 
####################################################### 
#                                                     # 
#                        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 1095 atoms, 535 common with TARGET 
           Number of atoms possible to evaluate: 527 
 
 
 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 . . . . . . . . . .    58.25           65.7   134    98.5   136     ARMSMC  
     WELL ORDERED  . . . . .    58.25           65.7   134    98.5   136     ARMSMC  
     NO INTER CONTACTS . . .    58.25           65.7   134    98.5   136     ARMSMC  
     SHIFTED CHAIN . . . . .    58.25           65.7   134    98.5   136     ARMSMC  
     ALTERNATIVE PARENT  . .    34.10            0.0     1   100.0     1     ARMSMC  
     SECONDARY STRUCTURE . .    22.75           93.1    72   100.0    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS    62.46           61.6   112    98.2   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    58.47           64.9   114    98.3   116     ARMSMC  
     BURIED  . . . . . . . .    56.97           70.0    20   100.0    20     ARMSMC  
     CORE  . . . . . . . . .    28.45           86.4    22   100.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    88.10           29.3    58    98.3    59     ARMSSC1 
     WELL ORDERED  . . . . .    88.10           29.3    58    98.3    59     ARMSSC1 
     NO INTER CONTACTS . . .    88.10           29.3    58    98.3    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .    89.61           24.0    50    98.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .    96.42           20.5    39    97.5    40     ARMSSC1 
     SHIFTED CHAIN . . . . .    88.10           29.3    58    98.3    59     ARMSSC1 
     ALTERNATIVE PARENT  . .    46.31            0.0     1   100.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .    83.00           28.1    32   100.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    81.38           35.4    48    98.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    86.57           29.4    51    98.1    52     ARMSSC1 
     BURIED  . . . . . . . .    98.49           28.6     7   100.0     7     ARMSSC1 
     CORE  . . . . . . . . .   115.00            0.0    10   100.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.91           34.8    46    97.9    47     ARMSSC2 
     WELL ORDERED  . . . . .    72.91           34.8    46    97.9    47     ARMSSC2 
     NO INTER CONTACTS . . .    72.91           34.8    46    97.9    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.21           33.3    36   100.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .    81.63           26.7    30    96.8    31     ARMSSC2 
     SHIFTED CHAIN . . . . .    72.91           34.8    46    97.9    47     ARMSSC2 
     ALTERNATIVE PARENT  . .    62.01            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    60.72           38.5    26   100.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    77.20           36.1    36    97.3    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    72.57           31.0    42    97.7    43     ARMSSC2 
     BURIED  . . . . . . . .    76.32           75.0     4   100.0     4     ARMSSC2 
     CORE  . . . . . . . . .    54.74           30.0    10   100.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.29           36.8    19   100.0    19     ARMSSC3 
     WELL ORDERED  . . . . .    79.29           36.8    19   100.0    19     ARMSSC3 
     NO INTER CONTACTS . . .    79.29           36.8    19   100.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .    81.36           41.2    17   100.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .    75.83           40.0    15   100.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .    79.29           36.8    19   100.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    58.66           50.0    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    92.04           30.8    13   100.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    81.22           35.3    17   100.0    17     ARMSSC3 
     BURIED  . . . . . . . .    60.45           50.0     2   100.0     2     ARMSSC3 
     CORE  . . . . . . . . .    39.46           50.0     6   100.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    55.72           50.0     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    55.72           50.0     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    55.72           50.0     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    55.72           50.0     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    55.72           50.0     6   100.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .    55.72           50.0     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    53.24           33.3     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    44.15           60.0     5   100.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    55.72           50.0     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    94.26            0.0     1   100.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.71635     r(1,2) =   0.60202     r(1,3) =   0.35272 
