
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        1.29     1.29
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        1.29     1.29
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    42      32_A - 73_A        0.99     1.41
  LCS_AVERAGE:     63.61

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     A    32_A     A    32_A     42   61   61     11   31   47   55   58   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     42   61   61     18   40   50   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     42   61   61     22   42   50   55   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     42   61   61     21   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     42   61   61     23   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     42   61   61     19   40   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     42   61   61      6   40   49   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     42   61   61     21   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     42   61   61      5   31   48   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     42   61   61     15   41   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     42   61   61     15   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     42   61   61     22   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     42   61   61     22   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     42   61   61     15   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     42   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     42   61   61     15   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     42   61   61     15   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     42   61   61     15   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     42   61   61     13   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     42   61   61     14   40   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     42   61   61     11   37   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     42   61   61     15   33   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     42   61   61     15   33   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     40   61   61     12   32   48   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     38   61   61      6   32   48   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     38   61   61      6   32   48   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     34   61   61      0    4   24   31   48   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     34   61   61      4    6    7   51   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     34   61   61      4   31   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     34   61   61      8   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     34   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     34   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     34   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     34   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     34   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     34   61   61     24   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     34   61   61     23   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     34   61   61     16   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     34   61   61     14   42   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     15   61   61      5   29   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     15   61   61      5   31   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     15   61   61      4   32   50   56   59   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  87.87  (  63.61  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     24     42     50     56     59     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  39.34  68.85  81.97  91.80  96.72  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.62   0.81   1.08   1.16   1.19   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29
GDT RMS_ALL_AT   1.75   1.49   1.39   1.31   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29   1.29

