
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.17     1.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.17     1.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    68       2_B - 69_B        0.99     1.19
  LCS_AVERAGE:     95.02

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     G     1_B     G     1_B     67   71   71      5    6   47   61   69   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     68   71   71      8   42   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     68   71   71     28   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     68   71   71     22   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     68   71   71     28   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     68   71   71     28   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     68   71   71     29   50   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     68   71   71     29   50   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     68   71   71      6   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     68   71   71     20   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     68   71   71     28   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     68   71   71     19   46   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     68   71   71     25   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     68   71   71     18   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     68   71   71     29   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     68   71   71     25   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     68   71   71     20   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     68   71   71     18   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     68   71   71     19   35   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     68   71   71     19   32   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     68   71   71     19   40   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     68   71   71     19   49   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     68   71   71     27   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     68   71   71     19   51   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     68   71   71     19   39   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     68   71   71     13   43   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     68   71   71     19   49   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     68   71   71     19   39   65   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     68   71   71     11   32   54   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     68   71   71     11   32   54   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     68   71   71     11   27   54   68   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     50   71   71     11   20   39   62   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     49   71   71     11   20   39   47   70   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.34  (  95.02  100.00  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     29     51     65     68     70     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  40.85  71.83  91.55  95.77  98.59  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.64   0.86   0.99   1.13   1.10   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17
GDT RMS_ALL_AT   1.51   1.33   1.25   1.19   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  E    71_B      E    71_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.735     0    0.447   0.447     5.312   59.405   59.405
LGA    S     2_B      S     2_B     1.444     0    0.027   0.715     2.809   79.286   74.524
LGA    V     3_B      V     3_B     0.740     0    0.029   1.044     3.047   90.476   79.932
LGA    S     4_B      S     4_B     0.787     0    0.039   0.160     1.179   85.952   85.952
LGA    K     5_B      K     5_B     1.303     0    0.059   0.822     5.866   81.429   60.370
LGA    W     6_B      W     6_B     1.107     0    0.031   0.128     1.551   81.429   81.463
LGA    S     7_B      S     7_B     0.847     0    0.037   0.042     0.933   90.476   90.476
LGA    T     8_B      T     8_B     0.489     0    0.014   0.070     0.827   97.619   94.558
LGA    D     9_B      D     9_B     0.191     0    0.020   0.762     3.177  100.000   84.940
LGA    E    10_B      E    10_B     0.724     0    0.012   0.370     2.331   90.476   83.651
LGA    V    11_B      V    11_B     0.483     0    0.014   0.060     0.616   95.238   95.918
LGA    S    12_B      S    12_B     0.592     0    0.031   0.102     0.993   92.857   92.063
LGA    E    13_B      E    13_B     1.175     0    0.018   0.785     4.500   83.690   68.466
LGA    F    14_B      F    14_B     1.179     0    0.047   0.136     2.229   81.429   76.840
LGA    I    15_B      I    15_B     0.707     0    0.017   0.684     2.430   90.476   88.452
LGA    Q    16_B      Q    16_B     1.226     0    0.052   0.155     2.140   81.429   78.624
LGA    S    17_B      S    17_B     1.493     0    0.009   0.014     1.584   79.286   78.571
LGA    L    18_B      L    18_B     1.241     0    0.042   0.101     1.297   81.429   83.690
LGA    P    19_B      P    19_B     1.451     0    0.013   0.389     2.377   81.429   77.823
LGA    G    20_B      G    20_B     1.427     0    0.033   0.033     1.464   81.429   81.429
LGA    C    21_B      C    21_B     0.920     0    0.046   0.053     1.136   88.214   88.968
