
#######################################################
#                                                     #
#                        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   43 (  366),  selected   35 , name one
# Molecule2: number of CA atoms  127 ( 1099),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      12_C - 52_C        1.90     1.90
  LCS_AVERAGE:     27.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      12_C - 52_C        1.90     1.90
  LCS_AVERAGE:     27.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      12_C - 27_C        0.88     2.43
  LCS_AVERAGE:     11.88

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     R    12_B     R    12_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    13_B     E    13_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    14_B     L    14_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    15_B     L    15_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    16_B     E    16_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    17_B     K    17_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    18_B     L    18_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     I    19_B     I    19_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    20_B     E    20_C     16   35   35     10   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     Y    21_B     Y    21_C     16   35   35     11   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    22_B     L    22_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    23_B     E    23_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    24_B     E    24_C     16   35   35     11   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    25_B     L    25_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    26_B     K    26_C     16   35   35     12   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    27_B     E    27_C     16   35   35      3    8   13   21   29   31   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    34_B     K    34_C     11   35   35      3    8   17   27   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    35_B     E    35_C     11   35   35      4    9   22   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    36_B     K    36_C     11   35   35      4    8   17   25   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    37_B     L    37_C     15   35   35      4   11   22   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    38_B     E    38_C     15   35   35      4   13   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    39_B     E    39_C     15   35   35      4   13   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    40_B     V    40_C     15   35   35      4   13   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     I    41_B     I    41_C     15   35   35      6   13   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    42_B     E    42_C     15   35   35      9   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     G    43_B     G    43_C     15   35   35      9   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    44_B     L    44_C     15   35   35      6   17   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    45_B     E    45_C     15   35   35      6   13   22   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     R    46_B     R    46_C     15   35   35      3   13   23   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    47_B     L    47_C     15   35   35      5   13   15   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    48_B     K    48_C     15   35   35      6   13   15   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    49_B     E    49_C     15   35   35      6   13   15   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    50_B     E    50_C     15   35   35      4   12   15   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    51_B     V    51_C     15   35   35      4   13   15   31   33   33   34   34   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D    52_B     D    52_C     14   35   35      3    3    3    3   14   16   31   33   34   35   35   35   35   35   35   35   35   35   35   35 
LCS_AVERAGE  LCS_A:  22.33  (  11.88   27.56   27.56 )

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     17     23     31     33     33     34     34     34     35     35     35     35     35     35     35     35     35     35     35 
GDT PERCENT_AT   9.45  13.39  18.11  24.41  25.98  25.98  26.77  26.77  26.77  27.56  27.56  27.56  27.56  27.56  27.56  27.56  27.56  27.56  27.56  27.56
GDT RMS_LOCAL    0.39   0.53   0.88   1.46   1.59   1.59   1.68   1.68   1.68   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90
GDT RMS_ALL_AT   2.52   2.31   2.19   1.94   1.91   1.91   1.92   1.92   1.92   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90   1.90

