
#######################################################
#                                                     #
#                        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        1.53     1.53
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        1.53     1.53
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35      57_A - 97_A        0.96     2.06
  LCS_AVERAGE:     48.45

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     23   61   61      7   26   43   50   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     23   61   61     12   30   43   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     23   61   61     15   30   44   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     23   61   61     13   29   46   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     23   61   61      7   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     23   61   61     14   34   46   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     23   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     23   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     23   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     23   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     23   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     23   61   61      8   28   44   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     23   61   61     15   28   44   51   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     23   61   61     13   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     23   61   61      3    4   31   47   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     23   61   61      3    4   32   47   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     13   61   61      3    6   12   34   51   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     21   61   61      3   11   38   51   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     35   61   61      3    8   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     35   61   61     15   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     35   61   61     18   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     35   61   61     14   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     35   61   61     18   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     35   61   61     18   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     35   61   61     18   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     35   61   61     18   33   48   52   56   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     35   61   61      0    3    4    5   26   35   55   59   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     35   61   61     14   31   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     35   61   61      3   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     35   61   61     11   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     35   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     35   61   61     15   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     35   61   61     17   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     35   61   61     18   36   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     35   61   61     11   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     35   61   61     13   33   48   52   57   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     15   61   61      3    4    4   31   41   60   60   60   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  82.82  (  48.45  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     18     36     48     52     57     60     60     60     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  29.51  59.02  78.69  85.25  93.44  98.36  98.36  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   0.64   0.92   1.02   1.27   1.39   1.39   1.39   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53
GDT RMS_ALL_AT   1.73   1.60   1.64   1.60   1.54   1.54   1.54   1.54   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53   1.53

