
#######################################################
#                                                     #
#                        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        1.71     1.71
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        1.71     1.71
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      11_A - 33_A        0.99     1.93
  LONGEST_CONTINUOUS_SEGMENT:    23      12_A - 34_A        0.79     1.98
  LCS_AVERAGE:     55.80

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      7   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      4   34   34      3   19   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      4   34   34      3   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      4   34   34      3    4    5    7   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A      4   34   34      3    4    5   18   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A      5   34   34      3    5    5   10   15   22   29   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A      5   34   34      3    6   16   22   29   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     21   34   34      8   17   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     21   34   34      8   19   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     21   34   34      3   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     23   34   34      3    3    4   26   30   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     23   34   34      9   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     23   34   34      5   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     23   34   34      8   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     23   34   34      6   16   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     23   34   34      8   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     23   34   34     10   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     23   34   34     10   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     23   34   34      4   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     23   34   34      6   20   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     23   34   34      3   10   26   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     23   34   34      6   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     23   34   34     11   21   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     23   34   34      5   19   27   29   31   33   33   34   34   34   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  85.27  (  55.80  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     11     21     27     29     31     33     33     34     34     34     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  32.35  61.76  79.41  85.29  91.18  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
GDT RMS_LOCAL    0.34   0.62   0.85   0.96   1.15   1.41   1.41   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71
GDT RMS_ALL_AT   2.01   1.94   1.85   1.83   1.78   1.73   1.73   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     0.546     0    0.030   0.653     3.387   90.595   82.302
LGA    G     2_B      G     2_A     1.262     0    0.110   0.110     1.449   83.690   83.690
LGA    P     3_B      P     3_A     2.076     0    0.529   0.504     2.813   70.833   66.054
LGA    N     4_B      N     4_A     2.305     0    0.462   1.109     8.447   59.881   37.738
LGA    G     5_B      G     5_A     2.606     0    0.534   0.534     2.846   67.381   67.381
LGA    G     6_B      G     6_A     5.679     0    0.321   0.321     5.679   28.929   28.929
LGA    V     7_B      V     7_A     3.512     0    0.055   0.088     4.898   54.524   48.027
LGA    C     8_B      C     8_A     1.134     0    0.172   0.311     2.006   77.262   75.794
LGA    P     9_B      P     9_A     1.016     0    0.180   0.441     1.271   83.690   85.306
LGA    V    10_B      V    10_A     1.269     0    0.578   0.577     4.262   69.762   59.456
LGA    L    11_B      L    11_A     2.692     3    0.288   0.300     4.795   73.214   40.536
LGA    I    12_B      I    12_A     0.581     0    0.347   1.204     3.430   85.952   76.726
LGA    Y    13_B      Y    13_A     0.733     0    0.065   1.230     7.213   92.857   63.175
LGA    L    14_B      L    14_A     0.445     0    0.035   0.912     2.695   97.619   87.619
LGA    C    15_B      C    15_A     0.635     0    0.113   0.180     1.093   90.595   92.143
LGA    R    16_B      R    16_A     0.951     0    0.226   1.077     4.029   90.476   76.061
LGA    R    17_B      R    17_A     0.528     0    0.055   0.266     4.240   95.238   74.545
LGA    D    18_B      D    18_A     0.464     0    0.058   0.332     1.561   92.976   89.524
LGA    S    19_B      S    19_A     1.167     0    0.040   0.612     3.231   88.214   80.714
LGA    D    20_B      D    20_A     0.461     0    0.033   0.509     1.743   97.619   93.036
LGA    C    21_B      C    21_A     0.550     0    0.060   0.673     3.625   95.238   84.286
LGA    P    22_B      P    22_A     1.025     0    0.056   0.081     1.908   83.690   80.272
LGA    G    23_B      G    23_A     1.187     0    0.084   0.084     1.187   81.429   81.429
LGA    E    24_B      E    24_A     1.520     0    0.124   0.793     3.078   77.143   72.222
LGA    C    25_B      C    25_A     1.270     0    0.081   0.148     1.375   81.429   81.429
LGA    I    26_B      I    26_A     1.314     0    0.137   1.008     4.081   79.286   68.988
LGA    C    27_B      C    27_A     0.651     0    0.072   0.081     1.121   88.214   92.143
LGA    L    28_B      L    28_A     1.062     0    0.037   0.093     1.580   85.952   82.619
LGA    G    29_B      G    29_A     1.600     0    0.110   0.110     2.034   72.976   72.976
LGA    N    30_B      N    30_A     2.310     0    0.187   0.354     3.634   73.095   64.345
LGA    G    31_B      G    31_A     0.726     0    0.066   0.066     1.244   92.976   92.976
LGA    Y    32_B      Y    32_A     0.672     0    0.089   0.154     1.255   92.857   85.238
LGA    C    33_B      C    33_A     0.746     0    0.063   0.096     1.791   90.476   87.540
LGA    G    34_B      G    34_A     1.290     0    0.353   0.353     1.850   81.548   81.548

# 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):     1.711          1.622                  2.168           81.401   74.611

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     34    1.71    86.765    93.486     1.877

LGA_LOCAL      RMSD:   1.711  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.711  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   1.711  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.538449 * X  +  -0.842630 * Y  +   0.006861 * Z  +   1.578639
  Y_new =   0.724225 * X  +   0.466918 * Y  +   0.507430 * Z  + -11.828959
  Z_new =  -0.430779 * X  +  -0.268256 * Y  +   0.861666 * Z  + -23.811909 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.931480  0.445356 -0.301812   [DEG:   53.3699   25.5170  -17.2925 ]
ZXZ:  3.128073  0.532253 -2.127756   [DEG:  179.2254   30.4959 -121.9115 ]
 
# END of job