# Checking swapping
#   possible swapping detected:  Y    47_A      Y    47_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    76_A      Y    76_A
#   possible swapping detected:  D    84_A      D    84_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     2.573     0    0.510   0.509     3.808   60.952   57.429
LGA    T    33_A      T    33_A     1.798     0    0.090   0.321     2.306   75.000   76.667
LGA    M    34_A      M    34_A     1.650     0    0.044   0.256     2.989   77.143   69.048
LGA    A    35_A      A    35_A     1.177     0    0.030   0.034     1.353   85.952   85.048
LGA    D    36_A      D    36_A     0.662     0    0.112   0.196     1.551   90.476   86.012
LGA    L    37_A      L    37_A     1.181     0    0.026   0.168     2.225   88.214   78.512
LGA    K    38_A      K    38_A     0.546     0    0.039   0.607     1.555   95.238   87.619
LGA    M    39_A      M    39_A     0.432     0    0.011   1.068     4.624   95.238   78.095
LGA    Q    40_A      Q    40_A     0.978     0    0.064   1.007     5.141   90.476   70.476
LGA    A    41_A      A    41_A     0.410     0    0.050   0.051     0.624   97.619   98.095
LGA    V    42_A      V    42_A     0.362     0    0.062   0.145     0.882  100.000   98.639
LGA    K    43_A      K    43_A     0.777     0    0.008   0.165     2.080   92.857   82.751
LGA    E    44_A      E    44_A     0.968     0    0.158   0.716     3.267   83.810   71.746
LGA    I    45_A      I    45_A     0.403     0    0.030   0.076     1.066   95.238   94.107
LGA    C    46_A      C    46_A     0.657     0    0.085   0.122     1.210   90.595   90.556
LGA    Y    47_A      Y    47_A     1.170     0    0.025   0.158     2.726   83.690   73.175
LGA    E    48_A      E    48_A     1.101     0    0.043   0.898     5.254   83.690   64.603
LGA    V    49_A      V    49_A     0.906     0    0.068   0.088     1.187   85.952   87.891
LGA    A    50_A      A    50_A     1.896     0    0.069   0.069     2.236   68.810   68.000
LGA    L    51_A      L    51_A     2.091     0    0.277   1.335     3.430   63.095   64.107
LGA    A    52_A      A    52_A     1.391     0    0.218   0.208     1.445   81.429   81.429
LGA    D    53_A      D    53_A     1.311     0    0.075   0.196     2.465   81.429   74.107
LGA    F    54_A      F    54_A     0.825     0    0.058   0.104     2.048   90.476   80.087
LGA    R    55_A      R    55_A     0.577     0    0.123   1.491    11.138   92.857   51.558
LGA    H    56_A      H    56_A     0.761     0    0.040   0.884     2.521   88.333   81.857
LGA    G    57_A      G    57_A     1.824     0    0.115   0.115     1.824   77.143   77.143
LGA    R    58_A      R    58_A     1.146     0    0.035   1.235     7.032   85.952   59.177
LGA    A    59_A      A    59_A     1.044     0    0.090   0.093     1.148   83.690   83.238
LGA    E    60_A      E    60_A     1.055     0    0.034   0.397     2.060   85.952   80.688
LGA    I    61_A      I    61_A     0.991     0    0.023   0.077     1.087   88.214   85.952
LGA    E    62_A      E    62_A     0.813     0    0.058   0.853     3.279   90.476   78.254
LGA    A    63_A      A    63_A     0.631     0    0.023   0.033     0.721   90.476   90.476
LGA    L    64_A      L    64_A     0.728     0    0.197   1.297     3.118   86.071   77.798
LGA    A    65_A      A    65_A     0.458     0    0.034   0.037     0.559   97.619   96.190
LGA    A    66_A      A    66_A     0.590     0    0.040   0.049     0.736   92.857   92.381
LGA    L    67_A      L    67_A     0.299     0    0.009   0.792     3.218   97.619   90.238
LGA    K    68_A      K    68_A     0.640     0    0.033   0.548     1.516   92.857   88.571
LGA    M    69_A      M    69_A     0.338     0    0.030   0.232     0.989  100.000   96.429
LGA    R    70_A      R    70_A     0.482     0    0.079   1.241     3.828   92.976   84.805
LGA    E    71_A      E    71_A     0.927     0    0.052   1.080     3.564   83.810   71.905
LGA    L    72_A      L    72_A     1.289     0    0.007   0.175     1.791   79.286   80.357
LGA    C    73_A      C    73_A     1.540     0    0.092   0.284     1.866   75.000   75.714
LGA    R    74_A      R    74_A     2.297     0    0.312   0.981     8.232   59.524   44.329
LGA    T    75_A      T    75_A     2.264     0    0.118   0.223     2.405   64.762   64.762
LGA    Y    76_A      Y    76_A     2.385     0    0.696   0.606     3.368   59.167   65.595
LGA    G    83_A      G    83_A     3.847     0    0.054   0.054     5.155   49.762   49.762
LGA    D    84_A      D    84_A     2.296     0    0.592   1.205     6.144   75.357   57.024
LGA    A    85_A      A    85_A     1.083     0    0.038   0.043     1.670   83.810   83.333
LGA    W    86_A      W    86_A     1.227     0    0.019   0.277     2.322   81.548   78.503
LGA    R    87_A      R    87_A     1.140     0    0.045   0.827     2.531   83.690   80.043
LGA    A    88_A      A    88_A     0.945     0    0.132   0.147     1.305   88.214   86.857
LGA    V    89_A      V    89_A     0.919     0    0.049   0.125     1.182   88.214   86.599
LGA    A    90_A      A    90_A     0.904     0    0.076   0.084     0.909   90.476   90.476
LGA    R    91_A      R    91_A     0.767     0    0.027   1.238     7.232   90.476   64.589
LGA    D    92_A      D    92_A     0.653     0    0.063   0.194     1.252   92.857   90.536
LGA    V    93_A      V    93_A     0.458     0    0.029   0.047     0.643   97.619   97.279
LGA    W    94_A      W    94_A     0.439     0    0.059   1.486     7.962   97.619   50.374
LGA    D    95_A      D    95_A     0.500     0    0.129   0.413     1.393  100.000   96.488
LGA    T    96_A      T    96_A     1.312     0    0.156   0.995     3.168   79.524   72.381
LGA    V    97_A      V    97_A     1.355     0    0.557   1.306     3.656   69.762   72.381
LGA    G    98_A      G    98_A     1.144     0    0.041   0.041     1.175   83.690   83.690

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     1.288          1.320                  2.181           84.830   78.294

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    1.29    90.164    95.305     4.394

LGA_LOCAL      RMSD:   1.288  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.288  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.288  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.091152 * X  +  -0.456432 * Y  +   0.885077 * Z  + -31.232801
  Y_new =  -0.849798 * X  +  -0.427702 * Y  +  -0.308083 * Z  +  54.372513
  Z_new =   0.519168 * X  +  -0.780219 * Y  +  -0.348889 * Z  +  10.799319 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.677651 -0.545877 -1.991293   [DEG:  -96.1223  -31.2765 -114.0927 ]
ZXZ:  1.235827  1.927181  2.554458   [DEG:   70.8077  110.4194  146.3597 ]
 
# END of job
