
#######################################################
#                                                     #
#                        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        1.32     1.32
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.32     1.32
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    43      15_B - 57_B        0.99     1.42
  LCS_AVERAGE:     60.39

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     15   61   61      6   22   46   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     15   61   61      9   12   36   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     15   61   61      9   13   24   51   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     15   61   61      9   13   46   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     15   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     15   61   61     15   30   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     15   61   61      9   31   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     15   61   61     19   28   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     15   61   61      9   24   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     15   61   61     19   31   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     15   61   61      9   22   37   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     15   61   61      7   12   27   52   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     15   61   61      7   23   36   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     41   61   61      7   27   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     43   61   61      7   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     43   61   61      7   31   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     43   61   61     11   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     43   61   61     14   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     43   61   61      4    9   49   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     43   61   61      7   30   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     43   61   61      5   28   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     43   61   61     11   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     43   61   61      7   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     43   61   61     12   32   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     43   61   61     13   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     43   61   61     13   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     43   61   61     13   30   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     43   61   61     13   30   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     43   61   61     13   30   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     43   61   61     13   23   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     43   61   61     10   23   30   54   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     43   61   61      5   23   50   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     43   61   61      5   30   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     43   61   61     15   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     43   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     42   61   61     19   27   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     40   61   61     19   28   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     40   61   61     19   33   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     40   61   61      3   29   50   56   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  86.80  (  60.39  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     19     33     50     56     59     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  31.15  54.10  81.97  91.80  96.72 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.72   0.97   1.14   1.23   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32
GDT RMS_ALL_AT   1.85   1.40   1.33   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32   1.32

