
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , 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:    61       1_B - 61_B        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        0.86     0.86
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        0.86     0.86
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B     61   61   61     10   37   48   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     61   61   61     20   38   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     61   61   61     20   41   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     61   61   61     20   46   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     61   61   61     20   45   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     61   61   61     20   45   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     61   61   61     20   45   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     61   61   61     20   46   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     61   61   61     19   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     61   61   61     19   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     61   61   61     23   45   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     61   61   61     11   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     61   61   61     12   34   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     61   61   61     12   42   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     61   61   61     23   34   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     61   61   61     20   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     61   61   61     23   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     61   61   61     20   43   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     61   61   61     12   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     61   61   61     22   47   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     23     47     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  37.70  77.05  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.65   0.82   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86
GDT RMS_ALL_AT   1.40   0.88   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86

# Checking swapping
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  D    24_B      D    24_B
#   possible swapping detected:  D    30_B      D    30_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  F    37_B      F    37_B
#   possible swapping detected:  D    38_B      D    38_B
#   possible swapping detected:  D    44_B      D    44_B
#   possible swapping detected:  D    46_B      D    46_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     2.089     0    0.605   1.029     5.101   60.476   51.667
LGA    Y     2_B      Y     2_B     1.692     0    0.040   0.116     1.937   77.143   74.286
LGA    I     3_B      I     3_B     0.712     0    0.011   0.656     2.153   95.238   88.512
LGA    R     4_B      R     4_B     0.902     0    0.030   0.419     4.413   90.476   70.433
LGA    E     5_B      E     5_B     1.345     0    0.025   0.357     2.870   81.429   72.222
LGA    L     6_B      L     6_B     0.956     0    0.022   0.224     1.632   90.476   84.881
LGA    R     7_B      R     7_B     0.672     0    0.022   0.574     4.596   92.857   74.589
LGA    A     8_B      A     8_B     1.149     0    0.043   0.044     1.668   88.214   85.143
LGA    A     9_B      A     9_B     0.907     0    0.006   0.005     1.271   90.476   88.667
LGA    L    10_B      L    10_B     0.664     0    0.014   0.082     1.750   92.857   85.000
LGA    I    11_B      I    11_B     1.008     0    0.008   0.040     1.831   85.952   80.476
LGA    L    12_B      L    12_B     0.941     0    0.016   0.074     1.819   90.476   83.810
LGA    L    13_B      L    13_B     0.435     0    0.005   0.060     1.338  100.000   91.845
LGA    A    14_B      A    14_B     0.731     0    0.007   0.012     1.041   92.857   90.571
LGA    L    15_B      L    15_B     1.160     0    0.026   0.284     2.835   88.214   77.560
LGA    K    16_B      K    16_B     0.508     0    0.028   0.727     4.638   95.238   73.386
LGA    K    17_B      K    17_B     0.391     0    0.027   0.658     2.046  100.000   86.032
LGA    Q    18_B      Q    18_B     0.979     0    0.046   1.434     5.522   85.952   64.550
LGA    H    19_B      H    19_B     1.216     0    0.027   0.480     2.658   81.429   75.714
LGA    A    20_B      A    20_B     0.991     0    0.025   0.030     0.991   90.476   90.476
