A      L    42_A     1.398     0    0.632   0.568     2.759   73.214   75.298
LGA    E    43_A      E    43_A     1.151     0    0.630   0.562     2.442   81.429   75.767
LGA    A    44_A      A    44_A     4.051     0    0.608   0.596     5.954   34.524   31.905
LGA    L    45_A      L    45_A     7.580     0    0.057   1.286    13.777   12.738    6.429
LGA    E    46_A      E    46_A     5.134     0    0.660   1.458     9.929   40.952   21.746
LGA    E    47_A      E    47_A     6.951     0    0.701   1.256    12.180   11.905    5.344

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       30     120    120  100.00     215    215  100.00               344
SUMMARY(RMSD_GDC):     9.367          9.459                 10.253            2.400    2.059

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   47  344    4.0     12    2.82     3.125     2.859     0.411

LGA_LOCAL      RMSD:   2.817  Number of atoms:   12  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  21.768  Number of assigned atoms:   30 
Std_ASGN_ATOMS RMSD:   9.367  Standard rmsd on all 30 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.169651 * X  +  -0.659386 * Y  +   0.732413 * Z  + -23.572096
  Y_new =   0.650027 * X  +  -0.633470 * Y  +  -0.419740 * Z  +   3.777241
  Z_new =   0.740732 * X  +   0.404879 * Y  +   0.536087 * Z  + -15.619888 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.826092 -0.834159  0.646852   [DEG:  104.6274  -47.7938   37.0619 ]
ZXZ:  1.050398  1.005001  1.070572   [DEG:   60.1834   57.5823   61.3393 ]
 
# END of job
