
#######################################################
#                                                     #
#                        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   51 (  434),  selected   45 , name one
# Molecule2: number of CA atoms  127 ( 1099),  selected   45 , 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:    28       2_C - 35_C        4.44    26.48
  LCS_AVERAGE:     20.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       3_C - 26_C        1.95    27.62
  LONGEST_CONTINUOUS_SEGMENT:    24       4_C - 27_C        1.96    27.77
  LCS_AVERAGE:     16.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       8_C - 26_C        0.95    28.06
  LONGEST_CONTINUOUS_SEGMENT:    19      34_C - 52_C        0.96    40.47
  LCS_AVERAGE:     13.68

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     P     2_B     P     2_C      7    9   28      3    5    7    9   10   16   20   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     I     3_B     I     3_C      7   24   28      4    6    7   16   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     Q     4_B     Q     4_C      7   24   28      4    6    7   10   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E     5_B     E     5_C      7   24   28      4    6    7    9   15   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E     6_B     E     6_C      7   24   28      4    6    7    9   16   22   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     I     7_B     I     7_C      7   24   28      4    6    7   10   16   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     Q     8_B     Q     8_C     19   24   28      4    6    7   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     K     9_B     K     9_C     19   24   28      3    5   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     K    10_B     K    10_C     19   24   28      4   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     V    11_B     V    11_C     19   24   28      4   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     R    12_B     R    12_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E    13_B     E    13_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     L    14_B     L    14_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     L    15_B     L    15_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E    16_B     E    16_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     K    17_B     K    17_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     L    18_B     L    18_C     19   24   28      7   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     I    19_B     I    19_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E    20_B     E    20_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     Y    21_B     Y    21_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     L    22_B     L    22_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E    23_B     E    23_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E    24_B     E    24_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     L    25_B     L    25_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     K    26_B     K    26_C     19   24   28     14   17   18   18   20   23   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     E    27_B     E    27_C     18   24   28      3    3    3    8   14   20   25   25   26   26   26   26   26   26   27   27   27   28   28   29 
LCS_GDT     K    34_B     K    34_C     19   19   28     11   16   18   18   19   19   19   19   19   19   19   19   23   25   27   27   27   28   28   29 
LCS_GDT     E    35_B     E    35_C     19   19   28     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   21   25   28   28   29 
LCS_GDT     K    36_B     K    36_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   24   26   29 
LCS_GDT     L    37_B     L    37_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     E    38_B     E    38_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     E    39_B     E    39_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     V    40_B     V    40_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     I    41_B     I    41_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     E    42_B     E    42_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     G    43_B     G    43_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     L    44_B     L    44_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     E    45_B     E    45_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     R    46_B     R    46_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     L    47_B     L    47_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     K    48_B     K    48_C     19   19   22     14   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     E    49_B     E    49_C     19   19   22      5   16   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     E    50_B     E    50_C     19   19   22      3   15   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     V    51_B     V    51_C     19   19   22      3   15   18   18   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_GDT     D    52_B     D    52_C     19   19   22      3    3    3    7   19   19   19   19   19   19   19   19   20   20   20   20   21   21   22   22 
LCS_AVERAGE  LCS_A:  16.97  (  13.68   16.97   20.26 )

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     14     17     18     18     20     23     25     25     26     26     26     26     26     26     27     27     27     28     28     29 
GDT PERCENT_AT  11.02  13.39  14.17  14.17  15.75  18.11  19.69  19.69  20.47  20.47  20.47  20.47  20.47  20.47  21.26  21.26  21.26  22.05  22.05  22.83
GDT RMS_LOCAL    0.34   0.47   0.62   0.62   1.11   1.80   2.03   2.03   2.26   2.26   2.26   2.26   2.26   2.26   3.21   3.21   3.21   4.44   4.44   5.42
GDT RMS_ALL_AT  27.93  27.98  40.61  40.61  28.01  27.70  27.65  27.65  27.70  27.70  27.70  27.70  27.70  27.70  27.17  27.17  27.17  26.48  26.48  25.83

