
#######################################################
#                                                     #
#                        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   34 (  238),  selected   34 , name one
# Molecule2: number of CA atoms   34 (  235),  selected   34 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    34       1_A - 34_A        2.53     2.53
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       4_A - 34_A        1.77     2.70
  LCS_AVERAGE:     85.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       6_A - 34_A        0.89     3.12
  LCS_AVERAGE:     74.74

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   34
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     S     1_B     S     1_A      4    8   34      4    4    4    6   11   13   18   20   28   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     2_B     G     2_A      4    8   34      4    4    5    9   11   25   28   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     3_B     P     3_A      5    8   34      4    4    5    9   11   13   18   27   31   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N     4_B     N     4_A      5   31   34      4    4    5    9   11   19   27   29   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     5_B     G     5_A      5   31   34      3    5   19   26   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G     6_B     G     6_A     29   31   34      3    3   23   27   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V     7_B     V     7_A     29   31   34      3    5   24   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C     8_B     C     8_A     29   31   34      5   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P     9_B     P     9_A     29   31   34     14   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     V    10_B     V    10_A     29   31   34     15   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    11_B     L    11_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    12_B     I    12_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    13_B     Y    13_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    14_B     L    14_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    15_B     C    15_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    16_B     R    16_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     R    17_B     R    17_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    18_B     D    18_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     S    19_B     S    19_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     D    20_B     D    20_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    21_B     C    21_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     P    22_B     P    22_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    23_B     G    23_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     E    24_B     E    24_A     29   31   34     15   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    25_B     C    25_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     I    26_B     I    26_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    27_B     C    27_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     L    28_B     L    28_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    29_B     G    29_A     29   31   34     16   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     N    30_B     N    30_A     29   31   34      4   14   24   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    31_B     G    31_A     29   31   34     16   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     Y    32_B     Y    32_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     C    33_B     C    33_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_GDT     G    34_B     G    34_A     29   31   34     20   26   26   28   29   30   30   30   32   33   34   34   34   34   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  86.65  (  74.74   85.21  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     20     26     26     28     29     30     30     30     32     33     34     34     34     34     34     34     34     34     34     34 
GDT PERCENT_AT  58.82  76.47  76.47  82.35  85.29  88.24  88.24  88.24  94.12  97.06 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.50   0.50   0.73   0.89   1.15   1.15   1.15   2.01   2.25   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53
GDT RMS_ALL_AT   3.04   3.16   3.16   3.22   3.12   2.93   2.93   2.93   2.61   2.57   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53   2.53

# Checking swapping
#   possible swapping detected:  E    24_B      E    24_A
#   possible swapping detected:  Y    32_B      Y    32_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_B      S     1_A     7.052     0    0.175   0.616     9.475    7.143    6.190
LGA    G     2_B      G     2_A     6.614     0    0.042   0.042     7.496   13.690   13.690
LGA    P     3_B      P     3_A     9.607     0    0.389   0.506    11.151    1.786    1.429
LGA    N     4_B      N     4_A     8.182     0    0.678   1.118     9.107    6.071    5.298
LGA    G     5_B      G     5_A     3.717     0    0.668   0.668     4.895   39.048   39.048
LGA    G     6_B      G     6_A     2.100     0    0.211   0.211     2.358   73.214   73.214
LGA    V     7_B      V     7_A     2.637     0    0.024   1.044     5.453   60.952   49.184
LGA    C     8_B      C     8_A     1.553     0    0.056   0.107     2.033   75.119   78.730
LGA    P     9_B      P     9_A     1.018     0    0.042   0.073     1.280   85.952   84.014
LGA    V    10_B      V    10_A     0.540     0    0.129   0.112     0.883   95.238   93.197
LGA    L    11_B      L    11_A     0.767     3    0.108   0.129     1.436   88.214   55.417
LGA    I    12_B      I    12_A     0.745     0    0.074   0.620     1.582   90.476   88.274
LGA    Y    13_B      Y    13_A     0.698     0    0.034   0.877     5.355   95.238   70.437
LGA    L    14_B      L    14_A     0.312     0    0.028   0.141     0.504  100.000   98.810
LGA    C    15_B      C    15_A     0.286     0    0.026   0.051     0.616  100.000   98.413
LGA    R    16_B      R    16_A     0.349     0    0.054   0.381     3.600  100.000   78.615
LGA    R    17_B      R    17_A     0.555     0    0.047   0.199     0.972   90.476   90.476
LGA    D    18_B      D    18_A     0.546     0    0.015   0.186     1.581   90.476   87.143
LGA    S    19_B      S    19_A     0.530     0    0.042   0.115     0.701   92.857   92.063
LGA    D    20_B      D    20_A     0.231     0    0.050   0.162     0.628  100.000   98.810
LGA    C    21_B      C    21_A     0.520     0    0.027   0.082     0.709   97.619   95.238
LGA    P    22_B      P    22_A     0.504     0    0.088   0.170     0.802   90.476   90.476
LGA    G    23_B      G    23_A     0.616     0    0.067   0.067     0.837   90.476   90.476
LGA    E    24_B      E    24_A     0.785     0    0.049   0.240     2.050   90.476   81.693
LGA    C    25_B      C    25_A     0.591     0    0.020   0.041     0.603   92.857   93.651
LGA    I    26_B      I    26_A     0.744     0    0.011   0.075     1.346   90.476   87.083
LGA    C    27_B      C    27_A     0.758     0    0.065   0.072     0.786   90.476   90.476
LGA    L    28_B      L    28_A     0.278     0    0.039   0.062     1.303   97.619   91.786
LGA    G    29_B      G    29_A     0.978     0    0.033   0.033     1.894   86.190   86.190
LGA    N    30_B      N    30_A     1.752     0    0.061   0.139     2.824   79.286   73.155
LGA    G    31_B      G    31_A     0.676     0    0.044   0.044     0.877   95.238   95.238
LGA    Y    32_B      Y    32_A     0.378     0    0.027   0.121     1.835  100.000   86.944
LGA    C    33_B      C    33_A     0.472     0    0.052   0.071     0.791   97.619   95.238
LGA    G    34_B      G    34_A     0.311     0    0.026   0.026     1.066   92.976   92.976

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       34     136    136  100.00     235    235  100.00                34
SUMMARY(RMSD_GDC):     2.535          2.562                  2.754           79.345   75.090

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   34    4.0     30    1.15    86.765    88.059     2.396

LGA_LOCAL      RMSD:   1.152  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.933  Number of assigned atoms:   34 
Std_ASGN_ATOMS RMSD:   2.535  Standard rmsd on all 34 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.768968 * X  +  -0.339899 * Y  +  -0.541440 * Z  + -11.988922
  Y_new =  -0.338044 * X  +   0.502657 * Y  +  -0.795652 * Z  +  -7.734394
  Z_new =   0.542600 * X  +   0.794861 * Y  +   0.271626 * Z  + -15.693779 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.414178 -0.573529  1.241510   [DEG:  -23.7306  -32.8608   71.1333 ]
ZXZ: -0.597517  1.295714  0.598976   [DEG:  -34.2352   74.2389   34.3188 ]
 
# END of job
