
#######################################################
#                                                     #
#                        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   35 (  261),  selected   35 , name one
# Molecule2: number of CA atoms  192 ( 1575),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      32_D - 66_D        4.96     4.96
  LCS_AVERAGE:     18.23

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      50_D - 66_D        1.71    16.69
  LCS_AVERAGE:      7.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      51_D - 66_D        0.49    16.78
  LCS_AVERAGE:      6.43

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     K    32_D     K    32_D     12   13   35      5   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     E    33_D     E    33_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     E    34_D     E    34_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     I    35_D     I    35_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     I    36_D     I    36_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     N    37_D     N    37_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     L    38_D     L    38_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     I    39_D     I    39_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     K    40_D     K    40_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     K    41_D     K    41_D     12   13   35      9   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     F    42_D     F    42_D     12   13   35      5   11   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     S    43_D     S    43_D     12   13   35      3    4   14   14   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     N    44_D     N    44_D      5   13   35      3    4    5   12   15   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     S    45_D     S    45_D      5    5   35      3    4    5    5    6   10   11   15   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     G    46_D     G    46_D      5    6   35      3    4    5    5    6   10   11   15   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     Q    47_D     Q    47_D      5    6   35      3    4    5    5    6   10   12   15   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     S    48_D     S    48_D      4    6   35      4    4    5    5    6    9   12   15   18   19   24   28   30   32   34   34   35   35   35   35 
LCS_GDT     G    49_D     G    49_D      4    6   35      4    4    5    5    6    7    9   15   18   19   23   27   29   32   34   34   35   35   35   35 
LCS_GDT     M    50_D     M    50_D      4   17   35      4    4    5    5    6    7    9   15   18   20   23   27   30   32   34   34   35   35   35   35 
LCS_GDT     S    51_D     S    51_D     16   17   35     10   16   16   16   16   16   16   16   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     A    52_D     A    52_D     16   17   35     12   16   16   16   16   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     P    53_D     P    53_D     16   17   35     12   16   16   16   16   16   16   16   17   17   18   24   26   29   32   33   35   35   35   35 
LCS_GDT     I    54_D     I    54_D     16   17   35     12   16   16   16   16   16   16   16   17   17   21   26   30   32   34   34   35   35   35   35 
LCS_GDT     T    55_D     T    55_D     16   17   35     12   16   16   16   16   16   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     A    56_D     A    56_D     16   17   35     12   16   16   16   16   17   17   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     S    57_D     S    57_D     16   17   35     12   16   16   16   16   16   16   18   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     I    58_D     I    58_D     16   17   35     12   16   16   16   16   16   16   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     I    59_D     I    59_D     16   17   35     12   16   16   16   16   16   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     T    60_D     T    60_D     16   17   35     12   16   16   16   16   16   17   18   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     N    61_D     N    61_D     16   17   35     12   16   16   16   16   17   17   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     C    62_D     C    62_D     16   17   35     12   16   16   16   16   16   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     I    63_D     I    63_D     16   17   35     12   16   16   16   16   16   16   16   17   17   20   25   30   32   34   34   35   35   35   35 
LCS_GDT     K    64_D     K    64_D     16   17   35     11   16   16   16   16   16   17   18   20   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     N    65_D     N    65_D     16   17   35     10   16   16   16   16   17   18   19   21   23   26   28   30   32   34   34   35   35   35   35 
LCS_GDT     L    66_D     L    66_D     16   17   35     10   16   16   16   16   16   16   16   18   22   22   24   26   28   34   34   35   35   35   35 
LCS_AVERAGE  LCS_A:  10.63  (   6.43    7.25   18.23 )

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     12     16     16     16     16     17     18     19     21     23     26     28     30     32     34     34     35     35     35     35 
GDT PERCENT_AT   6.25   8.33   8.33   8.33   8.33   8.85   9.38   9.90  10.94  11.98  13.54  14.58  15.63  16.67  17.71  17.71  18.23  18.23  18.23  18.23
GDT RMS_LOCAL    0.35   0.49   0.49   0.49   0.49   1.57   1.88   2.04   2.37   3.05   3.53   3.88   4.25   4.54   4.83   4.83   4.96   4.96   4.96   4.96
GDT RMS_ALL_AT  16.86  16.78  16.78  16.78  16.78   5.99   5.80   5.86   5.78   5.44   5.32   5.15   5.06   5.01   4.98   4.98   4.96   4.96   4.96   4.96