# Checking swapping
#   possible swapping detected:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  D    24_B      D    24_B
#   possible swapping detected:  F    37_B      F    37_B
#   possible swapping detected:  E    53_B      E    53_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     2.082     0    0.280   1.375     5.938   65.595   49.583
LGA    Y     2_B      Y     2_B     2.164     0    0.057   0.921     3.571   68.810   62.778
LGA    I     3_B      I     3_B     2.898     0    0.031   1.278     5.760   60.952   56.607
LGA    R     4_B      R     4_B     2.050     0    0.058   1.081     2.817   73.095   67.879
LGA    E     5_B      E     5_B     0.582     0    0.045   0.626     2.461   88.214   82.751
LGA    L     6_B      L     6_B     1.094     0    0.043   0.948     4.833   88.214   72.500
LGA    R     7_B      R     7_B     1.057     0    0.028   1.198     3.625   88.214   77.879
LGA    A     8_B      A     8_B     1.172     0    0.044   0.045     1.760   81.548   81.524
LGA    A     9_B      A     9_B     1.351     0    0.037   0.039     1.943   81.548   81.524
LGA    L    10_B      L    10_B     0.862     0    0.039   0.124     1.402   85.952   85.952
LGA    I    11_B      I    11_B     2.066     0    0.026   1.300     4.557   64.881   64.821
LGA    L    12_B      L    12_B     2.767     0    0.153   0.898     5.457   60.952   53.512
LGA    L    13_B      L    13_B     2.248     0    0.032   1.025     4.676   66.905   58.869
LGA    A    14_B      A    14_B     1.487     0    0.038   0.046     1.914   81.548   79.810
LGA    L    15_B      L    15_B     0.726     0    0.038   1.058     4.338   92.976   77.679
LGA    K    16_B      K    16_B     0.940     0    0.033   1.082     6.880   90.476   67.143
LGA    K    17_B      K    17_B     0.563     0    0.036   1.115     5.058   92.857   78.889
LGA    Q    18_B      Q    18_B     0.813     0    0.048   0.988     3.555   86.190   74.656
LGA    H    19_B      H    19_B     1.727     0    0.171   1.103     6.477   75.000   50.524
LGA    A    20_B      A    20_B     1.373     0    0.129   0.172     2.027   77.262   78.095
LGA    E    21_B      E    21_B     1.060     0    0.069   0.258     1.433   83.690   84.444
LGA    D    22_B      D    22_B     0.314     0    0.086   1.205     4.387   92.857   78.810
LGA    P    23_B      P    23_B     1.289     0    0.108   0.355     1.607   83.690   85.442
LGA    D    24_B      D    24_B     1.367     0    0.077   0.900     5.449   81.429   66.667
LGA    A    25_B      A    25_B     0.939     0    0.049   0.050     1.352   85.952   86.857
LGA    Q    26_B      Q    26_B     1.368     0    0.024   1.074     3.941   79.286   77.249
LGA    R    27_B      R    27_B     1.592     0    0.021   1.115     4.975   72.857   63.030
LGA    V    28_B      V    28_B     1.306     0    0.021   1.013     2.499   81.429   77.823
LGA    A    29_B      A    29_B     1.300     0    0.044   0.070     1.300   81.429   81.429
LGA    D    30_B      D    30_B     1.091     0    0.020   1.174     5.401   85.952   70.060
LGA    E    31_B      E    31_B     0.833     0    0.030   0.995     4.879   92.857   72.275
LGA    L    32_B      L    32_B     0.863     0    0.050   1.383     2.830   90.476   80.833
LGA    M    33_B      M    33_B     1.058     0    0.045   1.057     3.735   88.214   78.988
LGA    K    34_B      K    34_B     0.471     0    0.043   0.956     3.459   95.238   75.397
LGA    K    35_B      K    35_B     0.565     0    0.063   0.288     1.280   92.857   89.524
LGA    L    36_B      L    36_B     0.865     0    0.037   1.175     3.222   88.214   82.083
LGA    F    37_B      F    37_B     1.325     0    0.040   0.530     2.413   79.286   76.840
LGA    D    38_B      D    38_B     1.488     0    0.051   0.162     2.047   75.119   77.202
LGA    A    39_B      A    39_B     1.235     0    0.022   0.033     1.591   79.286   81.524
LGA    A    40_B      A    40_B     1.893     0    0.102   0.100     2.252   68.810   69.619
LGA    H    41_B      H    41_B     2.743     0    0.088   0.922     7.621   57.262   37.429
LGA    R    42_B      R    42_B     1.946     0    0.145   1.355     7.034   70.833   57.879
LGA    N    43_B      N    43_B     1.155     0    0.036   0.770     3.214   85.952   75.595
LGA    D    44_B      D    44_B     0.620     0    0.099   0.942     3.812   95.238   76.905
LGA    K    45_B      K    45_B     0.474     0    0.090   0.820     5.171  100.000   71.217
LGA    D    46_B      D    46_B     0.369     0    0.036   0.626     1.982  100.000   93.036
LGA    K    47_B      K    47_B     0.128     0    0.037   0.969     5.003  100.000   74.868
LGA    V    48_B      V    48_B     0.163     0    0.064   1.240     2.781  100.000   88.844
LGA    K    49_B      K    49_B     0.502     0    0.052   0.869     3.082   92.857   79.471
LGA    K    50_B      K    50_B     0.586     0    0.057   1.125     5.025   92.857   80.688
LGA    V    51_B      V    51_B     0.423     0    0.031   0.109     0.655   97.619   98.639
LGA    V    52_B      V    52_B     0.414     0    0.032   0.153     0.648   95.238   94.558
LGA    E    53_B      E    53_B     0.654     0    0.030   0.773     3.808   88.214   71.534
LGA    E    54_B      E    54_B     0.906     0    0.038   0.369     2.409   90.476   84.603
LGA    A    55_B      A    55_B     0.901     0    0.038   0.052     1.087   88.214   88.667
LGA    K    56_B      K    56_B     0.819     0    0.057   0.731     2.249   88.214   81.799
LGA    K    57_B      K    57_B     0.975     0    0.028   1.518     6.978   85.952   60.899
LGA    V    58_B      V    58_B     1.410     0    0.074   0.131     2.267   81.429   76.599
LGA    V    59_B      V    59_B     1.199     0    0.094   0.241     1.589   81.429   81.497
LGA    S    60_B      S    60_B     0.956     0    0.221   0.231     2.029   81.786   84.683
LGA    T    61_B      T    61_B     1.049     0    0.024   1.072     2.861   81.548   76.939

# 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):     1.316          1.312                  2.231           83.692   75.335

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    1.32    86.475    94.241     4.307

LGA_LOCAL      RMSD:   1.316  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.316  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.316  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.977864 * X  +  -0.208171 * Y  +   0.021116 * Z  +  -8.466328
  Y_new =  -0.206298 * X  +  -0.942330 * Y  +   0.263545 * Z  + -15.527316
  Z_new =  -0.034965 * X  +  -0.262068 * Y  +  -0.964416 * Z  +  36.506310 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.207919  0.034972 -2.876262   [DEG:  -11.9129    2.0037 -164.7977 ]
ZXZ:  3.061641  2.874022 -3.008958   [DEG:  175.4191  164.6693 -172.4006 ]
 
# END of job
