 
####################################################### 
#                                                     # 
#                        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/T0048.inter 
CONANA-PAIR            ../CONANA/T0048.pair 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0048.1dcp_E.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 923 atoms, MODEL 949 atoms, 922 common with TARGET 
           Number of atoms possible to evaluate: 773 
 
 
 CA-RMS TARGET<->PARENT(1dcp-E)	 1.412918 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    34.39           83.2   190    82.6   230     ARMSMC  
     WELL ORDERED  . . . . .    34.77           84.6   175    84.5   207     ARMSMC  
     NO INTER CONTACTS . . .    35.96           83.3   138    84.1   164     ARMSMC  
     SHIFTED CHAIN . . . . .    35.70           77.7   112    73.7   152     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    25.43           93.2   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    69.64           60.0    10    21.7    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    39.00           77.7   103    75.7   136     ARMSMC  
     BURIED  . . . . . . . .    27.98           89.7    87    92.6    94     ARMSMC  
     CORE  . . . . . . . . .    31.29           84.4   180    97.8   184     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    66.60           50.0    82    85.4    96     ARMSSC1 
     WELL ORDERED  . . . . .    62.69           59.1    66    89.2    74     ARMSSC1 
     NO INTER CONTACTS . . .    73.43           46.7    60    89.6    67     ARMSSC1 
     RELIABLE SIDE CHAINS  .    65.58           48.6    74    84.1    88     ARMSSC1 
     CHANGED ANGLES  . . . .    74.14           37.0    46    76.7    60     ARMSSC1 
     SHIFTED CHAIN . . . . .    68.71           37.5    48    77.4    62     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    68.56           54.0    50   100.0    50     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    33.61           75.0     4    23.5    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    66.72           43.2    44    77.2    57     ARMSSC1 
     BURIED  . . . . . . . .    66.47           57.9    38    97.4    39     ARMSSC1 
     CORE  . . . . . . . . .    67.86           48.7    78    98.7    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    63.22           48.4    64    85.3    75     ARMSSC2 
     WELL ORDERED  . . . . .    62.35           51.1    47    90.4    52     ARMSSC2 
     NO INTER CONTACTS . . .    64.23           51.1    45    90.0    50     ARMSSC2 
     RELIABLE SIDE CHAINS  .    62.62           50.0    46    85.2    54     ARMSSC2 
     CHANGED ANGLES  . . . .    72.98           36.4    44    80.0    55     ARMSSC2 
     SHIFTED CHAIN . . . . .    63.56           40.5    37    77.1    48     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    58.76           50.0    38   100.0    38     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    60.52           33.3     3    23.1    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    61.39           43.2    37    78.7    47     ARMSSC2 
     BURIED  . . . . . . . .    65.63           55.6    27    96.4    28     ARMSSC2 
     CORE  . . . . . . . . .    63.35           49.2    61    98.4    62     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    61.09           30.4    23    79.3    29     ARMSSC3 
     WELL ORDERED  . . . . .    62.18           25.0    12    92.3    13     ARMSSC3 
     NO INTER CONTACTS . . .    63.87           27.8    18    90.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    56.68           33.3    21    80.8    26     ARMSSC3 
     CHANGED ANGLES  . . . .    61.81           31.8    22    78.6    28     ARMSSC3 
     SHIFTED CHAIN . . . . .    60.05           31.2    16    72.7    22     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    61.22           23.5    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    78.11            0.0     1    14.3     7     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    60.51           29.4    17    73.9    23     ARMSSC3 
     BURIED  . . . . . . . .    62.70           33.3     6   100.0     6     ARMSSC3 
     CORE  . . . . . . . . .    60.20           31.8    22   100.0    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.17           20.0    10    76.9    13     ARMSSC4 
     WELL ORDERED  . . . . .    47.12           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    87.33           14.3     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    75.17           20.0    10    76.9    13     ARMSSC4 
     CHANGED ANGLES  . . . .    60.08           22.2     9    75.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    61.15           25.0     8    72.7    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    85.31           28.6     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     8.68          100.0     1    25.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    78.99           25.0     8    72.7    11     ARMSSC4 
     BURIED  . . . . . . . .    57.39            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    79.18           11.1     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.98489     r(1,2) =  -0.15733     r(1,3) =   0.07236 
 r(2,1) =  -0.15994     r(2,2) =   0.66626     r(2,3) =  -0.72836 
 r(3,1) =   0.06638     r(3,2) =  -0.72893     r(3,3) =  -0.68136 
THE OFFSET VECTOR: 
 v(1) =   0.64277     v(2) =  16.03871     v(3) =  34.38123 
 
