
#######################################################
#                                                     #
#                        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   63 (  505),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        2.77     2.77
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    47       6_C - 52_C        1.99     3.04
  LONGEST_CONTINUOUS_SEGMENT:    47       7_C - 53_C        1.91     2.95
  LONGEST_CONTINUOUS_SEGMENT:    47       8_C - 54_C        1.96     2.85
  LCS_AVERAGE:     89.54

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      29_C - 50_C        0.96     3.25
  LONGEST_CONTINUOUS_SEGMENT:    22      30_C - 51_C        0.97     3.14
  LCS_AVERAGE:     36.45

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      5   47   51      3    5    6   11   17   29   35   43   43   46   48   50   50   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C      5   47   51      3    5    6   13   28   33   36   43   43   46   47   50   50   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     19   47   51      7   19   29   36   41   42   44   45   46   46   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     19   47   51     10   24   36   39   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     19   47   51     12   28   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     19   47   51     12   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     19   47   51     15   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     19   47   51     12   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     19   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     19   47   51     15   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     19   47   51     10   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     19   47   51     15   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     19   47   51      4   29   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     19   47   51      3   22   31   37   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     12   47   51      5   11   13   20   38   42   44   45   46   48   49   49   50   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     22   47   51      5   22   30   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     22   47   51      5   11   25   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     22   47   51     10   24   36   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     22   47   51     14   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     22   47   51     15   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     22   47   51     18   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     22   47   51     11   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     22   47   51     14   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     22   47   51     14   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     22   47   51     14   31   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     22   47   51      6   28   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     22   47   51      5   28   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     22   47   51     10   26   37   40   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     10   47   51      4    5   18   33   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C      9   47   51      4    6   19   34   42   43   44   45   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C      7   47   51      3    5    8   12   14   22   37   44   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C      7   13   51      3    5    9   12   14   22   24   43   46   48   49   50   50   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C      7   13   51      3    5    8   12   13   18   24   33   40   48   49   50   50   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  75.33  (  36.45   89.54  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     31     37     40     42     43     44     45     46     48     49     50     50     51     51     51     51     51     51     51 
GDT PERCENT_AT  35.29  60.78  72.55  78.43  82.35  84.31  86.27  88.24  90.20  94.12  96.08  98.04  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.60   0.79   1.04   1.14   1.35   1.38   1.53   1.64   2.36   2.44   2.72   2.55   2.77   2.77   2.77   2.77   2.77   2.77   2.77
GDT RMS_ALL_AT   3.27   3.16   3.07   3.05   3.07   2.92   3.01   2.93   2.93   2.87   2.82   2.78   2.79   2.77   2.77   2.77   2.77   2.77   2.77   2.77

