 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_2.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_2.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_2.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_2.1aj4.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff  
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff  
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 1062 atoms, MODEL 1088 atoms, 536 common with TARGET 
           Number of atoms possible to evaluate: 528 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 3.538625 
 
 CA-RMS TARGET<->PARENT(1ncx)	 3.287245 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.396291 
 
 CA-RMS TARGET<->PARENT(1aj4)	 5.635736 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    55.75           70.9   134    98.5   136     ARMSMC  
     WELL ORDERED  . . . . .    55.75           70.9   134    98.5   136     ARMSMC  
     NO INTER CONTACTS . . .    55.75           70.9   134    98.5   136     ARMSMC  
     SHIFTED CHAIN . . . . .    55.75           70.9   134    98.5   136     ARMSMC  
     ALTERNATIVE PARENT  . .    24.70          100.0     1   100.0     1     ARMSMC  
     SECONDARY STRUCTURE . .    17.90           95.8    72   100.0    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS    59.40           67.9   112    98.2   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    55.08           70.2   114    98.3   116     ARMSMC  
     BURIED  . . . . . . . .    59.46           75.0    20   100.0    20     ARMSMC  
     CORE  . . . . . . . . .    31.14           86.4    22   100.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    96.70           31.0    58    98.3    59     ARMSSC1 
     WELL ORDERED  . . . . .    96.70           31.0    58    98.3    59     ARMSSC1 
     NO INTER CONTACTS . . .    96.70           31.0    58    98.3    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .    93.89           32.0    50    98.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .   102.88           23.1    39    97.5    40     ARMSSC1 
     SHIFTED CHAIN . . . . .    96.70           31.0    58    98.3    59     ARMSSC1 
     ALTERNATIVE PARENT  . .    52.80            0.0     1   100.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .    96.62           31.2    32   100.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    95.33           37.5    48    98.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    92.90           33.3    51    98.1    52     ARMSSC1 
     BURIED  . . . . . . . .   120.79           14.3     7   100.0     7     ARMSSC1 
     CORE  . . . . . . . . .   103.01            0.0    10   100.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    83.92           41.3    46    97.9    47     ARMSSC2 
     WELL ORDERED  . . . . .    83.92           41.3    46    97.9    47     ARMSSC2 
     NO INTER CONTACTS . . .    83.92           41.3    46    97.9    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .    72.83           47.2    36   100.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .    87.70           30.0    30    96.8    31     ARMSSC2 
     SHIFTED CHAIN . . . . .    83.92           41.3    46    97.9    47     ARMSSC2 
     ALTERNATIVE PARENT  . .    75.10            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    78.65           38.5    26   100.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    87.95           38.9    36    97.3    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    82.86           40.5    42    97.7    43     ARMSSC2 
     BURIED  . . . . . . . .    94.25           50.0     4   100.0     4     ARMSSC2 
     CORE  . . . . . . . . .    67.42           50.0    10   100.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.60           26.3    19   100.0    19     ARMSSC3 
     WELL ORDERED  . . . . .    78.60           26.3    19   100.0    19     ARMSSC3 
     NO INTER CONTACTS . . .    78.60           26.3    19   100.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .    80.77           23.5    17   100.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .    81.72           20.0    15   100.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .    78.60           26.3    19   100.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    75.63           33.3    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    75.64           23.1    13   100.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    77.91           29.4    17   100.0    17     ARMSSC3 
     BURIED  . . . . . . . .    84.28            0.0     2   100.0     2     ARMSSC3 
