
#######################################################
#                                                     #
#                        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   64 (  513),  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        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.90     1.90
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      20_B - 60_B        1.00     2.06
  LCS_AVERAGE:     57.35

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     21   61   61      4    7   12   22   31   46   53   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     21   61   61      9   18   20   23   35   54   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     21   61   61      9   18   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     21   61   61      9   18   37   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     21   61   61     10   18   20   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     21   61   61      8   18   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     21   61   61      9   21   37   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     21   61   61     10   18   32   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     21   61   61      9   22   38   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     21   61   61      9   18   33   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     21   61   61     10   18   23   44   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     21   61   61     10   18   20   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     21   61   61     10   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     21   61   61     10   18   22   40   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     21   61   61     10   18   20   40   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     21   61   61     10   18   38   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     21   61   61     10   18   33   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     21   61   61      9   18   20   34   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     40   61   61      5   17   25   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     41   61   61      9   22   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     41   61   61     16   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     41   61   61     12   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     41   61   61     12   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     41   61   61     18   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     41   61   61     13   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     41   61   61     12   31   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     41   61   61     18   29   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     41   61   61     10   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     41   61   61     18   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     41   61   61     10   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     41   61   61     10   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     41   61   61     11   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     41   61   61     11   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     41   61   61     19   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     41   61   61     18   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     41   61   61     13   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     41   61   61     13   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     41   61   61     11   33   41   46   53   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     41   61   61      8   31   41   46   51   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     41   61   61      7   10   36   44   49   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     41   61   61      7   10   34   42   49   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     41   61   61      7   10   17   39   49   53   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     35   61   61      7   10   12   27   35   53   59   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  85.78  (  57.35  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     41     46     53     55     59     60     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  31.15  54.10  67.21  75.41  86.89  90.16  96.72  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
GDT RMS_LOCAL    0.31   0.61   0.81   1.03   1.47   1.51   1.72   1.80   1.90   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   2.04   2.03   2.05   2.00   2.06   2.00   1.91   1.90   1.90   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:  D     1_B      D     1_B
#   possible swapping detected:  Y     2_B      Y     2_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     5.220     0    0.026   0.905     6.906   24.286   33.810
LGA    Y     2_B      Y     2_B     3.770     0    0.155   1.379     4.668   48.690   48.135
LGA    I     3_B      I     3_B     1.354     0    0.028   0.034     2.283   81.548   75.238
LGA    R     4_B      R     4_B     2.004     0    0.011   0.423     7.726   70.952   43.420
LGA    E     5_B      E     5_B     2.406     0    0.014   1.257     5.386   68.810   51.481
LGA    L     6_B      L     6_B     1.629     0    0.055   1.415     3.143   77.143   72.321
LGA    R     7_B      R     7_B     1.924     0    0.026   0.068     4.908   72.976   53.333
LGA    A     8_B      A     8_B     2.787     0    0.023   0.025     3.661   62.857   58.952
LGA    A     9_B      A     9_B     1.817     0    0.019   0.031     2.514   77.143   73.143