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  Y    28_C      Y    28_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     6.668     2    0.078   0.078     7.870   10.952    9.320
LGA    T     7_C      T     7_C     7.625     0    0.138   0.218     9.839   10.238    7.347
LGA    K     8_C      K     8_C     4.413     4    0.340   0.365     5.193   37.500   21.481
LGA    I     9_C      I     9_C     2.605     0    0.130   0.747     4.745   57.262   55.952
LGA    L    10_C      L    10_C     1.881     0    0.060   0.269     3.421   75.119   68.155
LGA    P    11_C      P    11_C     1.126     0    0.011   0.039     1.894   81.429   78.980
LGA    C    12_C      C    12_C     0.590     0    0.029   0.135     1.073   88.214   90.556
LGA    P    13_C      P    13_C     1.237     0    0.096   0.291     1.830   79.286   78.980
LGA    R    14_C      R    14_C     1.365     0    0.218   0.874     3.403   75.119   73.203
LGA    C    15_C      C    15_C     1.022     0    0.036   0.225     1.166   83.690   84.444
LGA    N    16_C      N    16_C     0.868     0    0.065   0.274     1.854   88.214   84.881
LGA    S    17_C      S    17_C     0.501     0    0.054   0.490     1.753   95.238   92.302
LGA    M    18_C      M    18_C     0.571     0    0.059   0.834     4.434   92.857   77.738
LGA    E    19_C      E    19_C     0.577     4    0.032   0.039     0.741   92.857   51.323
LGA    T    20_C      T    20_C     0.816     0    0.089   0.123     1.152   88.214   89.184
LGA    K    21_C      K    21_C     0.622     0    0.017   0.432     3.763   92.857   77.884
LGA    F    22_C      F    22_C     0.501     0    0.027   0.056     0.620   90.476   90.476
LGA    C    23_C      C    23_C     0.619     0    0.058   0.685     2.286   90.476   86.190
LGA    Y    24_C      Y    24_C     0.856     0    0.019   0.089     1.416   90.476   84.444
LGA    Y    25_C      Y    25_C     1.043     0    0.102   0.117     1.348   83.690   88.254
LGA    N    26_C      N    26_C     1.443     0    0.088   0.237     2.947   73.095   70.000
LGA    N    27_C      N    27_C     2.999     0    0.334   0.339     8.497   64.881   38.452
LGA    Y    28_C      Y    28_C     4.154     0    0.222   1.367     7.566   44.167   26.310
LGA    N    29_C      N    29_C     2.052     0    0.073   0.206     2.530   66.905   73.155
LGA    V    30_C      V    30_C     2.605     0    0.024   1.126     6.089   60.952   52.585
LGA    N    31_C      N    31_C     1.715     0    0.035   0.394     3.919   75.000   64.524
LGA    Q    32_C      Q    32_C     0.621     0    0.134   0.344     2.137   90.476   87.672
LGA    P    33_C      P    33_C     0.545     0    0.049   0.078     0.766   90.476   90.476
LGA    R    34_C      R    34_C     0.584     0    0.041   0.904     5.040   90.476   71.732
LGA    H    35_C      H    35_C     0.331     0    0.104   0.236     0.743   97.619   96.190
LGA    F    36_C      F    36_C     0.871     0    0.020   0.149     1.732   90.476   82.381
LGA    C    37_C      C    37_C     0.770     0    0.097   0.139     1.402   88.214   88.968
LGA    K    38_C      K    38_C     0.677     0    0.088   0.483     1.747   90.476   87.513
LGA    A    39_C      A    39_C     0.606     0    0.130   0.134     0.707   92.857   92.381
LGA    C    40_C      C    40_C     1.247     0    0.027   0.053     1.419   81.429   81.429
LGA    Q    41_C      Q    41_C     1.424     0    0.019   0.769     2.832   77.143   73.016
LGA    R    42_C      R    42_C     1.393     0    0.022   1.205     6.178   81.429   61.602
LGA    Y    43_C      Y    43_C     0.863     0    0.064   0.185     1.086   88.214   89.722
LGA    W    44_C      W    44_C     0.603     0    0.085   0.171     0.911   92.857   91.837
LGA    T    45_C      T    45_C     1.189     0    0.049   1.003     2.619   81.429   75.578
LGA    S    46_C      S    46_C     1.002     0    0.067   0.687     1.592   83.690   81.508
LGA    G    47_C      G    47_C     0.951     0    0.039   0.039     0.951   90.476   90.476
LGA    G    48_C      G    48_C     0.677     0    0.077   0.077     0.732   90.476   90.476
LGA    T    49_C      T    49_C     0.934     0    0.143   0.190     1.385   88.214   85.306
LGA    M    50_C      M    50_C     0.885     0    0.089   1.306     4.418   90.476   78.333
LGA    R    51_C      R    51_C     1.262     0    0.123   0.458     6.541   77.143   55.931
LGA    S    52_C      S    52_C     3.239     0    0.113   0.633     6.054   53.690   44.841
LGA    V    53_C      V    53_C     3.786     0    0.135   1.168     5.063   37.738   39.252
LGA    P    54_C      P    54_C     7.757     0    0.086   0.306     9.157    9.643    9.184
LGA    I    55_C      I    55_C     7.890     0    0.019   1.427     9.416    4.643    5.000
LGA    G    56_C      G    56_C     9.432     0    0.666   0.666     9.582    1.548    1.548

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     2.774          2.783                  3.046           73.539   68.009

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   51    4.0     45    1.53    81.863    86.189     2.757

LGA_LOCAL      RMSD:   1.532  Number of atoms:   45  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.934  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   2.774  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.439948 * X  +  -0.291351 * Y  +  -0.849447 * Z  + -28.604774
  Y_new =  -0.158548 * X  +  -0.956249 * Y  +   0.245867 * Z  + -10.390238
  Z_new =  -0.883916 * X  +   0.026509 * Y  +  -0.466893 * Z  +   2.854713 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.345891  1.084172  3.084876   [DEG:  -19.8181   62.1185  176.7504 ]
ZXZ: -1.852541  2.056570 -1.540815   [DEG: -106.1428  117.8328  -88.2822 ]
 
# END of job
