
#######################################################
#                                                     #
#                        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        4.37     4.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       5_A - 34_A        1.29     4.96
  LCS_AVERAGE:     79.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_A - 34_A        0.84     5.09
  LCS_AVERAGE:     71.19

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      3    5   34      3    3    3    4    5    5    5    7    8    9    9   11   12   13   13   14   14   16   17   26 
LCS_GDT     G     2_B     G     2_A      3    5   34      3    3    3    4    5    5    6    7    8    9    9   12   14   15   18   19   26   31   33   33 
LCS_GDT     P     3_B     P     3_A      3    5   34      3    3    3    4    5    6    7   10   11   17   20   25   29   31   32   32   32   32   33   33 
LCS_GDT     N     4_B     N     4_A      3    6   34      3    3    3    4    6    6    8   14   21   28   29   31   31   31   32   32   32   32   33   33 
LCS_GDT     G     5_B     G     5_A      3   30   34      1    3   13   22   28   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     G     6_B     G     6_A     24   30   34      1    4   22   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     V     7_B     V     7_A     28   30   34      3    5   23   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     C     8_B     C     8_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     P     9_B     P     9_A     28   30   34      9   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     V    10_B     V    10_A     28   30   34      3   19   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     L    11_B     L    11_A     28   30   34     12   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     I    12_B     I    12_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     Y    13_B     Y    13_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     L    14_B     L    14_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     C    15_B     C    15_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     R    16_B     R    16_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     R    17_B     R    17_A     28   30   34      6   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     D    18_B     D    18_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     S    19_B     S    19_A     28   30   34     13   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     D    20_B     D    20_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     C    21_B     C    21_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     P    22_B     P    22_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     G    23_B     G    23_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     E    24_B     E    24_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     C    25_B     C    25_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     I    26_B     I    26_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     C    27_B     C    27_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     L    28_B     L    28_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     G    29_B     G    29_A     28   30   34      5   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     N    30_B     N    30_A     28   30   34      3   10   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     G    31_B     G    31_A     28   30   34      6   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     Y    32_B     Y    32_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     C    33_B     C    33_A     28   30   34     18   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_GDT     G    34_B     G    34_A     28   30   34     13   25   26   27   29   29   29   30   30   30   30   31   31   31   32   32   32   32   33   33 
LCS_AVERAGE  LCS_A:  83.62  (  71.19   79.67  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     18     25     26     27     29     29     29     30     30     30     30     31     31     31     32     32     32     32     33     33 
GDT PERCENT_AT  52.94  73.53  76.47  79.41  85.29  85.29  85.29  88.24  88.24  88.24  88.24  91.18  91.18  91.18  94.12  94.12  94.12  94.12  97.06  97.06
GDT RMS_LOCAL    0.34   0.53   0.59   0.69   1.01   1.01   1.01   1.29   1.29   1.29   1.29   2.17   2.17   2.17   2.95   2.95   2.95   2.95   3.75   3.75
GDT RMS_ALL_AT   5.13   5.12   5.14   5.11   5.14   5.14   5.14   4.96   4.96   4.96   4.96   4.70   4.70   4.70   4.50   4.50   4.50   4.50   4.40   4.40

# Checking swapping
#   possible swapping detected:  Y    13_B      Y    13_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A    15.773     0    0.459   0.554    18.171    0.000    0.000
LGA    G     2_B      G     2_A    15.779     0    0.146   0.146    15.779    0.000    0.000
LGA    P     3_B      P     3_A    13.336     0    0.350   0.572    17.428    0.000    0.000
LGA    N     4_B      N     4_A    10.461     0    0.661   1.203    13.818    3.571    1.786
LGA    G     5_B      G     5_A     4.115     0    0.564   0.564     6.162   47.976   47.976
LGA    G     6_B      G     6_A     3.247     0    0.669   0.669     3.247   59.286   59.286
LGA    V     7_B      V     7_A     2.061     0    0.650   0.678     4.379   57.857   68.027
LGA    C     8_B      C     8_A     0.984     0    0.119   0.152     1.548   85.952   83.016
LGA    P     9_B      P     9_A     1.119     0    0.045   0.296     1.391   81.429   81.429
LGA    V    10_B      V    10_A     1.629     0    0.341   0.996     3.191   71.071   69.796
LGA    L    11_B      L    11_A     0.929     3    0.083   0.111     1.263   88.214   55.417
LGA    I    12_B      I    12_A     0.376     0    0.150   0.149     1.386   95.238   91.726
LGA    Y    13_B      Y    13_A     0.104     0    0.055   0.545     2.650  100.000   85.833
LGA    L    14_B      L    14_A     0.132     0    0.035   0.070     0.717  100.000   96.429
LGA    C    15_B      C    15_A     0.261     0    0.049   0.062     0.572  100.000   98.413
LGA    R    16_B      R    16_A     0.329     0    0.122   1.609     8.996  100.000   62.424
LGA    R    17_B      R    17_A     0.966     0    0.087   1.358     8.028   90.476   57.446
LGA    D    18_B      D    18_A     0.745     0    0.020   0.071     1.173   90.476   89.345
LGA    S    19_B      S    19_A     1.036     0    0.060   0.058     1.364   85.952   84.444
LGA    D    20_B      D    20_A     0.214     0    0.028   0.141     0.398  100.000  100.000
LGA    C    21_B      C    21_A     0.605     0    0.021   0.050     1.000   95.238   92.143
LGA    P    22_B      P    22_A     0.575     0    0.052   0.128     1.274   90.476   87.891
LGA    G    23_B      G    23_A     0.488     0    0.037   0.037     0.533   97.619   97.619
LGA    E    24_B      E    24_A     0.497     0    0.027   0.244     1.666   95.238   89.683
LGA    C    25_B      C    25_A     0.590     0    0.025   0.088     1.008   92.857   90.556
LGA    I    26_B      I    26_A     0.541     0    0.072   1.454     4.616   90.476   75.952
LGA    C    27_B      C    27_A     0.578     0    0.047   0.067     0.615   92.857   92.063
LGA    L    28_B      L    28_A     0.493     0    0.024   0.041     1.552   95.238   88.393
LGA    G    29_B      G    29_A     1.003     0    0.033   0.033     1.968   83.929   83.929
LGA    N    30_B      N    30_A     1.950     0    0.049   0.109     2.779   75.000   69.940
LGA    G    31_B      G    31_A     1.000     0    0.113   0.113     1.109   92.976   92.976
LGA    Y    32_B      Y    32_A     0.339     0    0.040   0.053     1.951  100.000   86.230
LGA    C    33_B      C    33_A     0.584     0    0.026   0.049     1.044   92.857   90.556
LGA    G    34_B      G    34_A     0.906     0    0.250   0.250     1.463   85.952   85.952

# 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):     4.367          4.283                  4.377           77.595   72.255

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     30    1.29    83.824    83.566     2.159

LGA_LOCAL      RMSD:   1.290  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.955  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   4.367  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.351510 * X  +  -0.919578 * Y  +   0.175548 * Z  +  -0.414120
  Y_new =  -0.108160 * X  +   0.146368 * Y  +   0.983299 * Z  +   7.303073
  Z_new =  -0.929915 * X  +  -0.364627 * Y  +  -0.048012 * Z  +  -5.955836 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.298508  1.194182 -1.701718   [DEG:  -17.1032   68.4216  -97.5012 ]
ZXZ:  2.964924  1.618827 -1.944481   [DEG:  169.8777   92.7519 -111.4105 ]
 
# END of job