     CORE  . . . . . . . . .    84.67           33.3     6   100.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.77           33.3     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    85.77           33.3     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    85.77           33.3     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    85.77           33.3     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    85.77           33.3     6   100.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .    85.77           33.3     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    64.97           33.3     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    61.15           40.0     5   100.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    85.77           33.3     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .   159.51            0.0     1   100.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.14016     r(1,2) =   0.95768     r(1,3) =  -0.25141 
 r(2,1) =  -0.98022     r(2,2) =  -0.09838     r(2,3) =   0.17172 
 r(3,1) =   0.13972     r(3,2) =   0.27051     r(3,3) =   0.95252 
THE OFFSET VECTOR: 
 v(1) = -12.52347     v(2) =   7.86556     v(3) = -32.54544 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.71           (Number of atoms:   26) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.42         68    98.6    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0945                            CRMSCA  
     WELL ORDERED  . . . . .    6.42         68    98.6    69     CRMSCA  
     NO INTER CONTACTS . . .    6.42         68    98.6    69     CRMSCA  
     SHIFTED CHAIN . . . . .    6.42         68    98.6    69     CRMSCA  
     ALTERNATIVE PARENT  . .   20.23          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .    5.69         36   100.0    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.63         57    98.3    58     CRMSCA  
     SURFACE . . . . . . . .    6.81         58    98.3    59     CRMSCA  
     BURIED  . . . . . . . .    3.45         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .    5.20         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.39        332    98.5   337     CRMSMC  
     WELL ORDERED  . . . . .    6.39        332    98.5   337     CRMSMC  
     NO INTER CONTACTS . . .    6.39        332    98.5   337     CRMSMC  
     SHIFTED CHAIN . . . . .    6.39        332    98.5   337     CRMSMC  
     ALTERNATIVE PARENT  . .   19.48          5   100.0     5     CRMSMC  
     SECONDARY STRUCTURE . .    5.68        176   100.0   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.62        278    98.2   283     CRMSMC  
     SURFACE . . . . . . . .    6.76        285    98.3   290     CRMSMC  
     BURIED  . . . . . . . .    3.32         47   100.0    47     CRMSMC  
     CORE  . . . . . . . . .    5.06         54   100.0    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.13        256    32.6   786     CRMSSC  
     WELL ORDERED  . . . . .    8.13        256    32.6   786     CRMSSC  
     NO INTER CONTACTS . . .    8.13        256    32.6   786     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.48        214    28.8   742     CRMSSC  
     CHANGED ANGLES  . . . .    8.52        155    98.1   158     CRMSSC  
     SECONDARY STRUCTURE . .    7.13        145    33.8   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.41        208    31.2   666     CRMSSC  
     SURFACE . . . . . . . .    8.51        230    33.4   689     CRMSSC  
     BURIED  . . . . . . . .    3.24         26    26.8    97     CRMSSC  
     CORE  . . . . . . . . .    6.81         48    40.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.21        528    49.7  1062     CRMSALL 
     WELL ORDERED  . . . . .    7.21        528    49.7  1062     CRMSALL 
     NO INTER CONTACTS . . .    7.21        528    49.7  1062     CRMSALL 
     SHIFTED CHAIN . . . . .    7.21        528    49.7  1062     CRMSALL 
     ALTERNATIVE PARENT  . .   20.61          7    50.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    6.39        289    50.4   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.44        436    48.6   898     CRMSALL 
     SURFACE . . . . . . . .    7.61        462    49.9   925     CRMSALL 
     BURIED  . . . . . . . .    3.35         66    48.2   137     CRMSALL 
     CORE  . . . . . . . . .    6.01         92    56.1   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    13.57      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.87     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     4.82     23    95.8    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    13.34     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     3.01    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     4.91    113    95.8   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    14.01     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.84    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     5.70    180    46.9   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.98      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.39     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     3.61     23    95.8    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.04     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.56    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     3.71    113    95.8   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.00     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.41    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     4.68    180    46.9   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.923      1.000       0.500     68    98.6    69     ERRCA  