# Checking swapping
#   possible swapping detected:  E     6_B      E     6_C
#   possible swapping detected:  E    16_B      E    16_C
#   possible swapping detected:  E    24_B      E    24_C
#   possible swapping detected:  E    27_B      E    27_C
#   possible swapping detected:  E    38_B      E    38_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     2_B      P     2_C     5.901     0    0.713   0.577     8.207   26.548   18.707
LGA    I     3_B      I     3_C     3.082     0    0.147   0.649     6.494   57.262   42.798
LGA    Q     4_B      Q     4_C     3.286     0    0.037   1.056     7.068   55.476   35.979
LGA    E     5_B      E     5_C     3.804     0    0.111   0.362     8.042   48.452   28.519
LGA    E     6_B      E     6_C     3.765     0    0.128   1.098     5.136   50.119   41.111
LGA    I     7_B      I     7_C     3.445     0    0.037   0.064     6.167   53.571   40.119
LGA    Q     8_B      Q     8_C     2.604     0    0.049   0.801     5.709   60.952   46.931
LGA    K     9_B      K     9_C     1.719     0    0.165   1.236     7.756   67.262   50.370
LGA    K    10_B      K    10_C     1.119     0    0.143   0.697     2.768   83.690   73.333
LGA    V    11_B      V    11_C     1.264     0    0.083   0.113     2.867   88.333   77.143
LGA    R    12_B      R    12_C     0.800     0    0.088   1.408     5.482   90.476   75.887
LGA    E    13_B      E    13_C     1.316     0    0.094   0.406     4.222   85.952   64.815
LGA    L    14_B      L    14_C     1.161     0    0.067   0.116     2.433   83.690   76.250
LGA    L    15_B      L    15_C     0.860     0    0.121   0.143     2.925   90.476   76.726
LGA    E    16_B      E    16_C     0.951     0    0.103   0.998     5.152   88.214   72.116
LGA    K    17_B      K    17_C     0.918     0    0.044   1.280     8.134   95.238   67.037
LGA    L    18_B      L    18_C     0.855     0    0.125   1.382     3.776   90.476   80.119
LGA    I    19_B      I    19_C     1.468     0    0.028   0.680     2.631   83.690   73.274
LGA    E    20_B      E    20_C     1.501     0    0.044   0.868     2.593   79.286   74.921
LGA    Y    21_B      Y    21_C     0.960     0    0.086   0.680     5.682   90.476   58.889
LGA    L    22_B      L    22_C     0.968     0    0.084   0.094     1.857   88.214   83.750
LGA    E    23_B      E    23_C     1.229     0    0.061   1.045     6.008   83.690   61.164
LGA    E    24_B      E    24_C     0.861     0    0.028   1.167     4.979   90.476   72.169
LGA    L    25_B      L    25_C     0.968     0    0.107   0.088     1.685   85.952   82.619
LGA    K    26_B      K    26_C     1.440     0    0.577   0.834     6.836   77.262   53.651
LGA    E    27_B      E    27_C     3.321     0    0.599   1.125    10.451   41.190   24.921
LGA    K    34_B      K    34_C    12.826     0    0.335   0.706    16.940    0.000    0.053
LGA    E    35_B      E    35_C    19.062     0    0.080   1.510    22.842    0.000    0.000
LGA    K    36_B      K    36_C    21.264     0    0.018   0.954    23.847    0.000    0.000
LGA    L    37_B      L    37_C    20.641     0    0.042   1.325    24.734    0.000    0.000
LGA    E    38_B      E    38_C    23.930     0    0.053   1.006    28.625    0.000    0.000
LGA    E    39_B      E    39_C    29.407     0    0.042   0.924    33.042    0.000    0.000
LGA    V    40_B      V    40_C    30.398     0    0.065   0.715    34.106    0.000    0.000
LGA    I    41_B      I    41_C    31.871     0    0.023   0.928    36.207    0.000    0.000
LGA    E    42_B      E    42_C    35.956     0    0.120   0.735    40.539    0.000    0.000
LGA    G    43_B      G    43_C    40.311     0    0.025   0.025    43.964    0.000    0.000
LGA    L    44_B      L    44_C    41.535     0    0.043   0.652    45.533    0.000    0.000
LGA    E    45_B      E    45_C    43.472     0    0.121   0.978    47.818    0.000    0.000
LGA    R    46_B      R    46_C    47.817     0    0.075   1.435    52.370    0.000    0.000
LGA    L    47_B      L    47_C    51.710     0    0.051   0.979    55.326    0.000    0.000
LGA    K    48_B      K    48_C    52.454     0    0.068   1.104    56.664    0.000    0.000
LGA    E    49_B      E    49_C    56.170     0    0.052   1.122    60.741    0.000    0.000
LGA    E    50_B      E    50_C    61.440     0    0.128   1.247    65.152    0.000    0.000
LGA    V    51_B      V    51_C    62.650     0    0.124   0.299    66.936    0.000    0.000
LGA    D    52_B      D    52_C    66.154     0    0.679   0.669    69.673    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     386    386  100.00               127
SUMMARY(RMSD_GDC):    20.169         20.456                 20.100           15.247   12.231

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   51  127    4.0     25    2.03    17.126    17.646     1.174

LGA_LOCAL      RMSD:   2.029  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  27.647  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:  20.169  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.521112 * X  +   0.510173 * Y  +   0.684226 * Z  +  18.998596
  Y_new =   0.258590 * X  +  -0.669623 * Y  +   0.696230 * Z  + -12.933867
  Z_new =   0.813372 * X  +   0.539748 * Y  +   0.217023 * Z  +  40.099438 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.680967 -0.949925  1.188497   [DEG:  153.6081  -54.4267   68.0959 ]
ZXZ:  2.364889  1.352033  0.984925   [DEG:  135.4982   77.4658   56.4320 ]
 
# END of job