 r(2,1) =   0.45976     r(2,2) =  -0.78752     r(2,3) =   0.41039 
 r(3,1) =   0.52484     r(3,2) =  -0.13182     r(3,3) =  -0.84093 
THE OFFSET VECTOR: 
 v(1) =   6.75622     v(2) =  -6.00412     v(3) = -11.42403 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.87           (Number of atoms:   29) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.86         68    98.6    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0862                            CRMSCA  
     WELL ORDERED  . . . . .    5.86         68    98.6    69     CRMSCA  
     NO INTER CONTACTS . . .    5.86         68    98.6    69     CRMSCA  
     SHIFTED CHAIN . . . . .    5.86         68    98.6    69     CRMSCA  
     ALTERNATIVE PARENT  . .   18.21          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .    5.01         36   100.0    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.04         57    98.3    58     CRMSCA  
     SURFACE . . . . . . . .    6.18         58    98.3    59     CRMSCA  
     BURIED  . . . . . . . .    3.53         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .    4.83         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.84        331    98.2   337     CRMSMC  
     WELL ORDERED  . . . . .    5.84        331    98.2   337     CRMSMC  
     NO INTER CONTACTS . . .    5.84        331    98.2   337     CRMSMC  
     SHIFTED CHAIN . . . . .    5.84        331    98.2   337     CRMSMC  
     ALTERNATIVE PARENT  . .   17.53          5   100.0     5     CRMSMC  
     SECONDARY STRUCTURE . .    5.01        176   100.0   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.04        277    97.9   283     CRMSMC  
     SURFACE . . . . . . . .    6.15        284    97.9   290     CRMSMC  
     BURIED  . . . . . . . .    3.36         47   100.0    47     CRMSMC  
     CORE  . . . . . . . . .    4.69         54   100.0    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    7.67        256    32.6   786     CRMSSC  
     WELL ORDERED  . . . . .    7.67        256    32.6   786     CRMSSC  
     NO INTER CONTACTS . . .    7.67        256    32.6   786     CRMSSC  
     RELIABLE SIDE CHAINS  .    7.98        214    28.8   742     CRMSSC  
     CHANGED ANGLES  . . . .    8.07        155    98.1   158     CRMSSC  
     SECONDARY STRUCTURE . .    6.61        145    33.8   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.84        208    31.2   666     CRMSSC  
     SURFACE . . . . . . . .    8.01        230    33.4   689     CRMSSC  
     BURIED  . . . . . . . .    3.43         26    26.8    97     CRMSSC  
     CORE  . . . . . . . . .    6.91         48    40.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.72        527    49.6  1062     CRMSALL 
     WELL ORDERED  . . . . .    6.72        527    49.6  1062     CRMSALL 
     NO INTER CONTACTS . . .    6.72        527    49.6  1062     CRMSALL 
     SHIFTED CHAIN . . . . .    6.72        527    49.6  1062     CRMSALL 
     ALTERNATIVE PARENT  . .   18.76          7    50.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    5.80        289    50.4   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.88        435    48.4   898     CRMSALL 
     SURFACE . . . . . . . .    7.07        461    49.8   925     CRMSALL 
     BURIED  . . . . . . . .    3.42         66    48.2   137     CRMSALL 
     CORE  . . . . . . . . .    5.92         92    56.1   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    11.75      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.87     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     4.81     23    95.8    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    11.57     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.97    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     4.86    112    94.9   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    12.33     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.68    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     5.63    179    46.6   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.13      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.27     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     3.17     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.43    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     3.72    112    94.9   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.05     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.22    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     4.62    179    46.6   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 . . . . . . . . . .    3.631      0.514       0.260     68    98.6    69     ERRCA  
