
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        1.31     1.31
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        1.31     1.31
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       4_A - 34_A        0.88     1.38
  LCS_AVERAGE:     84.43

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     1_B     S     1_A      4   34   34      4    4    4    5   15   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      4   34   34      4    4    4   26   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      7   34   34      4    9   19   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A     31   34   34      4    5   16   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A     31   34   34      3   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     31   34   34     15   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     31   34   34      5   19   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     31   34   34      9   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     31   34   34     16   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     31   34   34     15   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     31   34   34     16   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     31   34   34      7   17   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     31   34   34     18   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     31   34   34     20   28   30   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  94.81  (  84.43  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     20     28     30     30     33     33     34     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  58.82  82.35  88.24  88.24  97.06  97.06 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.31   0.49   0.59   0.59   1.16   1.16   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31
GDT RMS_ALL_AT   1.51   1.48   1.50   1.50   1.32   1.32   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31   1.31

# Checking swapping
#   possible swapping detected:  E    24_B      E    24_A
#   possible swapping detected:  Y    32_B      Y    32_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     3.673     0    0.283   0.689     5.003   42.381   46.270
LGA    G     2_B      G     2_A     2.944     0    0.027   0.027     3.031   55.357   55.357
LGA    P     3_B      P     3_A     2.638     0    0.349   0.391     3.596   60.952   55.306
LGA    N     4_B      N     4_A     2.609     0    0.661   1.161     5.912   54.048   48.512
LGA    G     5_B      G     5_A     0.933     0    0.676   0.676     3.106   80.476   80.476
LGA    G     6_B      G     6_A     1.224     0    0.085   0.085     2.133   77.262   77.262
LGA    V     7_B      V     7_A     1.837     0    0.051   0.065     2.757   77.143   69.660
LGA    C     8_B      C     8_A     1.403     0    0.038   0.045     1.631   79.286   80.000
LGA    P     9_B      P     9_A     0.714     0    0.055   0.080     0.975   90.476   90.476
LGA    V    10_B      V    10_A     0.836     0    0.175   0.173     1.187   88.214   86.599
LGA    L    11_B      L    11_A     1.126     3    0.150   0.180     1.788   81.548   50.952
LGA    I    12_B      I    12_A     0.638     0    0.101   0.652     1.967   90.476   90.655
LGA    Y    13_B      Y    13_A     0.675     0    0.036   0.738     4.284   90.476   73.492
LGA    L    14_B      L    14_A     0.570     0    0.054   0.158     0.979   90.476   91.667
LGA    C    15_B      C    15_A     0.381     0    0.026   0.058     0.622   97.619   96.825
LGA    R    16_B      R    16_A     0.390     0    0.017   1.097     6.532  100.000   70.823
LGA    R    17_B      R    17_A     0.366     0    0.055   0.252     0.893  100.000   96.537
LGA    D    18_B      D    18_A     0.281     0    0.016   0.173     1.297  100.000   95.298
LGA    S    19_B      S    19_A     0.212     0    0.029   0.045     0.391  100.000  100.000
LGA    D    20_B      D    20_A     0.146     0    0.077   0.552     1.557   97.619   91.905
LGA    C    21_B      C    21_A     0.552     0    0.040   0.081     0.657   92.857   92.063
LGA    P    22_B      P    22_A     0.656     0    0.119   0.173     0.984   90.476   90.476
LGA    G    23_B      G    23_A     0.821     0    0.067   0.067     1.124   88.214   88.214
LGA    E    24_B      E    24_A     1.256     0    0.048   0.603     3.916   81.429   68.307
LGA    C    25_B      C    25_A     0.782     0    0.031   0.048     0.878   92.857   92.063
LGA    I    26_B      I    26_A     0.682     0    0.009   0.088     0.838   90.476   90.476
LGA    C    27_B      C    27_A     0.728     0    0.053   0.053     0.823   90.476   90.476
LGA    L    28_B      L    28_A     0.638     0    0.036   0.073     1.035   88.214   92.917
LGA    G    29_B      G    29_A     1.280     0    0.020   0.020     1.861   81.548   81.548
LGA    N    30_B      N    30_A     1.541     0    0.060   0.103     2.308   79.286   76.131
LGA    G    31_B      G    31_A     0.682     0    0.021   0.021     0.892   90.476   90.476
LGA    Y    32_B      Y    32_A     0.584     0    0.027   0.137     2.078   90.476   81.667
LGA    C    33_B      C    33_A     0.545     0    0.067   0.081     0.918   90.476   90.476
LGA    G    34_B      G    34_A     0.550     0    0.024   0.024     1.187   88.214   88.214

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     1.309          1.373                  1.673           84.979   81.223

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    1.31    92.647    96.530     2.412

LGA_LOCAL      RMSD:   1.309  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.309  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   1.309  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.140176 * X  +   0.949405 * Y  +   0.281034 * Z  + -13.493957
  Y_new =   0.758783 * X  +  -0.079337 * Y  +   0.646494 * Z  +  -9.467894
  Z_new =   0.636081 * X  +   0.303867 * Y  +  -0.709271 * Z  + -21.467695 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.753475 -0.689409  2.736828   [DEG:  100.4667  -39.5002  156.8087 ]
ZXZ:  2.731531  2.359260  1.125134   [DEG:  156.5052  135.1757   64.4654 ]
 
# END of job