# Checking swapping
#   possible swapping detected:  E    16_B      E    16_C
#   possible swapping detected:  Y    21_B      Y    21_C
#   possible swapping detected:  E    24_B      E    24_C
#   possible swapping detected:  E    45_B      E    45_C
#   possible swapping detected:  E    49_B      E    49_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    12_B      R    12_C     1.041     0    0.194   1.176     5.766   85.952   66.883
LGA    E    13_B      E    13_C     0.509     0    0.161   0.294     2.673   90.476   78.201
LGA    L    14_B      L    14_C     0.881     0    0.086   1.422     4.755   90.476   71.012
LGA    L    15_B      L    15_C     0.761     0    0.064   0.097     1.388   90.476   85.952
LGA    E    16_B      E    16_C     1.116     0    0.066   0.865     1.900   83.690   81.481
LGA    K    17_B      K    17_C     0.965     0    0.056   1.225     5.392   90.476   68.942
LGA    L    18_B      L    18_C     1.050     0    0.066   1.417     3.108   83.690   77.679
LGA    I    19_B      I    19_C     1.354     0    0.016   0.820     2.428   81.429   75.119
LGA    E    20_B      E    20_C     1.545     0    0.014   0.763     2.184   79.286   79.683
LGA    Y    21_B      Y    21_C     1.141     0    0.050   0.857     4.074   85.952   73.135
LGA    L    22_B      L    22_C     0.930     0    0.023   0.092     1.289   88.214   84.821
LGA    E    23_B      E    23_C     0.727     0    0.072   0.286     1.004   88.214   89.471
LGA    E    24_B      E    24_C     0.877     0    0.039   1.307     4.549   90.476   73.968
LGA    L    25_B      L    25_C     0.987     0    0.118   1.104     3.390   90.476   80.952
LGA    K    26_B      K    26_C     1.148     0    0.655   0.633     5.289   77.262   60.741
LGA    E    27_B      E    27_C     3.332     0    0.596   1.008     8.218   46.905   29.683
LGA    K    34_B      K    34_C     2.487     0    0.313   0.711     4.678   72.976   58.201
LGA    E    35_B      E    35_C     1.795     0    0.019   0.469     2.655   70.833   65.767
LGA    K    36_B      K    36_C     2.731     0    0.014   1.071     3.668   60.952   58.201
LGA    L    37_B      L    37_C     1.556     0    0.051   0.135     2.233   70.833   79.524
LGA    E    38_B      E    38_C     1.808     0    0.025   0.389     2.189   72.857   71.958
LGA    E    39_B      E    39_C     2.031     0    0.100   1.016     6.922   70.833   50.265
LGA    V    40_B      V    40_C     1.877     0    0.096   1.173     4.372   72.857   69.116
LGA    I    41_B      I    41_C     1.826     0    0.028   0.211     2.078   72.857   71.845
LGA    E    42_B      E    42_C     1.161     0    0.181   0.167     1.497   81.429   89.630
LGA    G    43_B      G    43_C     1.105     0    0.024   0.024     1.105   85.952   85.952
LGA    L    44_B      L    44_C     0.922     0    0.073   1.235     4.936   83.810   66.071
LGA    E    45_B      E    45_C     1.436     0    0.101   0.751     4.833   81.429   65.979
LGA    R    46_B      R    46_C     1.006     0    0.050   0.578     4.631   77.381   63.420
LGA    L    47_B      L    47_C     2.079     0    0.058   0.972     2.645   67.024   69.107
LGA    K    48_B      K    48_C     2.320     0    0.118   0.777     3.875   64.762   58.307
LGA    E    49_B      E    49_C     2.499     0    0.101   0.669     4.465   60.952   52.857
LGA    E    50_B      E    50_C     2.445     0    0.244   0.946     5.294   59.167   51.693
LGA    V    51_B      V    51_C     2.568     0    0.319   1.221     5.464   46.310   54.286
LGA    D    52_B      D    52_C     5.818     0    0.121   0.244     7.354   22.262   17.440

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     302    302  100.00               127
SUMMARY(RMSD_GDC):     1.902          1.949                  2.626           20.779   18.719

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   43  127    4.0     34    1.68    23.031    25.190     1.913

LGA_LOCAL      RMSD:   1.677  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.923  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   1.902  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.436925 * X  +  -0.788899 * Y  +  -0.432129 * Z  +  65.975945
  Y_new =  -0.807639 * X  +   0.555567 * Y  +  -0.197645 * Z  +  14.325253
  Z_new =   0.395999 * X  +   0.262648 * Y  +  -0.879887 * Z  +  57.821861 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.066696 -0.407155  2.851511   [DEG: -118.4130  -23.3283  163.3795 ]
ZXZ: -1.141825  2.646421  0.985160   [DEG:  -65.4218  151.6287   56.4455 ]
 
# END of job