LGA    L    10_B      L    10_B     1.940     0    0.029   0.057     3.827   70.952   59.702
LGA    I    11_B      I    11_B     3.364     0    0.015   0.111     6.343   55.476   40.357
LGA    L    12_B      L    12_B     2.784     0    0.021   1.007     7.409   62.976   42.798
LGA    L    13_B      L    13_B     1.421     0    0.069   1.084     7.308   81.429   55.060
LGA    A    14_B      A    14_B     2.979     0    0.024   0.026     4.172   59.286   54.857
LGA    L    15_B      L    15_B     3.556     0    0.037   0.247     7.070   53.690   36.369
LGA    K    16_B      K    16_B     1.930     0    0.052   0.136     6.447   77.143   54.074
LGA    K    17_B      K    17_B     1.883     0    0.019   1.098     2.997   72.976   67.725
LGA    Q    18_B      Q    18_B     3.210     0    0.023   1.430     9.052   57.262   35.503
LGA    H    19_B      H    19_B     2.715     0    0.136   0.423     7.355   59.167   38.714
LGA    A    20_B      A    20_B     2.481     0    0.409   0.453     3.523   66.786   62.095
LGA    E    21_B      E    21_B     1.517     0    0.053   0.487     1.855   77.143   80.529
LGA    D    22_B      D    22_B     0.966     0    0.013   0.277     1.299   88.214   90.536
LGA    P    23_B      P    23_B     1.048     0    0.069   0.342     1.418   88.214   87.891
LGA    D    24_B      D    24_B     0.746     0    0.025   0.973     5.459   88.214   70.060
LGA    A    25_B      A    25_B     1.323     0    0.022   0.022     1.741   81.429   79.714
LGA    Q    26_B      Q    26_B     1.283     0    0.031   0.403     2.737   85.952   73.386
LGA    R    27_B      R    27_B     0.663     0    0.043   0.251     2.545   90.476   78.745
LGA    V    28_B      V    28_B     1.330     0    0.019   0.033     2.125   81.548   76.667
LGA    A    29_B      A    29_B     1.604     0    0.036   0.043     1.844   77.143   76.286
LGA    D    30_B      D    30_B     0.936     0    0.057   0.273     2.056   88.214   82.798
LGA    E    31_B      E    31_B     0.677     0    0.021   0.107     1.138   90.476   88.466
LGA    L    32_B      L    32_B     1.141     0    0.075   1.381     5.000   83.690   64.940
LGA    M    33_B      M    33_B     1.136     0    0.028   1.090     4.433   85.952   69.464
LGA    K    34_B      K    34_B     0.635     0    0.020   0.224     2.120   95.238   86.772
LGA    K    35_B      K    35_B     0.196     0    0.064   0.287     1.076   97.619   95.820
LGA    L    36_B      L    36_B     1.016     0    0.223   0.234     1.325   88.214   84.821
LGA    F    37_B      F    37_B     1.194     0    0.136   1.269     7.403   77.143   48.701
LGA    D    38_B      D    38_B     1.278     0    0.390   0.770     4.140   77.262   66.845
LGA    A    39_B      A    39_B     0.512     0    0.072   0.068     1.045   88.214   90.571
LGA    A    40_B      A    40_B     0.712     0    0.095   0.103     1.405   85.952   86.857
LGA    H    41_B      H    41_B     1.319     0    0.097   0.910     3.413   79.286   70.905
LGA    R    42_B      R    42_B     0.669     0    0.013   0.758     3.164   90.476   84.632
LGA    N    43_B      N    43_B     0.941     0    0.076   0.797     2.628   88.214   79.643
LGA    D    44_B      D    44_B     0.607     0    0.021   0.105     0.745   92.857   92.857
LGA    K    45_B      K    45_B     0.849     0    0.017   0.318     3.285   90.476   77.407
LGA    D    46_B      D    46_B     0.797     0    0.012   0.889     4.401   90.476   72.083
LGA    K    47_B      K    47_B     0.320     0    0.020   0.289     2.097  100.000   90.053
LGA    V    48_B      V    48_B     0.157     0    0.009   0.079     0.326  100.000  100.000
LGA    K    49_B      K    49_B     0.329     0    0.062   0.985     6.541   97.619   71.587
LGA    K    50_B      K    50_B     0.391     0    0.017   0.170     1.190  100.000   94.762
LGA    V    51_B      V    51_B     0.511     0    0.038   0.059     0.567   92.857   93.197
LGA    V    52_B      V    52_B     0.665     0    0.040   0.093     1.418   95.238   89.320
LGA    E    53_B      E    53_B     0.365     0    0.008   0.423     0.889   97.619   96.825
LGA    E    54_B      E    54_B     0.556     0    0.013   0.931     4.731   92.857   73.122
LGA    A    55_B      A    55_B     0.509     0    0.016   0.026     0.997   92.857   94.286
LGA    K    56_B      K    56_B     1.059     0    0.007   0.393     2.202   81.548   79.630
LGA    K    57_B      K    57_B     1.513     0    0.018   0.586     2.106   72.976   77.672
LGA    V    58_B      V    58_B     2.283     0    0.117   0.165     3.250   61.190   61.633
LGA    V    59_B      V    59_B     2.753     0    0.069   0.148     3.120   57.262   57.211
LGA    S    60_B      S    60_B     3.242     0    0.058   0.603     4.144   46.905   54.365
LGA    T    61_B      T    61_B     4.125     0    0.174   1.115     5.118   38.690   37.347

# 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):     1.895          1.835                  2.679           78.316   70.254

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   61    4.0     60    1.80    81.967    90.466     3.166

LGA_LOCAL      RMSD:   1.795  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.902  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.895  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.341652 * X  +  -0.874420 * Y  +   0.344476 * Z  +  14.918104
  Y_new =  -0.357203 * X  +  -0.218210 * Y  +  -0.908180 * Z  + -10.508336
  Z_new =   0.869299 * X  +  -0.433329 * Y  +  -0.237793 * Z  +   6.570042 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.333946 -1.053782 -2.072686   [DEG: -133.7253  -60.3773 -118.7562 ]
ZXZ:  0.362538  1.810890  2.033228   [DEG:   20.7719  103.7563  116.4954 ]
 
# END of job
