
#######################################################
#                                                     #
#                        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        2.86     2.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       3_A - 34_A        1.72     2.97
  LCS_AVERAGE:     89.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27       8_A - 34_A        0.98     3.15
  LCS_AVERAGE:     65.92

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    4   34      4    4    4    6    6    6    6    6    7   10   18   18   21   26   27   30   32   34   34   34 
LCS_GDT     G     2_B     G     2_A      4    4   34      4    4    4    6    8   13   17   23   28   31   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     P     3_B     P     3_A      4   32   34      4    4    5    7   15   22   28   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     N     4_B     N     4_A      4   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G     5_B     G     5_A      5   32   34      4    4    6    8   27   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G     6_B     G     6_A      6   32   34      4   16   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     V     7_B     V     7_A      6   32   34      4    7   15   26   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C     8_B     C     8_A     27   32   34      4   22   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     P     9_B     P     9_A     27   32   34      7   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     V    10_B     V    10_A     27   32   34      3    6   11   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     L    11_B     L    11_A     27   32   34      3    6   12   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     I    12_B     I    12_A     27   32   34      7   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     27   32   34      6   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     L    14_B     L    14_A     27   32   34      6   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    15_B     C    15_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     R    16_B     R    16_A     27   32   34      6   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     R    17_B     R    17_A     27   32   34      6   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     D    18_B     D    18_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     S    19_B     S    19_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     D    20_B     D    20_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    21_B     C    21_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     P    22_B     P    22_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    23_B     G    23_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     E    24_B     E    24_A     27   32   34      9   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    25_B     C    25_A     27   32   34     11   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     I    26_B     I    26_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    27_B     C    27_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     L    28_B     L    28_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    29_B     G    29_A     27   32   34      5   22   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     N    30_B     N    30_A     27   32   34      5   10   24   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    31_B     G    31_A     27   32   34      4   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     27   32   34     12   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     C    33_B     C    33_A     27   32   34      4   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_GDT     G    34_B     G    34_A     27   32   34      4   23   26   27   29   30   31   32   32   32   33   33   33   33   33   33   33   34   34   34 
LCS_AVERAGE  LCS_A:  85.06  (  65.92   89.27  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     12     23     26     27     29     30     31     32     32     32     33     33     33     33     33     33     33     34     34     34 
GDT PERCENT_AT  35.29  67.65  76.47  79.41  85.29  88.24  91.18  94.12  94.12  94.12  97.06  97.06  97.06  97.06  97.06  97.06  97.06 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.64   0.82   0.85   1.05   1.19   1.35   1.72   1.72   1.72   2.09   2.09   2.09   2.09   2.09   2.09   2.09   2.86   2.86   2.86
GDT RMS_ALL_AT   3.14   3.12   3.17   3.16   3.15   3.17   3.10   2.97   2.97   2.97   2.90   2.90   2.90   2.90   2.90   2.90   2.90   2.86   2.86   2.86

# 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    12.339     0    0.276   0.917    13.961    0.000    0.000
LGA    G     2_B      G     2_A     7.379     0    0.045   0.045     8.586   11.786   11.786
LGA    P     3_B      P     3_A     5.712     0    0.512   0.605     7.876   32.976   22.313
LGA    N     4_B      N     4_A     0.141     0    0.502   0.868     6.246   71.905   56.131
LGA    G     5_B      G     5_A     3.022     0    0.496   0.496     3.022   67.262   67.262
LGA    G     6_B      G     6_A     2.636     0    0.089   0.089     2.955   59.048   59.048
LGA    V     7_B      V     7_A     3.701     0    0.049   0.072     6.363   50.119   37.891
LGA    C     8_B      C     8_A     1.301     0    0.209   0.758     2.113   77.262   78.651
LGA    P     9_B      P     9_A     0.765     0    0.672   0.598     2.571   82.143   85.782
LGA    V    10_B      V    10_A     2.332     0    0.294   0.281     3.183   63.095   59.524
LGA    L    11_B      L    11_A     2.155     3    0.067   0.076     2.333   68.810   42.500
LGA    I    12_B      I    12_A     0.996     0    0.170   0.697     2.511   83.690   82.917
LGA    Y    13_B      Y    13_A     1.191     0    0.075   0.220     4.505   85.952   63.690
LGA    L    14_B      L    14_A     0.726     0    0.064   0.154     1.717   88.214   86.071
LGA    C    15_B      C    15_A     0.354     0    0.068   0.129     0.728   95.238   96.825
LGA    R    16_B      R    16_A     0.767     0    0.205   1.000     5.096   90.476   67.532
LGA    R    17_B      R    17_A     0.581     0    0.058   1.433     9.261   90.476   59.048
LGA    D    18_B      D    18_A     0.497     0    0.041   0.150     0.590   92.857   94.048
LGA    S    19_B      S    19_A     0.637     0    0.078   0.598     2.245   90.476   86.190
LGA    D    20_B      D    20_A     0.724     0    0.037   0.880     2.371   90.476   83.929
LGA    C    21_B      C    21_A     0.551     0    0.042   0.160     1.449   92.857   92.143
LGA    P    22_B      P    22_A     0.996     0    0.053   0.155     1.343   90.476   86.599
LGA    G    23_B      G    23_A     0.492     0    0.030   0.030     0.798   97.619   97.619
LGA    E    24_B      E    24_A     0.793     0    0.163   1.196     5.866   95.238   67.037
LGA    C    25_B      C    25_A     0.700     0    0.042   0.129     0.764   92.857   93.651
LGA    I    26_B      I    26_A     0.452     0    0.045   1.107     2.703   97.619   84.464
LGA    C    27_B      C    27_A     0.307     0    0.028   0.056     0.716   97.619   98.413
LGA    L    28_B      L    28_A     0.874     0    0.047   0.867     2.439   85.952   79.464
LGA    G    29_B      G    29_A     1.677     0    0.110   0.110     1.996   75.000   75.000
LGA    N    30_B      N    30_A     2.112     0    0.213   1.176     3.473   77.381   67.321
LGA    G    31_B      G    31_A     0.842     0    0.077   0.077     1.308   92.976   92.976
LGA    Y    32_B      Y    32_A     0.524     0    0.075   0.060     1.571   90.476   84.484
LGA    C    33_B      C    33_A     0.635     0    0.049   0.192     1.779   90.476   87.540
LGA    G    34_B      G    34_A     1.338     0    0.679   0.679     3.925   69.762   69.762

# 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):     2.861          2.811                  3.142           77.605   71.106

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     32    1.72    84.559    87.979     1.763

LGA_LOCAL      RMSD:   1.715  Number of atoms:   32  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.975  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   2.861  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.342428 * X  +  -0.168135 * Y  +  -0.924377 * Z  +  -5.806246
  Y_new =  -0.846717 * X  +   0.371182 * Y  +  -0.381174 * Z  +  -5.088496
  Z_new =   0.407201 * X  +   0.913211 * Y  +  -0.015260 * Z  + -16.733727 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.186487 -0.419387  1.587505   [DEG:  -67.9807  -24.0291   90.9573 ]
ZXZ: -1.179682  1.586057  0.419439   [DEG:  -67.5908   90.8743   24.0321 ]
 
# END of job