     WELL ORDERED  . . . . .    3.631      0.514       0.260     68    98.6    69     ERRCA  
     NO INTER CONTACTS . . .    3.631      0.514       0.260     68    98.6    69     ERRCA  
     SHIFTED CHAIN . . . . .    3.631      0.514       0.260     68    98.6    69     ERRCA  
     ALTERNATIVE PARENT  . .   17.214      0.896       0.448      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    2.921      0.470       0.241     36   100.0    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    3.676      0.507       0.257     57    98.3    58     ERRCA  
     SURFACE . . . . . . . .    3.925      0.535       0.268     58    98.3    59     ERRCA  
     BURIED  . . . . . . . .    1.926      0.392       0.218     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    3.401      0.552       0.276     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.626      0.514       0.260    331    98.2   337     ERRMC  
     WELL ORDERED  . . . . .    3.626      0.514       0.260    331    98.2   337     ERRMC  
     NO INTER CONTACTS . . .    3.626      0.514       0.260    331    98.2   337     ERRMC  
     SHIFTED CHAIN . . . . .    3.626      0.514       0.260    331    98.2   337     ERRMC  
     ALTERNATIVE PARENT  . .   16.389      0.890       0.445      5   100.0     5     ERRMC  
     SECONDARY STRUCTURE . .    2.901      0.459       0.235    176   100.0   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    3.702      0.509       0.258    277    97.9   283     ERRMC  
     SURFACE . . . . . . . .    3.928      0.537       0.270    284    97.9   290     ERRMC  
     BURIED  . . . . . . . .    1.798      0.374       0.199     47   100.0    47     ERRMC  
     CORE  . . . . . . . . .    3.236      0.538       0.269     54   100.0    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.410      0.638       0.321    256    32.6   786     ERRSC  
     WELL ORDERED  . . . . .    5.410      0.638       0.321    256    32.6   786     ERRSC  
     NO INTER CONTACTS . . .    5.410      0.638       0.321    256    32.6   786     ERRSC  
     RELIABLE SIDE CHAINS  .    5.622      0.639       0.321    214    28.8   742     ERRSC  
     CHANGED ANGLES  . . . .    5.762      0.657       0.331    155    98.1   158     ERRSC  
     SHIFTED CHAIN . . . . .    5.410      0.638       0.321    256    32.6   786     ERRSC  
     ALTERNATIVE PARENT  . .   19.802      0.908       0.454      3    30.0    10     ERRSC  
     SECONDARY STRUCTURE . .    4.519      0.600       0.300    145    33.8   429     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.463      0.636       0.320    208    31.2   666     ERRSC  
     SURFACE . . . . . . . .    5.775      0.656       0.328    230    33.4   689     ERRSC  
     BURIED  . . . . . . . .    2.174      0.482       0.255     26    26.8    97     ERRSC  
     CORE  . . . . . . . . .    5.180      0.648       0.324     48    40.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.425      0.569       0.287    527    49.6  1062     ERRALL 
     WELL ORDERED  . . . . .    4.425      0.569       0.287    527    49.6  1062     ERRALL 
     NO INTER CONTACTS . . .    4.425      0.569       0.287    527    49.6  1062     ERRALL 
     SHIFTED CHAIN . . . . .    4.425      0.569       0.287    527    49.6  1062     ERRALL 
     ALTERNATIVE PARENT  . .   17.573      0.896       0.448      7    50.0    14     ERRALL 
     SECONDARY STRUCTURE . .    3.644      0.522       0.265    289    50.4   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.471      0.564       0.285    435    48.4   898     ERRALL 
     SURFACE . . . . . . . .    4.779      0.591       0.297    461    49.8   925     ERRALL 
     BURIED  . . . . . . . .    1.947      0.413       0.220     66    48.2   137     ERRALL 
     CORE  . . . . . . . . .    4.203      0.590       0.295     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)         1        18        35        43        60      68      69   DISTCA 
CA  (P)      1.45     26.09     50.72     62.32     86.96              69   DISTCA 
CA  (RMS)    0.54      1.57      2.07      2.50      4.29                   DISTCA 
 
ALL (N)        12       100       190       297       451     527    1062   DISTALL 
ALL (P)      1.13      9.42     17.89     27.97     42.47            1062   DISTALL 
ALL (RMS)    0.75      1.50      2.03      2.85      4.77                   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          4.83          6.04          RMSLSI 
 
 
 
END of the results output 