LGA    E    21_B      E    21_B     0.688     0    0.047   0.242     1.674   90.476   86.508
LGA    D    22_B      D    22_B     0.786     0    0.015   0.592     1.896   90.476   87.143
LGA    P    23_B      P    23_B     0.624     0    0.082   0.117     1.176   92.857   87.959
LGA    D    24_B      D    24_B     0.530     0    0.050   0.104     1.185   92.857   90.536
LGA    A    25_B      A    25_B     0.557     0    0.007   0.007     0.620   92.857   92.381
LGA    Q    26_B      Q    26_B     0.370     0    0.007   0.183     0.684  100.000   98.942
LGA    R    27_B      R    27_B     0.373     0    0.011   0.848     3.629   97.619   85.844
LGA    V    28_B      V    28_B     0.478     0    0.009   0.014     0.555   97.619   94.558
LGA    A    29_B      A    29_B     0.492     0    0.019   0.023     0.541   95.238   96.190
LGA    D    30_B      D    30_B     0.584     0    0.028   0.758     2.557   90.476   84.048
LGA    E    31_B      E    31_B     0.573     0    0.007   0.544     2.729   92.857   84.868
LGA    L    32_B      L    32_B     0.483     0    0.013   0.097     0.541   92.857   94.048
LGA    M    33_B      M    33_B     0.593     0    0.005   0.943     2.716   90.476   84.048
LGA    K    34_B      K    34_B     0.448     0    0.033   0.332     2.470  100.000   90.899
LGA    K    35_B      K    35_B     0.177     0    0.005   0.296     0.987  100.000   96.825
LGA    L    36_B      L    36_B     0.233     0    0.013   1.375     3.309  100.000   83.988
LGA    F    37_B      F    37_B     0.229     0    0.012   0.493     2.130  100.000   88.442
LGA    D    38_B      D    38_B     0.404     0    0.022   0.826     3.915   97.619   78.929
LGA    A    39_B      A    39_B     0.484     0    0.004   0.007     0.597   97.619   96.190
LGA    A    40_B      A    40_B     0.328     0    0.070   0.074     0.509  100.000   98.095
LGA    H    41_B      H    41_B     0.441     0    0.050   0.808     3.360   95.238   79.762
LGA    R    42_B      R    42_B     0.704     0    0.031   1.022     3.572   90.476   80.736
LGA    N    43_B      N    43_B     0.452     0    0.010   0.803     3.418   95.238   83.571
LGA    D    44_B      D    44_B     0.917     0    0.052   0.253     1.140   90.476   88.214
LGA    K    45_B      K    45_B     1.041     0    0.051   0.838     5.564   81.429   61.640
LGA    D    46_B      D    46_B     1.219     0    0.026   0.463     2.549   81.429   76.250
LGA    K    47_B      K    47_B     0.778     0    0.013   0.219     1.409   90.476   88.466
LGA    V    48_B      V    48_B     0.806     0    0.013   0.064     0.959   90.476   90.476
LGA    K    49_B      K    49_B     1.066     0    0.017   0.903     5.825   83.690   62.116
LGA    K    50_B      K    50_B     1.174     0    0.006   0.414     2.322   81.429   79.577
LGA    V    51_B      V    51_B     1.163     0    0.023   0.029     1.396   81.429   81.429
LGA    V    52_B      V    52_B     0.931     0    0.007   0.069     0.991   90.476   90.476
LGA    E    53_B      E    53_B     1.002     0    0.009   0.483     2.400   83.690   78.677
LGA    E    54_B      E    54_B     1.220     0    0.010   0.642     1.350   81.429   81.429
LGA    A    55_B      A    55_B     1.015     0    0.014   0.015     1.061   85.952   86.857
LGA    K    56_B      K    56_B     0.681     0    0.004   0.383     1.265   90.476   88.466
LGA    K    57_B      K    57_B     0.987     0    0.024   0.048     2.046   90.476   81.693
LGA    V    58_B      V    58_B     1.260     0    0.094   0.184     2.245   81.429   75.442
LGA    V    59_B      V    59_B     0.837     0    0.033   0.172     0.906   90.476   90.476
LGA    S    60_B      S    60_B     0.408     0    0.125   0.176     0.719   95.238   95.238
LGA    T    61_B      T    61_B     0.324     0    0.026   0.056     0.730  100.000   95.918

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     0.857          0.856                  1.506           90.714   84.052

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    0.86    94.262    98.066     6.372

LGA_LOCAL      RMSD:   0.857  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.857  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.857  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.014069 * X  +  -0.590406 * Y  +   0.806984 * Z  +   1.691275
  Y_new =   0.997046 * X  +  -0.069224 * Y  +  -0.033263 * Z  + -10.399971
  Z_new =   0.075501 * X  +   0.804132 * Y  +   0.589636 * Z  +   2.014435 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.584906 -0.075573  0.938097   [DEG:   90.8084   -4.3300   53.7490 ]
ZXZ:  1.529600  0.940188  0.093617   [DEG:   87.6396   53.8688    5.3639 ]
 
# END of job