     WELL ORDERED  . . . . .    4.923      1.000       0.500     68    98.6    69     ERRCA  
     NO INTER CONTACTS . . .    4.923      1.000       0.500     68    98.6    69     ERRCA  
     SHIFTED CHAIN . . . . .    4.923      1.000       0.500     68    98.6    69     ERRCA  
     ALTERNATIVE PARENT  . .   20.227      1.000       0.500      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    4.318      1.000       0.500     36   100.0    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.957      1.000       0.500     57    98.3    58     ERRCA  
     SURFACE . . . . . . . .    5.304      1.000       0.500     58    98.3    59     ERRCA  
     BURIED  . . . . . . . .    2.717      1.000       0.500     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    4.747      1.000       0.500     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.937      1.000       0.500    332    98.5   337     ERRMC  
     WELL ORDERED  . . . . .    4.937      1.000       0.500    332    98.5   337     ERRMC  
     NO INTER CONTACTS . . .    4.937      1.000       0.500    332    98.5   337     ERRMC  
     SHIFTED CHAIN . . . . .    4.937      1.000       0.500    332    98.5   337     ERRMC  
     ALTERNATIVE PARENT  . .   19.373      1.000       0.500      5   100.0     5     ERRMC  
     SECONDARY STRUCTURE . .    4.311      1.000       0.500    176   100.0   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.005      1.000       0.500    278    98.2   283     ERRMC  
     SURFACE . . . . . . . .    5.310      1.000       0.500    285    98.3   290     ERRMC  
     BURIED  . . . . . . . .    2.674      1.000       0.500     47   100.0    47     ERRMC  
     CORE  . . . . . . . . .    4.586      1.000       0.500     54   100.0    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.683      1.000       0.500    256    32.6   786     ERRSC  
     WELL ORDERED  . . . . .    6.683      1.000       0.500    256    32.6   786     ERRSC  
     NO INTER CONTACTS . . .    6.683      1.000       0.500    256    32.6   786     ERRSC  
     RELIABLE SIDE CHAINS  .    6.916      1.000       0.500    214    28.8   742     ERRSC  
     CHANGED ANGLES  . . . .    6.970      1.000       0.500    155    98.1   158     ERRSC  
     SHIFTED CHAIN . . . . .    6.683      1.000       0.500    256    32.6   786     ERRSC  
     ALTERNATIVE PARENT  . .   22.590      1.000       0.500      3    30.0    10     ERRSC  
     SECONDARY STRUCTURE . .    5.818      1.000       0.500    145    33.8   429     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.790      1.000       0.500    208    31.2   666     ERRSC  
     SURFACE . . . . . . . .    7.111      1.000       0.500    230    33.4   689     ERRSC  
     BURIED  . . . . . . . .    2.894      1.000       0.500     26    26.8    97     ERRSC  
     CORE  . . . . . . . . .    6.221      1.000       0.500     48    40.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.716      1.000       0.500    528    49.7  1062     ERRALL 
     WELL ORDERED  . . . . .    5.716      1.000       0.500    528    49.7  1062     ERRALL 
     NO INTER CONTACTS . . .    5.716      1.000       0.500    528    49.7  1062     ERRALL 
     SHIFTED CHAIN . . . . .    5.716      1.000       0.500    528    49.7  1062     ERRALL 
     ALTERNATIVE PARENT  . .   20.464      1.000       0.500      7    50.0    14     ERRALL 
     SECONDARY STRUCTURE . .    4.998      1.000       0.500    289    50.4   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.782      1.000       0.500    436    48.6   898     ERRALL 
     SURFACE . . . . . . . .    6.136      1.000       0.500    462    49.9   925     ERRALL 
     BURIED  . . . . . . . .    2.778      1.000       0.500     66    48.2   137     ERRALL 
     CORE  . . . . . . . . .    5.404      1.000       0.500     92    56.1   164     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)         3        19        29        43        59      68      69   DISTCA 
CA  (P)      4.35     27.54     42.03     62.32     85.51              69   DISTCA 
CA  (RMS)    0.95      1.45      1.84      2.61      4.33                   DISTCA 
 
ALL (N)        15       105       182       289       441     528    1062   DISTALL 
ALL (P)      1.41      9.89     17.14     27.21     41.53            1062   DISTALL 
ALL (RMS)    0.73      1.47      1.98      2.88      4.78                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)          11            11            57          RMSLSI 
CA  (P)       15.94         15.94         82.61          RMSLSI 
CA  (RMS)      1.81          5.20          6.63          RMSLSI 
 
 
 
END of the results output 