# Checking swapping
#   possible swapping detected:  E    44_A      E    44_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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     2.445     0    0.501   0.500     3.865   62.857   58.952
LGA    T    33_A      T    33_A     1.764     0    0.089   0.320     2.130   75.000   75.442
LGA    M    34_A      M    34_A     1.590     0    0.052   0.241     2.685   79.405   70.179
LGA    A    35_A      A    35_A     1.276     0    0.056   0.060     1.608   85.952   83.333
LGA    D    36_A      D    36_A     0.864     0    0.093   0.194     1.913   88.214   83.810
LGA    L    37_A      L    37_A     1.248     0    0.049   0.165     2.460   88.214   77.500
LGA    K    38_A      K    38_A     0.644     0    0.164   0.659     1.937   95.238   88.624
LGA    M    39_A      M    39_A     0.181     0    0.035   1.163     6.035  100.000   79.881
LGA    Q    40_A      Q    40_A     0.751     0    0.030   0.828     2.883   90.476   81.958
LGA    A    41_A      A    41_A     0.573     0    0.046   0.047     0.693   95.238   94.286
LGA    V    42_A      V    42_A     0.174     0    0.082   0.140     0.653   97.619   97.279
LGA    K    43_A      K    43_A     0.775     0    0.018   0.099     1.928   92.857   83.651
LGA    E    44_A      E    44_A     1.067     0    0.154   0.290     1.880   81.548   83.492
LGA    I    45_A      I    45_A     0.500     0    0.041   0.071     1.064   92.857   92.917
LGA    C    46_A      C    46_A     0.756     0    0.097   0.140     1.383   85.952   87.460
LGA    Y    47_A      Y    47_A     1.192     0    0.058   1.287     9.797   83.690   46.667
LGA    E    48_A      E    48_A     1.017     0    0.022   0.915     3.159   83.690   75.291
LGA    V    49_A      V    49_A     1.277     0    0.039   0.054     1.566   79.286   80.204
LGA    A    50_A      A    50_A     1.889     0    0.101   0.109     2.565   66.905   68.095
LGA    L    51_A      L    51_A     2.152     0    0.200   0.309     3.089   63.095   64.940
LGA    A    52_A      A    52_A     1.083     0    0.629   0.598     2.478   79.524   81.714
LGA    D    53_A      D    53_A     2.649     0    0.385   1.038     6.918   59.286   45.417
LGA    F    54_A      F    54_A     2.694     0    0.200   0.489     3.334   59.048   56.580
LGA    R    55_A      R    55_A     3.119     0    0.042   1.485     9.778   55.476   38.355
LGA    H    56_A      H    56_A     2.288     0    0.652   1.106     3.988   57.500   55.952
LGA    G    57_A      G    57_A     1.592     0    0.195   0.195     2.659   68.929   68.929
LGA    R    58_A      R    58_A     1.674     0    0.100   1.183    10.014   77.143   43.939
LGA    A    59_A      A    59_A     1.079     0    0.038   0.041     1.395   85.952   86.857
LGA    E    60_A      E    60_A     0.885     0    0.044   0.980     4.962   90.476   68.730
LGA    I    61_A      I    61_A     0.976     0    0.027   0.092     0.994   90.476   90.476
LGA    E    62_A      E    62_A     0.834     0    0.016   0.878     1.921   90.476   83.598
LGA    A    63_A      A    63_A     0.473     0    0.015   0.024     0.673   97.619   96.190
LGA    L    64_A      L    64_A     0.655     0    0.173   0.453     1.262   88.214   89.405
LGA    A    65_A      A    65_A     0.436     0    0.018   0.019     0.591   97.619   96.190
LGA    A    66_A      A    66_A     0.327     0    0.041   0.050     0.479  100.000  100.000
LGA    L    67_A      L    67_A     0.240     0    0.009   0.799     3.210   97.619   89.048
LGA    K    68_A      K    68_A     0.680     0    0.033   0.547     1.825   90.476   84.550
LGA    M    69_A      M    69_A     0.486     0    0.021   0.508     1.283   97.619   94.107
LGA    R    70_A      R    70_A     0.496     0    0.080   1.185     2.592   92.976   85.238
LGA    E    71_A      E    71_A     1.005     0    0.050   1.250     5.669   81.548   63.386
LGA    L    72_A      L    72_A     1.397     0    0.012   0.162     1.800   79.286   80.357
LGA    C    73_A      C    73_A     1.458     0    0.081   0.251     1.667   77.143   77.143
LGA    R    74_A      R    74_A     2.024     0    0.309   0.992     8.067   59.524   45.455
LGA    T    75_A      T    75_A     2.080     0    0.116   0.217     2.251   66.786   67.075
LGA    Y    76_A      Y    76_A     2.362     0    0.696   0.615     3.273   61.071   65.556
LGA    G    83_A      G    83_A     5.284     0    0.226   0.226     5.626   33.571   33.571
LGA    D    84_A      D    84_A     1.635     0    0.366   1.094     3.852   73.214   65.893
LGA    A    85_A      A    85_A     0.716     0    0.016   0.021     1.037   88.214   88.667
LGA    W    86_A      W    86_A     1.153     0    0.131   1.189     7.303   83.690   51.429
LGA    R    87_A      R    87_A     1.146     0    0.033   1.190     8.218   81.429   51.905
LGA    A    88_A      A    88_A     0.958     0    0.149   0.164     1.273   85.952   85.048
LGA    V    89_A      V    89_A     0.613     0    0.070   0.142     0.795   90.476   90.476
LGA    A    90_A      A    90_A     0.422     0    0.071   0.076     0.527   95.238   96.190
LGA    R    91_A      R    91_A     0.333     0    0.020   1.252     7.480  100.000   69.264
LGA    D    92_A      D    92_A     0.531     0    0.064   0.169     1.233   92.857   90.536
LGA    V    93_A      V    93_A     0.644     0    0.014   0.060     0.862   90.476   90.476
LGA    W    94_A      W    94_A     0.800     0    0.033   1.504     7.198   88.214   49.592
LGA    D    95_A      D    95_A     0.847     0    0.172   0.447     1.529   90.476   86.012
LGA    T    96_A      T    96_A     1.723     0    0.101   1.141     3.554   75.000   68.707
LGA    V    97_A      V    97_A     1.869     0    0.473   1.101     3.730   68.929   66.463
LGA    G    98_A      G    98_A     2.851     0    0.041   0.041     2.851   69.048   69.048

# 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):     1.530          1.533                  2.603           81.913   75.106

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     60    1.39    85.656    93.428     4.022

LGA_LOCAL      RMSD:   1.392  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.537  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.530  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.837795 * X  +  -0.268809 * Y  +   0.475228 * Z  +   3.978258
  Y_new =  -0.484389 * X  +  -0.767564 * Y  +   0.419778 * Z  +  64.149559
  Z_new =   0.251928 * X  +  -0.581883 * Y  +  -0.773269 * Z  +  14.929081 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.524214 -0.254672 -2.496495   [DEG:  -30.0352  -14.5916 -143.0386 ]
ZXZ:  2.294319  2.454777  2.733006   [DEG:  131.4548  140.6483  156.5897 ]
 
# END of job
