
#######################################################
#                                                     #
#                        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        0.52     0.52
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.52     0.52
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61      32_A - 98_A        0.52     0.52
  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     A    32_A     A    32_A     61   61   61     50   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    33_A     T    33_A     61   61   61     50   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    34_A     M    34_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    35_A     A    35_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    36_A     D    36_A     61   61   61      6   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    37_A     L    37_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    38_A     K    38_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    39_A     M    39_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    40_A     Q    40_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    41_A     A    41_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    42_A     V    42_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    43_A     K    43_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    44_A     E    44_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    45_A     I    45_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    46_A     C    46_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    47_A     Y    47_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    48_A     E    48_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    49_A     V    49_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    50_A     A    50_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    51_A     L    51_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    52_A     A    52_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    53_A     D    53_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    54_A     F    54_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    55_A     R    55_A     61   61   61     47   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    56_A     H    56_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    57_A     G    57_A     61   61   61     19   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    58_A     R    58_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    59_A     A    59_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    60_A     E    60_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    61_A     I    61_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    62_A     E    62_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    63_A     A    63_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    64_A     L    64_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    65_A     A    65_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    66_A     A    66_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    67_A     L    67_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    68_A     K    68_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    69_A     M    69_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    70_A     R    70_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    71_A     E    71_A     61   61   61     50   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    72_A     L    72_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     C    73_A     C    73_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    74_A     R    74_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    75_A     T    75_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y    76_A     Y    76_A     61   61   61      5   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    83_A     G    83_A     61   61   61      5   49   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    84_A     D    84_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    85_A     A    85_A     61   61   61     35   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    86_A     W    86_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    87_A     R    87_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    88_A     A    88_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    89_A     V    89_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    90_A     A    90_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    91_A     R    91_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    92_A     D    92_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    93_A     V    93_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     W    94_A     W    94_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    95_A     D    95_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    96_A     T    96_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    97_A     V    97_A     61   61   61     51   59   60   60   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     G    98_A     G    98_A     61   61   61      3    3    3   57   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     51     59     60     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  83.61  96.72  98.36  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.39   0.42   0.42   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52
GDT RMS_ALL_AT   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52   0.52

