
#######################################################
#                                                     #
#                        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   52 (  390),  selected   52 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   52 , 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:    41       2_A - 42_A        4.71     9.33
  LCS_AVERAGE:     65.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       4_A - 22_A        1.96    19.01
  LCS_AVERAGE:     25.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       5_A - 19_A        0.80    19.61
  LONGEST_CONTINUOUS_SEGMENT:    15      26_A - 40_A        0.35    14.22
  LCS_AVERAGE:     19.29

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   52
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     2_A     D     2_A      3    5   41      3    3    3    4    5    9   13   20   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     K     3_A     K     3_A      3    6   41      3    3    3    4    6    8   13   15   24   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A     4_A     A     4_A      4   19   41      3    3    5   11   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A     5_A     A     5_A     15   19   41      4   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     C     6_A     C     6_A     15   19   41      8   14   15   16   17   17   18   20   22   24   30   35   38   39   40   40   41   41   41   43 
LCS_GDT     A     7_A     A     7_A     15   19   41      8   14   15   16   17   17   18   20   22   25   31   35   38   39   40   40   41   41   43   43 
LCS_GDT     D     8_A     D     8_A     15   19   41      6   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     G     9_A     G     9_A     15   19   41      8   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     I    10_A     I    10_A     15   19   41      8   14   15   16   17   17   18   20   22   24   30   35   38   39   40   40   41   41   43   43 
LCS_GDT     A    11_A     A    11_A     15   19   41      8   14   15   16   17   17   18   20   20   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A    12_A     A    12_A     15   19   41      8   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     V    13_A     V    13_A     15   19   41      8   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     K    14_A     K    14_A     15   19   41      8   14   15   16   17   17   18   20   24   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A    15_A     A    15_A     15   19   41      8   14   15   16   17   17   18   20   20   25   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     R    16_A     R    16_A     15   19   41      7   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     V    17_A     V    17_A     15   19   41      4   14   15   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     E    18_A     E    18_A     15   19   41      8   14   15   16   17   17   18   20   24   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     K    19_A     K    19_A     15   19   41      4    9   15   16   17   17   18   20   20   20   26   31   37   39   40   40   41   41   43   43 
LCS_GDT     L    20_A     L    20_A     13   19   41      4    9   12   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A    21_A     A    21_A      4   19   41      3    4    6   16   17   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     P    22_A     P    22_A      4   19   41      3    5    8    8   13   17   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     E    23_A     E    23_A      4    8   41      3    4    6    7    8   17   18   20   24   28   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A    24_A     A    24_A      4    8   41      3    4    6    8   12   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     V    25_A     V    25_A      4   16   41      3    5    6    8   12   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     P    26_A     P    26_A     15   16   41     13   15   15   15   15   15   17   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     Q    27_A     Q    27_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     K    28_A     K    28_A     15   16   41     13   15   15   15   15   15   16   17   21   25   29   36   38   39   40   40   41   41   43   43 
LCS_GDT     L    29_A     L    29_A     15   16   41     13   15   15   15   15   15   16   20   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     K    30_A     K    30_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     R    31_A     R    31_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A    32_A     A    32_A     15   16   41     13   15   15   15   15   15   17   20   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     L    33_A     L    33_A     15   16   41     13   15   15   15   15   15   17   20   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     K    34_A     K    34_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     I    35_A     I    35_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     A    36_A     A    36_A     15   16   41     13   15   15   15   15   15   17   20   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     E    37_A     E    37_A     15   16   41     13   15   15   15   15   15   16   18   21   27   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     R    38_A     R    38_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   42   43 
LCS_GDT     E    39_A     E    39_A     15   16   41     13   15   15   15   15   15   18   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     Q    40_A     Q    40_A     15   16   41     13   15   15   15   15   15   17   18   23   27   34   36   37   39   40   40   41   41   43   43 
LCS_GDT     G    41_A     G    41_A      3   16   41      3    3    3    6   10   14   17   22   27   29   34   36   38   39   40   40   41   41   43   43 
LCS_GDT     E    42_A     E    42_A      3    4   41      4    5    5    5    5    9   12   14   21   25   32   33   36   37   40   40   41   41   43   43 
LCS_GDT     G    43_A     G    43_A      3   11   36      4    5    5    5    5    9   13   17   20   25   27   28   28   31   34   36   38   40   43   43 
LCS_GDT     E    44_A     E    44_A     10   11   33      7   10   10   10   10   10   13   17   21   25   27   28   29   30   34   36   38   40   43   43 
LCS_GDT     F    45_A     F    45_A     10   11   31      7   10   10   10   10   10   12   16   20   25   27   28   29   30   31   32   37   40   43   43 
LCS_GDT     D    46_A     D    46_A     10   11   31      7   10   10   10   10   10   13   17   21   25   27   28   29   30   31   31   31   32   35   37 
LCS_GDT     E    47_A     E    47_A     10   11   31      7   10   10   10   10   10   13   17   21   25   27   28   29   30   31   31   31   32   35   37 
LCS_GDT     C    48_A     C    48_A     10   11   31      7   10   10   10   10   10   13   17   21   25   27   28   29   30   31   33   36   39   43   43 
LCS_GDT     L    49_A     L    49_A     10   11   31      7   10   10   10   10   10   13   17   21   25   27   28   29   30   31   31   31   32   35   36 
LCS_GDT     E    50_A     E    50_A     10   11   31      7   10   10   10   10   10   13   17   21   25   27   28   29   30   31   31   31   32   32   34 
LCS_GDT     A    51_A     A    51_A     10   11   31      7   10   10   10   10   10   12   12   21   25   27   28   29   30   31   31   31   32   37   39 
LCS_GDT     L    52_A     L    52_A     10   11   31      7   10   10   10   10   10   12   17   21   25   27   28   29   30   31   31   31   32   37   39 
LCS_GDT     D    53_A     D    53_A     10   11   31      7   10   10   10   10   10   13   17   21   25   27   28   29   30   31   31   31   32   32   34 
LCS_AVERAGE  LCS_A:  36.50  (  19.29   25.16   65.03 )

