
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      12_A - 32_A        4.85    17.64
  LONGEST_CONTINUOUS_SEGMENT:    21      13_A - 33_A        4.34    18.34
  LCS_AVERAGE:     53.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      14_A - 27_A        1.94    18.73
  LCS_AVERAGE:     31.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      18_A - 25_A        0.91    18.53
  LCS_AVERAGE:     17.72

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      5    7   10      4    5    5    6    6    7    8    8    8    9    9    9    9    9    9   11   11   11   11   11 
LCS_GDT     R     2_A     R     2_A      5    7   10      4    5    5    6    6    7    8    8    8    9    9    9    9    9   10   11   11   11   11   11 
LCS_GDT     Q     3_A     Q     3_A      5    7   10      4    5    5    6    6    7    8    8    8    9    9    9    9    9   10   11   11   11   11   11 
LCS_GDT     S     4_A     S     4_A      5    7   10      4    5    5    6    6    7    8    8    8    9    9    9    9    9   10   11   11   11   11   11 
LCS_GDT     S     5_A     S     5_A      5    7   11      3    5    5    6    6    7    8    8    8    9    9    9   10   10   10   11   11   11   11   11 
LCS_GDT     A     6_A     A     6_A      4    7   11      3    4    5    6    6    7    8    8    8    9    9    9   10   10   10   11   11   11   11   14 
LCS_GDT     T     7_A     T     7_A      4    7   11      3    4    4    5    6    7    8    8    8    9    9    9   10   11   11   13   13   14   16   16 
LCS_GDT     S     8_A     S     8_A      4    4   11      3    4    4    4    4    6    8    8    8    9    9    9   10   11   12   13   13   14   16   17 
LCS_GDT     S     9_A     S     9_A      5    7   11      3    4    5    5    6    7    8    8    8    9    9    9   10   11   12   13   13   14   16   16 
LCS_GDT     F    10_A     F    10_A      5    7   11      3    4    5    6    6    7    8    8    8    9    9    9   10   11   12   13   13   15   17   17 
LCS_GDT     G    11_A     G    11_A      5    7   18      3    4    5    6    6    7    8    8    8    9   11   12   14   14   16   17   17   18   20   20 
LCS_GDT     G    12_A     G    12_A      5    7   21      3    4    5    6    6    7    8    8   11   12   15   15   16   18   19   19   20   21   22   22 
LCS_GDT     L    13_A     L    13_A      5    7   21      3    4    5    6    6    9   11   12   14   14   17   18   19   20   21   21   21   21   22   22 
LCS_GDT     G    14_A     G    14_A      4   14   21      3    4   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     G    15_A     G    15_A      4   14   21      3    5   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     G    16_A     G    16_A      3   14   21      3    3    4    5    7   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     S    17_A     S    17_A      4   14   21      3    3    8   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     V    18_A     V    18_A      8   14   21      4    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     R    19_A     R    19_A      8   14   21      4    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     F    20_A     F    20_A      8   14   21      3    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     G    21_A     G    21_A      8   14   21      4    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     P    22_A     P    22_A      8   14   21      4    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     G    23_A     G    23_A      8   14   21      4    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     V    24_A     V    24_A      8   14   21      4    7   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     A    25_A     A    25_A      8   14   21      4    4   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     F    26_A     F    26_A      7   14   21      4    6   11   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     R    27_A     R    27_A      7   14   21      4    6    8   11   13   13   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     A    28_A     A    28_A      7   12   21      4    6    7    8    9   11   12   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     P    29_A     P    29_A      7    9   21      4    6    7    8   10   12   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     S    30_A     S    30_A      7    9   21      4    6    7    8   10   12   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     I    31_A     I    31_A      7    9   21      3    6    7    7    9   12   13   14   16   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     H    32_A     H    32_A      7    9   21      3    4    7    7    7    9   11   13   15   18   19   19   19   20   21   21   21   21   22   22 
LCS_GDT     G    33_A     G    33_A      3    8   21      3    3    4    4    5    8    8   10   11   11   11   13   14   15   21   21   21   21   22   22 
LCS_AVERAGE  LCS_A:  34.25  (  17.72   31.22   53.81 )

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      4      7     11     11     13     13     13     14     16     18     19     19     19     20     21     21     21     21     22     22 
GDT PERCENT_AT  12.12  21.21  33.33  33.33  39.39  39.39  39.39  42.42  48.48  54.55  57.58  57.58  57.58  60.61  63.64  63.64  63.64  63.64  66.67  66.67
GDT RMS_LOCAL    0.18   0.54   1.09   1.09   1.52   1.52   1.52   1.94   2.85   3.26   3.46   3.46   3.46   3.98   4.34   4.34   4.34   4.34   5.10   5.10
GDT RMS_ALL_AT  20.64  18.32  18.65  18.65  18.58  18.58  18.58  18.73  18.56  18.78  18.77  18.77  18.77  18.30  18.34  18.34  18.34  18.34  17.72  17.72