LGA    E    22_B      E    22_B     1.051     0    0.059   0.775     4.409   85.952   69.841
LGA    E    23_B      E    23_B     0.754     0    0.087   0.826     3.541   90.476   79.524
LGA    H    24_B      H    24_B     0.698     0    0.070   0.105     1.430   90.476   85.952
LGA    G    25_B      G    25_B     0.756     0    0.040   0.040     0.857   90.476   90.476
LGA    K    26_B      K    26_B     0.898     0    0.010   0.766     1.616   90.476   84.497
LGA    V    27_B      V    27_B     1.168     0    0.044   1.068     3.688   85.952   78.571
LGA    F    28_B      F    28_B     0.558     0    0.012   0.207     1.613   90.476   88.095
LGA    K    29_B      K    29_B     0.767     0    0.010   1.053     3.434   85.952   75.450
LGA    D    30_B      D    30_B     1.455     0    0.051   0.076     1.815   79.286   76.071
LGA    E    31_B      E    31_B     1.225     0    0.017   0.137     1.779   81.429   78.571
LGA    Q    32_B      Q    32_B     1.246     0    0.020   0.822     4.314   81.429   67.831
LGA    I    33_B      I    33_B     0.668     0    0.064   0.064     0.781   92.857   91.667
LGA    D    34_B      D    34_B     0.735     0    0.015   0.127     1.462   90.476   88.214
LGA    G    35_B      G    35_B     0.823     0    0.075   0.075     0.823   90.476   90.476
LGA    E    36_B      E    36_B     1.041     0    0.016   0.067     2.257   85.952   77.831
LGA    A    37_B      A    37_B     0.818     0    0.024   0.023     0.861   90.476   90.476
LGA    F    38_B      F    38_B     0.497     0    0.055   0.207     0.890   97.619   93.939
LGA    L    39_B      L    39_B     0.330     0    0.105   0.182     0.794   97.619   95.238
LGA    L    40_B      L    40_B     0.170     0    0.014   0.077     0.575  100.000   97.619
LGA    M    41_B      M    41_B     0.429     0    0.062   0.149     0.941  100.000   95.238
LGA    T    42_B      T    42_B     0.645     0    0.021   0.048     0.732   90.476   90.476
LGA    Q    43_B      Q    43_B     0.687     0    0.025   0.142     2.042   90.476   83.651
LGA    T    44_B      T    44_B     0.624     0    0.038   0.103     0.900   92.857   91.837
LGA    D    45_B      D    45_B     0.581     0    0.015   0.111     0.994   90.476   90.476
LGA    I    46_B      I    46_B     0.640     0    0.033   0.071     0.804   90.476   90.476
LGA    V    47_B      V    47_B     0.890     0    0.047   0.053     1.159   90.476   87.891
LGA    K    48_B      K    48_B     1.386     0    0.064   0.810     5.211   79.286   66.243
LGA    I    49_B      I    49_B     1.364     0    0.044   0.092     1.798   81.429   78.214
LGA    M    50_B      M    50_B     0.983     0    0.026   0.272     1.574   88.214   86.012
LGA    S    51_B      S    51_B     0.937     0    0.023   0.040     1.365   88.214   85.952
LGA    I    52_B      I    52_B     0.563     0    0.046   0.045     0.710   90.476   90.476
LGA    K    53_B      K    53_B     0.893     0    0.024   0.644     2.702   90.476   83.069
LGA    E    54_B      E    54_B     1.079     0    0.018   0.548     2.522   81.429   75.926
LGA    G    55_B      G    55_B     1.225     0    0.061   0.061     1.366   81.429   81.429
LGA    P    56_B      P    56_B     0.901     0    0.013   0.295     1.007   90.476   89.184
LGA    A    57_B      A    57_B     0.742     0    0.023   0.021     0.847   90.476   90.476
LGA    E    58_B      E    58_B     0.845     0    0.011   0.816     3.619   90.476   76.667
LGA    K    59_B      K    59_B     0.982     0    0.018   0.103     1.430   90.476   85.450
LGA    I    60_B      I    60_B     0.594     0    0.019   0.066     0.693   92.857   91.667
LGA    F    61_B      F    61_B     0.324     0    0.062   0.102     0.621  100.000   97.403
LGA    N    62_B      N    62_B     0.678     0    0.017   0.046     1.436   90.476   85.952
LGA    S    63_B      S    63_B     1.181     0    0.011   0.047     1.565   83.690   81.508
LGA    I    64_B      I    64_B     0.990     0    0.011   0.076     1.279   88.214   88.214
LGA    L    65_B      L    65_B     0.516     0    0.025   0.134     0.952   90.476   92.857
LGA    M    66_B      M    66_B     1.391     0    0.027   0.803     4.673   79.405   63.571
LGA    F    67_B      F    67_B     2.034     0    0.042   1.294     5.252   64.881   58.615
LGA    K    68_B      K    68_B     1.956     0    0.011   0.971     2.512   68.810   68.413
LGA    A    69_B      A    69_B     2.045     0    0.076   0.080     2.356   66.786   68.000
LGA    A    70_B      A    70_B     2.968     0    0.183   0.200     3.137   53.571   54.286
LGA    E    71_B      E    71_B     3.317     0    0.025   0.664     3.414   50.000   52.434

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.169          1.186                  1.542           86.036   82.092

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.17    91.901    96.670     5.597

LGA_LOCAL      RMSD:   1.169  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.169  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.169  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.104031 * X  +  -0.971782 * Y  +  -0.211701 * Z  +  25.180651
  Y_new =  -0.493956 * X  +  -0.134266 * Y  +   0.859058 * Z  +  40.720551
  Z_new =  -0.863241 * X  +   0.193940 * Y  +  -0.466050 * Z  +  -8.533567 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.778370  1.041655  2.747255   [DEG: -101.8931   59.6825  157.4061 ]
ZXZ: -2.899973  2.055617 -1.349801   [DEG: -166.1562  117.7782  -77.3379 ]
 
# END of job