# Checking swapping
#   possible swapping detected:  E    33_D      E    33_D
#   possible swapping detected:  F    42_D      F    42_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    32_D      K    32_D     0.515     0    0.031   0.079     2.333   90.476   83.651
LGA    E    33_D      E    33_D     0.547     0    0.163   0.719     2.929   95.238   78.624
LGA    E    34_D      E    34_D     0.907     0    0.040   0.847     3.957   90.476   72.540
LGA    I    35_D      I    35_D     1.307     0    0.040   0.075     2.381   81.429   74.107
LGA    I    36_D      I    36_D     1.183     0    0.011   0.631     3.597   83.690   75.655
LGA    N    37_D      N    37_D     0.749     0    0.066   0.073     1.815   92.857   85.000
LGA    L    38_D      L    38_D     0.350     0    0.019   1.411     3.182   95.238   82.381
LGA    I    39_D      I    39_D     1.465     0    0.022   0.700     3.430   77.143   71.131
LGA    K    40_D      K    40_D     1.659     0    0.131   0.118     2.661   71.071   75.873
LGA    K    41_D      K    41_D     1.371     0    0.097   0.654     5.011   77.143   67.989
LGA    F    42_D      F    42_D     1.672     0    0.206   1.386     8.337   75.119   44.675
LGA    S    43_D      S    43_D     1.198     0    0.589   0.879     2.691   77.619   76.111
LGA    N    44_D      N    44_D     3.432     0    0.315   0.688     5.968   40.595   45.357
LGA    S    45_D      S    45_D     8.502     0    0.696   0.617    10.994    5.119    5.079
LGA    G    46_D      G    46_D    10.803     0    0.265   0.265    11.932    0.357    0.357
LGA    Q    47_D      Q    47_D    10.163     0    0.487   1.379    14.427    1.548    0.847
LGA    S    48_D      S    48_D    10.246     0    0.440   0.734    12.256    0.119    0.079
LGA    G    49_D      G    49_D    11.546     0    0.045   0.045    11.546    0.000    0.000
LGA    M    50_D      M    50_D    10.850     0    0.332   0.928    14.465    1.548    0.774
LGA    S    51_D      S    51_D     7.526     0    0.653   0.566     8.810   14.405   11.587
LGA    A    52_D      A    52_D     1.249     0    0.037   0.040     3.176   61.429   60.571
LGA    P    53_D      P    53_D     7.684     0    0.127   0.137    10.247   11.429    8.503
LGA    I    54_D      I    54_D     8.510     0    0.092   1.237    14.810   11.071    5.536
LGA    T    55_D      T    55_D     3.794     0    0.028   0.054     6.795   57.262   41.565
LGA    A    56_D      A    56_D     3.687     0    0.050   0.047     6.088   48.333   42.095
LGA    S    57_D      S    57_D     6.663     0    0.059   0.059    10.808   22.976   15.794
LGA    I    58_D      I    58_D     4.426     0    0.085   0.106    10.831   50.952   28.869
LGA    I    59_D      I    59_D     3.632     0    0.027   0.049     8.272   49.881   31.250
LGA    T    60_D      T    60_D     6.579     0    0.053   1.096    10.372   19.881   11.973
LGA    N    61_D      N    61_D     4.791     0    0.013   0.848    10.131   46.190   25.655
LGA    C    62_D      C    62_D     2.374     0    0.019   0.770     7.242   62.857   48.810
LGA    I    63_D      I    63_D     7.550     0    0.034   0.065    12.118   12.024    6.071
LGA    K    64_D      K    64_D     7.726     0    0.040   0.972    14.890   13.810    6.455
LGA    N    65_D      N    65_D     1.728     0    0.027   0.192     6.534   67.143   48.750
LGA    L    66_D      L    66_D     6.153     0    0.032   0.100    10.722   18.810   10.774

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     261    261  100.00               192
SUMMARY(RMSD_GDC):     4.965          4.633                  5.870            8.465    7.003

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35  192    4.0     19    2.04    11.068    10.019     0.886

LGA_LOCAL      RMSD:   2.043  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.857  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   4.965  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.097192 * X  +  -0.619752 * Y  +   0.778756 * Z  + -14.914912
  Y_new =  -0.509388 * X  +   0.703186 * Y  +   0.496038 * Z  + -21.850611
  Z_new =  -0.855031 * X  +  -0.348478 * Y  +  -0.384038 * Z  + -42.084232 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.759333  1.025610 -2.404702   [DEG: -100.8023   58.7631 -137.7793 ]
ZXZ:  2.137951  1.964962 -1.957804   [DEG:  122.4956  112.5840 -112.1739 ]
 
# END of job