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     13     15     15     16     17     17     18     22     27     29     34     36     38     39     40     40     41     41     43     43 
GDT PERCENT_AT  21.67  25.00  25.00  26.67  28.33  28.33  30.00  36.67  45.00  48.33  56.67  60.00  63.33  65.00  66.67  66.67  68.33  68.33  71.67  71.67
GDT RMS_LOCAL    0.25   0.35   0.35   1.01   1.15   1.15   1.56   3.03   3.42   3.69   3.98   4.12   4.37   4.42   4.53   4.53   4.71   4.71   5.81   5.42
GDT RMS_ALL_AT  14.39  14.22  14.22  19.67  19.63  19.63  19.36   9.85   9.47   9.50   9.37   9.35   9.59   9.46   9.54   9.54   9.33   9.33   8.49   8.91

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  D     8_A      D     8_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    37_A      E    37_A
#   possible swapping detected:  E    42_A      E    42_A
#   possible swapping detected:  D    46_A      D    46_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     2_A      D     2_A     5.172     0    0.648   1.298     7.901   21.429   30.238
LGA    K     3_A      K     3_A     5.602     0    0.035   0.572     6.495   23.810   22.646
LGA    A     4_A      A     4_A     4.438     0    0.426   0.448     4.989   40.714   38.857
LGA    A     5_A      A     5_A     1.353     0    0.428   0.447     3.266   65.714   67.143
LGA    C     6_A      C     6_A     7.328     0    0.071   0.816    12.454   13.333    8.968
LGA    A     7_A      A     7_A     7.982     0    0.050   0.065     9.339   11.905    9.810
LGA    D     8_A      D     8_A     3.201     0    0.125   0.842     4.998   54.167   49.167
LGA    G     9_A      G     9_A     3.460     0    0.110   0.110     4.454   47.262   47.262
LGA    I    10_A      I    10_A     7.438     0    0.037   0.070    12.863   13.452    6.786
LGA    A    11_A      A    11_A     6.679     0    0.000   0.026     7.706   22.024   19.048
LGA    A    12_A      A    12_A     2.085     0    0.063   0.070     2.843   73.452   71.714
LGA    V    13_A      V    13_A     3.469     0    0.036   0.065     7.476   54.048   37.279
LGA    K    14_A      K    14_A     6.515     0    0.000   0.207    16.162   19.524    8.995
LGA    A    15_A      A    15_A     6.134     0    0.057   0.051     7.327   24.048   21.238
LGA    R    16_A      R    16_A     2.988     0    0.078   1.442    10.006   65.119   32.554
LGA    V    17_A      V    17_A     3.126     0    0.082   0.064     7.548   61.429   41.088
LGA    E    18_A      E    18_A     6.079     0    0.111   1.039    14.020   23.214   10.635
LGA    K    19_A      K    19_A     6.705     0    0.073   1.052    13.611   17.738    8.571
LGA    L    20_A      L    20_A     3.846     0    0.632   1.525     8.838   56.071   34.881
LGA    A    21_A      A    21_A     1.773     0    0.077   0.099     3.546   75.119   68.762
LGA    P    22_A      P    22_A     3.236     0    0.213   0.436     5.121   50.357   44.966
LGA    E    23_A      E    23_A     5.576     0    0.192   1.321    12.681   31.786   15.238
LGA    A    24_A      A    24_A     3.299     0    0.184   0.176     5.003   52.024   46.857
LGA    V    25_A      V    25_A     1.191     0    0.631   1.440     4.230   73.214   66.939
LGA    P    26_A      P    26_A     3.871     0    0.603   0.679     6.472   53.810   40.000
LGA    Q    27_A      Q    27_A     2.265     0    0.046   0.124     6.112   62.976   40.688
