
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       1_A - 60_A        0.37     0.37
  LCS_AVERAGE:    100.00

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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_A     D     1_A     60   60   60     44   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     60   60   60     43   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A     60   60   60     32   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     60   60   60     52   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     60   60   60     52   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     60   60   60     53   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     60   60   60     31   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60   60 
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     53     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60     60 
GDT PERCENT_AT  88.33 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37
GDT RMS_ALL_AT   0.38   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37   0.37

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     0.727     0    0.198   0.840     3.280   90.476   78.869
LGA    D     2_A      D     2_A     0.283     0    0.015   0.515     2.401  100.000   93.214
LGA    K     3_A      K     3_A     0.332     0    0.019   0.542     1.580  100.000   91.852
LGA    A     4_A      A     4_A     0.410     0    0.050   0.059     0.506  100.000   98.095
LGA    A     5_A      A     5_A     0.205     0    0.045   0.063     0.426  100.000  100.000
LGA    C     6_A      C     6_A     0.128     0    0.025   0.056     0.155  100.000  100.000
LGA    A     7_A      A     7_A     0.172     0    0.032   0.044     0.250  100.000  100.000
LGA    D     8_A      D     8_A     0.242     0    0.019   0.154     0.654  100.000   97.619
LGA    G     9_A      G     9_A     0.149     0    0.050   0.050     0.239  100.000  100.000
LGA    I    10_A      I    10_A     0.200     0    0.024   0.052     0.345  100.000  100.000
LGA    A    11_A      A    11_A     0.229     0    0.034   0.046     0.285  100.000  100.000
LGA    A    12_A      A    12_A     0.104     0    0.012   0.016     0.316  100.000  100.000
LGA    V    13_A      V    13_A     0.300     0    0.027   0.050     0.438  100.000  100.000
LGA    K    14_A      K    14_A     0.312     0    0.086   0.185     0.675   97.619   96.825
LGA    A    15_A      A    15_A     0.220     0    0.054   0.051     0.414  100.000  100.000
LGA    R    16_A      R    16_A     0.285     0    0.016   0.945     3.987  100.000   88.312
LGA    V    17_A      V    17_A     0.317     0    0.039   0.050     0.358  100.000  100.000
LGA    E    18_A      E    18_A     0.244     0    0.021   0.654     3.298  100.000   81.852
LGA    K    19_A      K    19_A     0.324     0    0.038   1.069     5.009   97.619   80.423
LGA    L    20_A      L    20_A     0.379     0    0.031   0.146     0.489  100.000  100.000
LGA    A    21_A      A    21_A     0.469     0    0.019   0.025     0.507   97.619   96.190
LGA    P    22_A      P    22_A     0.588     0    0.051   0.072     0.903   90.476   91.837
LGA    E    23_A      E    23_A     0.633     0    0.077   1.131     3.299   90.476   80.106
LGA    A    24_A      A    24_A     0.524     0    0.091   0.103     0.658   92.857   92.381
LGA    V    25_A      V    25_A     0.229     0    0.030   0.078     0.304  100.000  100.000
LGA    P    26_A      P    26_A     0.271     0    0.032   0.086     0.417  100.000  100.000
LGA    Q    27_A      Q    27_A     0.309     0    0.006   0.994     3.846  100.000   83.968
LGA    K    28_A      K    28_A     0.206     0    0.066   0.830     3.740  100.000   80.476
LGA    L    29_A      L    29_A     0.264     0    0.024   1.120     2.730  100.000   89.286
LGA    K    30_A      K    30_A     0.432     0    0.015   0.089     0.717  100.000   96.825
LGA    R    31_A      R    31_A     0.411     0    0.046   0.811     2.244  100.000   88.442
LGA    A    32_A      A    32_A     0.391     0    0.043   0.058     0.413  100.000  100.000
LGA    L    33_A      L    33_A     0.399     0    0.034   0.049     0.456  100.000  100.000
LGA    K    34_A      K    34_A     0.360     0    0.054   0.625     2.670  100.000   91.058
LGA    I    35_A      I    35_A     0.362     0    0.090   0.090     0.522   97.619   98.810
LGA    A    36_A      A    36_A     0.384     0    0.016   0.018     0.449  100.000  100.000
LGA    E    37_A      E    37_A     0.306     0    0.022   0.442     1.155  100.000   95.873
LGA    R    38_A      R    38_A     0.268     0    0.064   0.982     4.150  100.000   82.684
LGA    E    39_A      E    39_A     0.314     0    0.029   1.123     4.028  100.000   83.280
LGA    Q    40_A      Q    40_A     0.283     0    0.046   0.271     0.894  100.000   97.884
LGA    G    41_A      G    41_A     0.155     0    0.052   0.052     0.245  100.000  100.000
LGA    E    42_A      E    42_A     0.461     0    0.134   0.574     1.760  100.000   92.751
LGA    G    43_A      G    43_A     0.344     0    0.049   0.049     0.478  100.000  100.000
LGA    E    44_A      E    44_A     0.250     0    0.037   0.831     3.405  100.000   85.767
LGA    F    45_A      F    45_A     0.380     0    0.017   0.069     0.446  100.000  100.000
LGA    D    46_A      D    46_A     0.502     0    0.071   1.231     4.249   97.619   81.964
LGA    E    47_A      E    47_A     0.383     0    0.034   0.600     2.007  100.000   92.963
LGA    C    48_A      C    48_A     0.010     0    0.014   0.073     0.181  100.000  100.000
LGA    L    49_A      L    49_A     0.146     0    0.026   0.101     0.385  100.000  100.000
LGA    E    50_A      E    50_A     0.069     0    0.035   0.391     1.254  100.000   96.878
LGA    A    51_A      A    51_A     0.116     0    0.014   0.028     0.215  100.000  100.000
LGA    L    52_A      L    52_A     0.251     0    0.014   0.052     0.467  100.000  100.000
LGA    D    53_A      D    53_A     0.240     0    0.054   0.174     0.624  100.000   97.619
LGA    D    54_A      D    54_A     0.220     0    0.017   0.475     1.712  100.000   93.095
LGA    A    55_A      A    55_A     0.362     0    0.006   0.010     0.495  100.000  100.000
LGA    K    56_A      K    56_A     0.646     0    0.034   0.650     1.433   97.619   90.635
LGA    R    57_A      R    57_A     0.237     0    0.012   0.453     1.715  100.000   92.511
LGA    A    58_A      A    58_A     0.578     0    0.025   0.030     0.889   92.857   92.381
LGA    L    59_A      L    59_A     0.463     0    0.062   0.195     1.174  100.000   94.107
LGA    P    60_A      P    60_A     0.937     0    0.033   0.344     1.229   90.476   89.184

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     0.367          0.370                  1.005           98.889   94.267

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     60    0.37   100.000   100.000    12.851

LGA_LOCAL      RMSD:   0.367  Number of atoms:   60  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.367  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   0.367  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.722791 * X  +   0.555571 * Y  +   0.410992 * Z  +  12.123074
  Y_new =  -0.557980 * X  +  -0.820044 * Y  +   0.127228 * Z  +  10.002833
  Z_new =   0.407715 * X  +  -0.137366 * Y  +   0.902718 * Z  +   6.674759 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.484172 -0.419951 -0.151011   [DEG: -142.3326  -24.0614   -8.6523 ]
ZXZ:  1.871004  0.444752  1.895768   [DEG:  107.2006   25.4824  108.6195 ]
 
# END of job
