 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0064.inter 
CONANA-PAIR            ../CONANA/T0064.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0064.1r69.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0064.2cro.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 845 atoms, MODEL 914 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 743 
 
 
 CA-RMS TARGET<->PARENT(1r69)	 1.473148 
 
 CA-RMS TARGET<->PARENT(2cro)	 1.394009 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    33.02           84.9   152    75.6   201     ARMSMC  
     WELL ORDERED  . . . . .    33.75           86.6   134    83.2   161     ARMSMC  
     NO INTER CONTACTS . . .    26.52           87.2    86    81.9   105     ARMSMC  
     SHIFTED CHAIN . . . . .    40.77           78.3    92    65.2   141     ARMSMC  
     ALTERNATIVE PARENT  . .    27.06           66.7     3    75.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    23.70           93.1   101    79.5   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    52.27           77.5    40    44.9    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    35.10           85.4   103    68.2   151     ARMSMC  
     BURIED  . . . . . . . .    28.14           83.7    49    98.0    50     ARMSMC  
     CORE  . . . . . . . . .    22.45           87.5   112   100.0   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.53           52.1    71    78.0    91     ARMSSC1 
     WELL ORDERED  . . . . .    71.68           60.0    45    83.3    54     ARMSSC1 
     NO INTER CONTACTS . . .    85.71           42.1    38    84.4    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    79.70           49.2    65    77.4    84     ARMSSC1 
     CHANGED ANGLES  . . . .    85.62           44.7    47    71.2    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    78.30           45.5    44    68.8    64     ARMSSC1 
     ALTERNATIVE PARENT  . .     5.54          100.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    85.80           42.6    47    82.5    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    73.70           50.0    22    52.4    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    73.17           55.1    49    71.0    69     ARMSSC1 
     BURIED  . . . . . . . .    86.47           45.5    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    79.19           53.1    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.01           41.5    53    82.8    64     ARMSSC2 
     WELL ORDERED  . . . . .    75.80           51.9    27    96.4    28     ARMSSC2 
     NO INTER CONTACTS . . .    88.80           35.7    28    84.8    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    69.25           45.0    40    81.6    49     ARMSSC2 
     CHANGED ANGLES  . . . .    78.59           36.1    36    76.6    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    82.78           42.4    33    75.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    10.43          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    84.11           41.7    36    85.7    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    81.03           41.2    17    60.7    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    75.56           39.5    38    77.6    49     ARMSSC2 
     BURIED  . . . . . . . .    80.57           46.7    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    75.04           41.7    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    82.65           36.0    25    80.6    31     ARMSSC3 
     WELL ORDERED  . . . . .    87.89           44.4     9    90.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    89.02           30.8    13    86.7    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    87.19           33.3    21    80.8    26     ARMSSC3 
     CHANGED ANGLES  . . . .    90.03           33.3    18    75.0    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    68.77           42.9    14    70.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    88.74           31.6    19    82.6    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    73.52           25.0     8    57.1    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    74.01           36.4    22    78.6    28     ARMSSC3 
     BURIED  . . . . . . . .   129.42           33.3     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    86.61           41.2    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.67           30.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .   113.20            0.0     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    77.26           40.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    85.67           30.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .    81.63           33.3     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    87.99           25.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    81.14           28.6     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   119.86            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    76.96           37.5     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .   114.04            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    80.99           33.3     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.13647     r(1,2) =   0.97636     r(1,3) =  -0.16760 
 r(2,1) =  -0.24045     r(2,2) =  -0.13148     r(2,3) =  -0.96172 
 r(3,1) =  -0.96102     r(3,2) =   0.17155     r(3,3) =   0.21682 
THE OFFSET VECTOR: 
 v(1) =  18.06858     v(2) =  64.75222     v(3) =  33.03933 
 
