
#######################################################
#                                                     #
#                        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     49   59   60   61   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     31   59   60   61   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     49   59   60   61   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     49   59   60   61   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   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     34   59   60   61   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     49   59   60   61   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     20   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     47   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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      6   59   60   61   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      7   44   60   61   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     49   59   60   61   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     34   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     49   59   60   61   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     19   59   60   61   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     49   59   60   61   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   61   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     49     59     60     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  80.33  96.72  98.36 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.41   0.45   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
GDT RMS_ALL_AT   0.53   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     0.366     0    0.450   0.456     1.925   90.833   87.238
LGA    T    33_A      T    33_A     0.712     0    0.075   0.307     1.211   90.476   89.184
LGA    M    34_A      M    34_A     0.510     0    0.053   1.125     2.576   92.857   85.357
LGA    A    35_A      A    35_A     0.487     0    0.094   0.110     0.910   95.238   94.286
LGA    D    36_A      D    36_A     1.031     0    0.125   0.312     2.985   92.976   78.929
LGA    L    37_A      L    37_A     0.173     0    0.033   0.176     0.626  100.000   98.810
LGA    K    38_A      K    38_A     0.472     0    0.065   0.670     1.831   97.619   89.735
LGA    M    39_A      M    39_A     0.455     0    0.019   0.861     2.740  100.000   88.095
LGA    Q    40_A      Q    40_A     0.306     0    0.009   0.805     3.915  100.000   84.180
LGA    A    41_A      A    41_A     0.354     0    0.077   0.087     0.551  100.000   98.095
LGA    V    42_A      V    42_A     0.420     0    0.074   0.122     0.696   97.619   98.639
LGA    K    43_A      K    43_A     0.378     0    0.005   0.097     0.572   97.619   96.825
LGA    E    44_A      E    44_A     0.355     0    0.166   0.234     1.082   92.976   96.878
LGA    I    45_A      I    45_A     0.160     0    0.022   0.098     0.766  100.000   98.810
LGA    C    46_A      C    46_A     0.193     0    0.112   0.122     0.690   97.619   98.413
LGA    Y    47_A      Y    47_A     0.054     0    0.057   0.119     1.611  100.000   89.960
LGA    E    48_A      E    48_A     0.204     0    0.014   0.832     2.421  100.000   85.238
LGA    V    49_A      V    49_A     0.413     0    0.059   0.073     0.607  100.000   98.639
LGA    A    50_A      A    50_A     0.305     0    0.054   0.051     0.458  100.000  100.000
LGA    L    51_A      L    51_A     0.444     0    0.120   0.263     2.105   97.619   87.500
LGA    A    52_A      A    52_A     0.445     0    0.027   0.027     0.582  100.000   98.095
LGA    D    53_A      D    53_A     0.208     0    0.028   0.152     0.778  100.000   96.429
LGA    F    54_A      F    54_A     0.318     0    0.066   0.074     0.524   97.619   99.134
LGA    R    55_A      R    55_A     0.780     0    0.115   1.486    10.292   95.238   53.636
LGA    H    56_A      H    56_A     0.251     0    0.078   0.395     0.944   97.619   96.190
LGA    G    57_A      G    57_A     0.613     0    0.065   0.065     0.613   97.619   97.619
LGA    R    58_A      R    58_A     0.411     0    0.056   1.106     5.085   97.619   74.632
LGA    A    59_A      A    59_A     0.281     0    0.055   0.051     0.341  100.000  100.000
LGA    E    60_A      E    60_A     0.147     0    0.017   0.433     1.039  100.000   94.815
LGA    I    61_A      I    61_A     0.267     0    0.018   0.075     0.471  100.000  100.000
LGA    E    62_A      E    62_A     0.208     0    0.028   0.214     0.820  100.000   96.825
LGA    A    63_A      A    63_A     0.400     0    0.020   0.021     0.490  100.000  100.000
LGA    L    64_A      L    64_A     0.354     0    0.219   0.441     1.800   97.619   88.512
LGA    A    65_A      A    65_A     0.236     0    0.021   0.021     0.477  100.000  100.000
LGA    A    66_A      A    66_A     0.479     0    0.049   0.051     0.689   97.619   96.190
LGA    L    67_A      L    67_A     0.256     0    0.034   0.766     2.957  100.000   91.131
LGA    K    68_A      K    68_A     0.228     0    0.037   0.256     1.749  100.000   92.857
LGA    M    69_A      M    69_A     0.371     0    0.023   0.549     1.473  100.000   95.357
LGA    R    70_A      R    70_A     0.283     0    0.084   1.250     3.141   97.619   84.589
LGA    E    71_A      E    71_A     0.543     0    0.094   0.670     2.202   97.619   89.788
LGA    L    72_A      L    72_A     0.449     0    0.026   0.170     0.635  100.000   98.810
LGA    C    73_A      C    73_A     0.321     0    0.088   0.252     1.100  100.000   96.905
LGA    R    74_A      R    74_A     0.486     0    0.287   1.397     9.247   90.833   60.476
LGA    T    75_A      T    75_A     0.420     0    0.139   0.204     1.440   97.619   93.265
LGA    Y    76_A      Y    76_A     0.744     0    0.670   0.648     2.406   84.048   86.825
LGA    G    83_A      G    83_A     1.303     0    0.238   0.238     1.303   85.952   85.952
LGA    D    84_A      D    84_A     0.207     0    0.065   0.467     1.095   95.238   94.107
LGA    A    85_A      A    85_A     0.573     0    0.040   0.040     0.876   95.238   94.286
LGA    W    86_A      W    86_A     0.330     0    0.042   0.071     0.884   97.619   93.197
LGA    R    87_A      R    87_A     0.465     0    0.017   0.324     0.899   97.619   93.074
LGA    A    88_A      A    88_A     0.330     0    0.145   0.167     0.988   97.619   98.095
LGA    V    89_A      V    89_A     0.282     0    0.071   0.120     0.542   97.619   97.279
LGA    A    90_A      A    90_A     0.376     0    0.056   0.064     0.464  100.000  100.000
LGA    R    91_A      R    91_A     0.328     0    0.044   0.467     1.314  100.000   94.026
LGA    D    92_A      D    92_A     0.132     0    0.044   0.274     1.026  100.000   97.679
LGA    V    93_A      V    93_A     0.260     0    0.019   0.064     0.484  100.000  100.000
LGA    W    94_A      W    94_A     0.348     0    0.023   0.097     0.559  100.000   95.238
LGA    D    95_A      D    95_A     0.434     0    0.121   0.475     1.024   92.976   94.107
LGA    T    96_A      T    96_A     0.596     0    0.041   1.155     2.612   97.619   86.122
LGA    V    97_A      V    97_A     0.600     0    0.435   0.350     2.151   86.429   88.163
LGA    G    98_A      G    98_A     2.105     0    0.119   0.119     2.105   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):     0.520          0.545                  1.326           96.942   92.059

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     61    0.52    99.180    99.619     9.834

LGA_LOCAL      RMSD:   0.520  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.520  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   0.520  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.681505 * X  +   0.509324 * Y  +  -0.525490 * Z  +   1.799682
  Y_new =  -0.713333 * X  +  -0.301981 * Y  +   0.632427 * Z  +  22.910036
  Z_new =   0.163422 * X  +   0.805852 * Y  +   0.569119 * Z  + -12.250990 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.333380 -0.164158  0.955899   [DEG: -133.6928   -9.4056   54.7690 ]
ZXZ: -2.448285  0.965362  0.200081   [DEG: -140.2764   55.3112   11.4638 ]
 
# END of job