# Checking swapping
#   possible swapping detected:  E    48_A      E    48_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     0.516     0    0.439   0.441     2.131   90.595   85.429
LGA    T    33_A      T    33_A     0.574     0    0.079   0.310     1.170   92.857   90.544
LGA    M    34_A      M    34_A     0.427     0    0.038   1.115     2.648   97.619   87.738
LGA    A    35_A      A    35_A     0.449     0    0.091   0.108     0.876   95.238   94.286
LGA    D    36_A      D    36_A     0.935     0    0.118   0.348     2.932   95.238   81.131
LGA    L    37_A      L    37_A     0.192     0    0.026   0.162     0.565  100.000   98.810
LGA    K    38_A      K    38_A     0.441     0    0.052   0.691     1.842   97.619   90.688
LGA    M    39_A      M    39_A     0.392     0    0.019   0.845     2.607  100.000   90.238
LGA    Q    40_A      Q    40_A     0.274     0    0.008   0.854     4.201  100.000   83.492
LGA    A    41_A      A    41_A     0.306     0    0.087   0.098     0.530  100.000   98.095
LGA    V    42_A      V    42_A     0.379     0    0.071   0.125     0.609   97.619   98.639
LGA    K    43_A      K    43_A     0.314     0    0.008   0.085     0.449  100.000  100.000
LGA    E    44_A      E    44_A     0.305     0    0.169   0.250     1.031   95.357   97.937
LGA    I    45_A      I    45_A     0.130     0    0.013   0.096     0.713  100.000   98.810
LGA    C    46_A      C    46_A     0.140     0    0.116   0.126     0.655   97.619   98.413
LGA    Y    47_A      Y    47_A     0.052     0    0.050   0.104     1.570  100.000   90.714
LGA    E    48_A      E    48_A     0.198     0    0.018   0.853     2.663  100.000   83.492
LGA    V    49_A      V    49_A     0.378     0    0.056   0.070     0.575  100.000   98.639
LGA    A    50_A      A    50_A     0.386     0    0.071   0.068     0.640   97.619   98.095
LGA    L    51_A      L    51_A     0.444     0    0.129   0.261     2.174   97.619   86.488
LGA    A    52_A      A    52_A     0.365     0    0.058   0.054     0.621   97.619   98.095
LGA    D    53_A      D    53_A     0.234     0    0.048   0.249     1.143   97.619   94.107
LGA    F    54_A      F    54_A     0.269     0    0.070   0.077     0.572   97.619   99.134
LGA    R    55_A      R    55_A     0.707     0    0.131   1.290     8.197   97.619   56.623
LGA    H    56_A      H    56_A     0.282     0    0.064   0.331     1.000   97.619   96.190
LGA    G    57_A      G    57_A     0.605     0    0.060   0.060     0.605   97.619   97.619
LGA    R    58_A      R    58_A     0.411     0    0.052   1.104     5.132   97.619   73.333
LGA    A    59_A      A    59_A     0.285     0    0.050   0.047     0.357  100.000  100.000
LGA    E    60_A      E    60_A     0.161     0    0.010   0.556     1.799  100.000   93.810
LGA    I    61_A      I    61_A     0.278     0    0.017   0.100     0.525  100.000   98.810
LGA    E    62_A      E    62_A     0.230     0    0.032   0.213     0.883  100.000   96.825
LGA    A    63_A      A    63_A     0.404     0    0.019   0.020     0.512  100.000   98.095
LGA    L    64_A      L    64_A     0.364     0    0.221   0.448     1.889   97.619   88.512
LGA    A    65_A      A    65_A     0.238     0    0.017   0.019     0.475  100.000  100.000
LGA    A    66_A      A    66_A     0.485     0    0.043   0.045     0.707   97.619   96.190
LGA    L    67_A      L    67_A     0.269     0    0.037   0.751     2.887  100.000   90.000
LGA    K    68_A      K    68_A     0.200     0    0.039   0.240     1.576  100.000   93.862
LGA    M    69_A      M    69_A     0.334     0    0.035   0.558     1.365  100.000   95.357
LGA    R    70_A      R    70_A     0.249     0    0.073   1.278     3.140  100.000   84.762
LGA    E    71_A      E    71_A     0.526     0    0.137   0.666     1.969   97.619   90.688
LGA    L    72_A      L    72_A     0.422     0    0.030   0.186     0.645  100.000   98.810
LGA    C    73_A      C    73_A     0.355     0    0.064   0.216     1.037  100.000   96.905
LGA    R    74_A      R    74_A     0.471     0    0.316   0.951     7.120   90.833   63.333
LGA    T    75_A      T    75_A     0.444     0    0.132   0.202     1.446  100.000   94.626
LGA    Y    76_A      Y    76_A     0.797     0    0.686   0.617     2.299   84.048   86.825
LGA    G    83_A      G    83_A     1.205     0    0.233   0.233     1.205   85.952   85.952
LGA    D    84_A      D    84_A     0.250     0    0.061   0.569     1.550   97.619   91.845
LGA    A    85_A      A    85_A     0.611     0    0.039   0.039     0.958   95.238   94.286
LGA    W    86_A      W    86_A     0.372     0    0.037   0.080     0.864  100.000   95.918
LGA    R    87_A      R    87_A     0.410     0    0.018   0.409     1.102   97.619   92.251
LGA    A    88_A      A    88_A     0.259     0    0.142   0.164     0.942   97.619   98.095
LGA    V    89_A      V    89_A     0.253     0    0.066   0.104     0.489  100.000  100.000
LGA    A    90_A      A    90_A     0.323     0    0.059   0.069     0.450  100.000  100.000
LGA    R    91_A      R    91_A     0.229     0    0.044   1.232     5.700  100.000   79.740
LGA    D    92_A      D    92_A     0.112     0    0.053   0.191     0.637  100.000   98.810
LGA    V    93_A      V    93_A     0.247     0    0.021   0.054     0.451  100.000  100.000
LGA    W    94_A      W    94_A     0.280     0    0.022   0.081     0.666  100.000   93.878
LGA    D    95_A      D    95_A     0.313     0    0.105   0.447     0.946   97.619   96.429
LGA    T    96_A      T    96_A     0.481     0    0.047   1.158     2.511  100.000   87.483
LGA    V    97_A      V    97_A     0.439     0    0.440   0.352     1.928   90.833   90.680
LGA    G    98_A      G    98_A     2.391     0    0.506   0.506     2.391   77.381   77.381

# 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):     0.517          0.529                  1.270           97.475   92.081

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    0.52    98.770    99.504     9.887

LGA_LOCAL      RMSD:   0.517  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.517  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.517  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.741612 * X  +   0.321845 * Y  +   0.588581 * Z  +   4.078501
  Y_new =  -0.655957 * X  +   0.164187 * Y  +   0.736725 * Z  +  23.083849
  Z_new =   0.140473 * X  +  -0.932448 * Y  +   0.332879 * Z  +  -9.750434 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.724186 -0.140939 -1.227903   [DEG:  -41.4928   -8.0752  -70.3537 ]
ZXZ:  2.467513  1.231441  2.992067   [DEG:  141.3781   70.5564  171.4328 ]
 
# END of job