 Number of iteration 33                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.03           (Number of atoms:   58) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   12.84         90    87.4   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1427                            CRMSCA  
     WELL ORDERED  . . . . .   13.18         79    92.9    85     CRMSCA  
     NO INTER CONTACTS . . .    7.12         48    88.9    54     CRMSCA  
     SHIFTED CHAIN . . . . .   15.72         60    82.2    73     CRMSCA  
     ALTERNATIVE PARENT  . .    2.93          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .   14.67         61    93.8    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   20.86         34    72.3    47     CRMSCA  
     SURFACE . . . . . . . .   15.09         65    83.3    78     CRMSCA  
     BURIED  . . . . . . . .    1.02         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    0.92         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   12.84        446    87.3   511     CRMSMC  
     WELL ORDERED  . . . . .   12.93        389    92.6   420     CRMSMC  
     NO INTER CONTACTS . . .    6.97        237    88.8   267     CRMSMC  
     SHIFTED CHAIN . . . . .   15.70        298    82.1   363     CRMSMC  
     ALTERNATIVE PARENT  . .    3.21         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .   14.71        304    93.8   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   20.82        169    72.2   234     CRMSMC  
     SURFACE . . . . . . . .   15.10        322    83.2   387     CRMSMC  
     BURIED  . . . . . . . .    1.13        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    0.98        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   14.24        383    88.5   433     CRMSSC  
     WELL ORDERED  . . . . .   13.48        232    93.5   248     CRMSSC  
     NO INTER CONTACTS . . .    8.22        188    89.5   210     CRMSSC  
     RELIABLE SIDE CHAINS  .   14.82        331    89.2   371     CRMSSC  
     CHANGED ANGLES  . . . .   15.98        245    87.2   281     CRMSSC  
     SECONDARY STRUCTURE . .   16.35        281    94.6   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS   21.64        163    76.5   213     CRMSSC  
     SURFACE . . . . . . . .   16.18        294    85.5   344     CRMSSC  
     BURIED  . . . . . . . .    2.74         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    2.47        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   13.55        743    87.9   845     CRMSALL 
     WELL ORDERED  . . . . .   13.14        552    93.1   593     CRMSALL 
     NO INTER CONTACTS . . .    7.67        380    89.2   426     CRMSALL 
     SHIFTED CHAIN . . . . .   16.49        499    83.0   601     CRMSALL 
     ALTERNATIVE PARENT  . .    3.31         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .   15.56        525    94.3   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS   21.24        299    74.6   401     CRMSALL 
     SURFACE . . . . . . . .   15.64        554    84.5   656     CRMSALL 
     BURIED  . . . . . . . .    2.03        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    1.86        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.18      4    66.7     6      40-TNPSIQ-45   
 CA  LOOP  2    22.54     29    72.5    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.18     20    66.7    30      40-TNPSIQ-45   
 MC  LOOP  2    22.52    144    72.4   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.10     31    68.9    45      40-TNPSIQ-45   
 ALL LOOP  2    22.71    260    74.7   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.10      4    66.7     6      40-TNPSIQ-45   
 CA  LOOP  2     6.65     29    72.5    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.17     20    66.7    30      40-TNPSIQ-45   
 MC  LOOP  2     6.61    144    72.4   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.97     31    68.9    45      40-TNPSIQ-45   
 ALL LOOP  2     7.51    260    74.7   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.156      0.528       0.487     90    87.4   103     ERRCA  
     WELL ORDERED  . . . . .    6.404      0.549       0.509     79    92.9    85     ERRCA  
     NO INTER CONTACTS . . .    3.179      0.501       0.526     48    88.9    54     ERRCA  
     SHIFTED CHAIN . . . . .    8.037      0.458       0.371     60    82.2    73     ERRCA  
     ALTERNATIVE PARENT  . .    0.731      0.131       0.089      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    7.524      0.548       0.484     61    93.8    65     ERRCA  
     LARGE SHIFTS/INSERTIONS   12.722      0.442       0.223     34    72.3    47     ERRCA  
     SURFACE . . . . . . . .    7.728      0.524       0.439     65    83.3    78     ERRCA  
     BURIED  . . . . . . . .    2.068      0.541       0.612     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    2.169      0.581       0.647     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.131      0.519       0.478    446    87.3   511     ERRMC  
     WELL ORDERED  . . . . .    6.237      0.538       0.503    389    92.6   420     ERRMC  
     NO INTER CONTACTS . . .    3.114      0.491       0.516    237    88.8   267     ERRMC  
     SHIFTED CHAIN . . . . .    8.022      0.458       0.368    298    82.1   363     ERRMC  
     ALTERNATIVE PARENT  . .    0.593      0.096       0.055     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    7.532      0.542       0.479    304    93.8   324     ERRMC  
     LARGE SHIFTS/INSERTIONS   12.696      0.443       0.223    169    72.2   234     ERRMC  
     SURFACE . . . . . . . .    7.714      0.515       0.431    322    83.2   387     ERRMC  
     BURIED  . . . . . . . .    2.021      0.529       0.599    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    2.126      0.565       0.633    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.664      0.423       0.384    383    88.5   433     ERRSC  
     WELL ORDERED  . . . . .    6.459      0.454       0.420    232    93.5   248     ERRSC  
     NO INTER CONTACTS . . .    3.450      0.372       0.390    188    89.5   210     ERRSC  
     RELIABLE SIDE CHAINS  .    6.935      0.422       0.376    331    89.2   371     ERRSC  
     CHANGED ANGLES  . . . .    7.505      0.375       0.314    245    87.2   281     ERRSC  
     SHIFTED CHAIN . . . . .    8.332      0.376       0.288    259    83.8   309     ERRSC  
     ALTERNATIVE PARENT  . .    1.093      0.135       0.128      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .    7.959      0.420       0.354    281    94.6   297     ERRSC  
     LARGE SHIFTS/INSERTIONS   11.722      0.365       0.187    163    76.5   213     ERRSC  
     SURFACE . . . . . . . .    7.904      0.424       0.357    294    85.5   344     ERRSC  
     BURIED  . . . . . . . .    2.568      0.417       0.472     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    2.916      0.465       0.529    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.401      0.473       0.433    743    87.9   845     ERRALL 
     WELL ORDERED  . . . . .    6.324      0.507       0.472    552    93.1   593     ERRALL 
     NO INTER CONTACTS . . .    3.320      0.437       0.457    380    89.2   426     ERRALL 
     SHIFTED CHAIN . . . . .    8.176      0.419       0.330    499    83.0   601     ERRALL 
     ALTERNATIVE PARENT  . .    0.807      0.113       0.088     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .    7.739      0.481       0.416    525    94.3   557     ERRALL 
     LARGE SHIFTS/INSERTIONS   12.142      0.401       0.204    299    74.6   401     ERRALL 
     SURFACE . . . . . . . .    7.798      0.469       0.393    554    84.5   656     ERRALL 
     BURIED  . . . . . . . .    2.306      0.486       0.548    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    2.535      0.522       0.587    444   100.0   444     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)        41        55        57        62        66      90     103   DISTCA 
CA  (P)     39.81     53.40     55.34     60.19     64.08             103   DISTCA 
CA  (RMS)    0.69      0.87      0.95      1.38      2.55                   DISTCA 
 
ALL (N)       220       361       406       478       521     743     845   DISTALL 
ALL (P)     26.04     42.72     48.05     56.57     61.66             845   DISTALL 
ALL (RMS)    0.70      1.05      1.27      1.91      2.94                   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)          56            56            34          RMSLSI 
CA  (P)       54.37         54.37         33.01          RMSLSI 
CA  (RMS)      1.04          0.92         20.86          RMSLSI 
 
 
 
END of the results output 