LGA    K    28_A      K    28_A     5.757     0    0.027   0.933    10.677   26.310   12.804
LGA    L    29_A      L    29_A     5.524     0    0.054   0.928     7.705   29.048   21.845
LGA    K    30_A      K    30_A     2.254     0    0.000   0.842    10.601   69.048   41.058
LGA    R    31_A      R    31_A     2.624     0    0.081   0.919    11.679   65.119   30.823
LGA    A    32_A      A    32_A     5.112     0    0.016   0.000     7.130   33.095   28.476
LGA    L    33_A      L    33_A     5.197     0    0.043   0.787    10.677   34.524   20.060
LGA    K    34_A      K    34_A     2.923     0    0.024   0.990    11.551   61.071   36.561
LGA    I    35_A      I    35_A     2.177     0    0.084   0.074     7.205   73.214   48.452
LGA    A    36_A      A    36_A     5.150     0    0.072   0.071     7.025   31.786   27.429
LGA    E    37_A      E    37_A     5.805     0    0.076   1.016    11.773   27.619   13.439
LGA    R    38_A      R    38_A     3.093     0    0.077   1.462     7.772   59.405   35.714
LGA    E    39_A      E    39_A     2.613     0    0.171   0.394     8.462   54.762   32.910
LGA    Q    40_A      Q    40_A     6.595     0    0.350   1.208    12.972   19.048    9.418
LGA    G    41_A      G    41_A     4.508     0    0.558   0.558     8.053   21.667   21.667
LGA    E    42_A      E    42_A    10.518     0    0.262   1.007    14.790    1.190    0.688
LGA    G    43_A      G    43_A    15.317     0    0.323   0.323    18.405    0.000    0.000
LGA    E    44_A      E    44_A    15.247     0    0.503   0.476    15.247    0.000    0.000
LGA    F    45_A      F    45_A    16.248     0    0.113   1.366    19.345    0.000    0.000
LGA    D    46_A      D    46_A    22.445     0    0.114   1.038    24.700    0.000    0.000
LGA    E    47_A      E    47_A    20.672     0    0.066   0.543    23.112    0.000    0.000
LGA    C    48_A      C    48_A    15.412     0    0.050   0.821    16.968    0.000    0.000
LGA    L    49_A      L    49_A    20.020     0    0.107   1.392    24.452    0.000    0.000
LGA    E    50_A      E    50_A    23.557     0    0.079   1.018    29.479    0.000    0.000
LGA    A    51_A      A    51_A    18.753     0    0.100   0.111    20.134    0.000    0.000
LGA    L    52_A      L    52_A    17.186     0    0.075   1.410    19.145    0.000    0.000
LGA    D    53_A      D    53_A    23.249     0    0.562   1.543    27.393    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       52     208    208  100.00     390    390  100.00                60
SUMMARY(RMSD_GDC):     8.037          7.871                  9.797           28.577   21.195

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   52   60    4.0     22    3.03    38.750    35.976     0.704

LGA_LOCAL      RMSD:   3.027  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.849  Number of assigned atoms:   52 
Std_ASGN_ATOMS RMSD:   8.037  Standard rmsd on all 52 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.983046 * X  +  -0.021812 * Y  +  -0.182054 * Z  + -221.315765
  Y_new =  -0.115738 * X  +   0.696282 * Y  +  -0.708376 * Z  + 187.910645
  Z_new =   0.142212 * X  +   0.717437 * Y  +   0.681953 * Z  + -484.813812 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.117194 -0.142696  0.810750   [DEG:   -6.7147   -8.1759   46.4525 ]
ZXZ: -0.251558  0.820367  0.195686   [DEG:  -14.4132   47.0036   11.2120 ]
 
# END of job