 Number of iteration 36                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.25           (Number of atoms:   80) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.46         96    82.8   116     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0256                            CRMSCA  
     WELL ORDERED  . . . . .    2.47         88    83.8   105     CRMSCA  
     NO INTER CONTACTS . . .    2.44         70    85.4    82     CRMSCA  
     SHIFTED CHAIN . . . . .    2.54         57    74.0    77     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.27         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    1.10          3   100.0     3     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.60          5    20.8    24     CRMSCA  
     SURFACE . . . . . . . .    3.00         52    75.4    69     CRMSCA  
     BURIED  . . . . . . . .    1.60         44    93.6    47     CRMSCA  
     CORE  . . . . . . . . .    2.00         91    98.9    92     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.52        473    82.5   573     CRMSMC  
     WELL ORDERED  . . . . .    2.46        435    83.7   520     CRMSMC  
     NO INTER CONTACTS . . .    2.48        347    85.3   407     CRMSMC  
     SHIFTED CHAIN . . . . .    2.61        280    73.7   380     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.33        293   100.0   293     CRMSMC  
     SHIFTED SS UNITS  . . .    1.08         15   100.0    15     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.68         24    20.3   118     CRMSMC  
     SURFACE . . . . . . . .    3.10        255    74.8   341     CRMSMC  
     BURIED  . . . . . . . .    1.59        218    94.0   232     CRMSMC  
     CORE  . . . . . . . . .    2.07        449    98.7   455     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.56        390    85.0   459     CRMSSC  
     WELL ORDERED  . . . . .    3.35        305    89.7   340     CRMSSC  
     NO INTER CONTACTS . . .    3.71        289    90.6   319     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.63        324    85.0   381     CRMSSC  
     CHANGED ANGLES  . . . .    3.76        198    79.8   248     CRMSSC  
     SECONDARY STRUCTURE . .    3.10        239   100.0   239     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.50         18    22.2    81     CRMSSC  
     SURFACE . . . . . . . .    3.82        206    76.3   270     CRMSSC  
     BURIED  . . . . . . . .    3.24        184    97.4   189     CRMSSC  
     CORE  . . . . . . . . .    3.25        372    98.4   378     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.06        773    83.7   923     CRMSALL 
     WELL ORDERED  . . . . .    2.90        659    86.3   764     CRMSALL 
     NO INTER CONTACTS . . .    3.14        568    87.8   647     CRMSALL 
     SHIFTED CHAIN . . . . .    3.06        449    75.0   599     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    2.73        475   100.0   475     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.98         38    21.5   177     CRMSALL 
     SURFACE . . . . . . . .    3.44        413    75.6   546     CRMSALL 
     BURIED  . . . . . . . .    2.56        360    95.5   377     CRMSALL 
     CORE  . . . . . . . . .    2.71        735    98.5   746     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0    15       3-ALTQAHCEACRADAP-17   
 CA  LOOP  2     6.60      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     0.00      0     0.0     4     115-EGRK-118  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    75       3-ALTQAHCEACRADAP-17   
 MC  LOOP  2     6.68     24   100.0    24      38-VRDGI-42   
 MC  LOOP  3     0.00      0     0.0    19     115-EGRK-118  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0   106       3-ALTQAHCEACRADAP-17   
 ALL LOOP  2     6.98     38   100.0    38      38-VRDGI-42   
 ALL LOOP  3     0.00      0     0.0    33     115-EGRK-118  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     1.84      5   100.0     5      38-VRDGI-42   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.87     24   100.0    24      38-VRDGI-42   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     3.12     38   100.0    38      38-VRDGI-42   
 WARNING! LOOP  3 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.979      0.252       0.164     96    82.8   116     ERRCA  