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    20_A      F    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    36.277     0    0.034   0.313    37.757    0.000    0.000
LGA    R     2_A      R     2_A    34.932     0    0.124   0.804    35.010    0.000    0.000
LGA    Q     3_A      Q     3_A    34.536     0    0.057   0.733    37.068    0.000    0.000
LGA    S     4_A      S     4_A    32.600     0    0.090   0.680    33.181    0.000    0.000
LGA    S     5_A      S     5_A    32.147     0    0.546   0.570    34.486    0.000    0.000
LGA    A     6_A      A     6_A    31.460     0    0.156   0.184    32.041    0.000    0.000
LGA    T     7_A      T     7_A    28.977     0    0.127   1.324    31.419    0.000    0.000
LGA    S     8_A      S     8_A    27.050     0    0.493   0.742    28.646    0.000    0.000
LGA    S     9_A      S     9_A    25.961     0    0.609   0.729    26.233    0.000    0.000
LGA    F    10_A      F    10_A    20.768     0    0.574   1.211    22.509    0.000    0.000
LGA    G    11_A      G    11_A    17.443     0    0.257   0.257    18.741    0.000    0.000
LGA    G    12_A      G    12_A    12.922     0    0.030   0.030    14.740    0.000    0.000
LGA    L    13_A      L    13_A     8.487     0    0.190   0.201    12.542    9.762    5.060
LGA    G    14_A      G    14_A     2.451     0    0.629   0.629     4.919   64.762   64.762
LGA    G    15_A      G    15_A     1.003     0    0.329   0.329     3.456   69.286   69.286
LGA    G    16_A      G    16_A     4.394     0    0.624   0.624     4.394   52.262   52.262
LGA    S    17_A      S    17_A     2.103     0    0.027   0.692     4.488   65.238   59.206
LGA    V    18_A      V    18_A     1.606     0    0.220   1.075     3.505   81.548   71.293
LGA    R    19_A      R    19_A     1.129     0    0.243   0.623     1.914   85.952   81.515
LGA    F    20_A      F    20_A     1.684     0    0.100   0.167     3.862   70.833   59.004
LGA    G    21_A      G    21_A     0.865     0    0.099   0.099     1.477   88.214   88.214
LGA    P    22_A      P    22_A     1.049     0    0.618   0.758     3.061   75.833   73.401
LGA    G    23_A      G    23_A     1.025     0    0.594   0.594     2.457   79.524   79.524
LGA    V    24_A      V    24_A     1.076     0    0.038   1.144     3.791   85.952   76.190
LGA    A    25_A      A    25_A     1.873     0    0.071   0.099     2.874   75.000   71.429
LGA    F    26_A      F    26_A     1.221     0    0.183   1.299     6.460   86.190   61.126
LGA    R    27_A      R    27_A     2.489     0    0.040   1.109     8.201   51.786   29.221
LGA    A    28_A      A    28_A     6.330     0    0.014   0.022     7.749   17.857   16.952
LGA    P    29_A      P    29_A    11.314     0    0.024   0.038    13.301    0.119    0.068
LGA    S    30_A      S    30_A    11.971     0    0.080   0.715    16.378    0.000    0.000
LGA    I    31_A      I    31_A    16.245     0    0.527   1.397    17.783    0.000    0.000
LGA    H    32_A      H    32_A    18.564     0    0.039   0.809    21.080    0.000    0.000
LGA    G    33_A      G    33_A    23.808     0    0.531   0.531    27.700    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):    14.150         14.099                 14.406           32.125   29.046

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     14    1.94    40.152    40.381     0.686

LGA_LOCAL      RMSD:   1.940  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  18.728  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  14.150  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.992806 * X  +   0.090272 * Y  +   0.078661 * Z  +  -9.013206
  Y_new =   0.084463 * X  +  -0.993653 * Y  +   0.074293 * Z  +  -3.385619
  Z_new =   0.084869 * X  +  -0.067115 * Y  +  -0.994129 * Z  +   0.050585 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.084870 -0.084971 -3.074184   [DEG:    4.8627   -4.8685 -176.1378 ]
ZXZ:  2.327644  3.033181  2.239907   [DEG:  133.3642  173.7885  128.3372 ]
 
# END of job