     WELL ORDERED  . . . . .    0.951      0.241       0.159     88    83.8   105     ERRCA  
     NO INTER CONTACTS . . .    0.968      0.250       0.165     70    85.4    82     ERRCA  
     SHIFTED CHAIN . . . . .    1.055      0.267       0.158     57    74.0    77     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    0.815      0.221       0.164     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.199      0.687       0.344      5    20.8    24     ERRCA  
     SURFACE . . . . . . . .    1.358      0.302       0.181     52    75.4    69     ERRCA  
     BURIED  . . . . . . . .    0.530      0.192       0.143     44    93.6    47     ERRCA  
     CORE  . . . . . . . . .    0.747      0.228       0.154     91    98.9    92     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.005      0.251       0.158    473    82.5   573     ERRMC  
     WELL ORDERED  . . . . .    0.954      0.240       0.154    435    83.7   520     ERRMC  
     NO INTER CONTACTS . . .    0.985      0.248       0.157    347    85.3   407     ERRMC  
     SHIFTED CHAIN . . . . .    1.101      0.272       0.157    280    73.7   380     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    0.834      0.220       0.156    293   100.0   293     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.226      0.682       0.341     24    20.3   118     ERRMC  
     SURFACE . . . . . . . .    1.418      0.306       0.180    255    74.8   341     ERRMC  
     BURIED  . . . . . . . .    0.522      0.188       0.131    218    94.0   232     ERRMC  
     CORE  . . . . . . . . .    0.779      0.228       0.148    449    98.7   455     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.759      0.343       0.183    390    85.0   459     ERRSC  
     WELL ORDERED  . . . . .    1.621      0.326       0.177    305    89.7   340     ERRSC  
     NO INTER CONTACTS . . .    1.888      0.360       0.194    289    90.6   319     ERRSC  
     RELIABLE SIDE CHAINS  .    1.786      0.343       0.184    324    85.0   381     ERRSC  
     CHANGED ANGLES  . . . .    2.067      0.400       0.202    198    79.8   248     ERRSC  
     SHIFTED CHAIN . . . . .    1.770      0.362       0.187    222    76.3   291     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    1.484      0.316       0.173    239   100.0   239     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.197      0.619       0.309     18    22.2    81     ERRSC  
     SURFACE . . . . . . . .    1.966      0.369       0.189    206    76.3   270     ERRSC  
     BURIED  . . . . . . . .    1.527      0.314       0.176    184    97.4   189     ERRSC  
     CORE  . . . . . . . . .    1.592      0.330       0.176    372    98.4   378     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.371      0.297       0.171    773    83.7   923     ERRALL 
     WELL ORDERED  . . . . .    1.260      0.280       0.166    659    86.3   764     ERRALL 
     NO INTER CONTACTS . . .    1.425      0.303       0.176    568    87.8   647     ERRALL 
     SHIFTED CHAIN . . . . .    1.414      0.314       0.171    449    75.0   599     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.153      0.267       0.166    475   100.0   475     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.140      0.650       0.325     38    21.5   177     ERRALL 
     SURFACE . . . . . . . .    1.671      0.337       0.185    413    75.6   546     ERRALL 
     BURIED  . . . . . . . .    1.028      0.252       0.155    360    95.5   377     ERRALL 
     CORE  . . . . . . . . .    1.176      0.279       0.163    735    98.5   746     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)        31        76        85        89        96      96     116   DISTCA 
CA  (P)     26.72     65.52     73.28     76.72     82.76             116   DISTCA 
CA  (RMS)    0.73      1.18      1.40      1.59      2.46                   DISTCA 
 
ALL (N)       179       517       607       694       766     773     923   DISTALL 
ALL (P)     19.39     56.01     65.76     75.19     82.99             923   DISTALL 
ALL (RMS)    0.75      1.22      1.47      1.93      2.84                   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)          92            91             5          RMSLSI 
CA  (P)       79.31         78.45          4.31          RMSLSI 
CA  (RMS)      1.19          2.00          6.60          RMSLSI 
 
 
 
END of the results output 
