 
####################################################### 
#                                                     # 
#                        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 938 atoms, 923 common with TARGET 
           Number of atoms possible to evaluate: 800 
 
 
 CA-RMS TARGET<->PARENT(1dcp-E)	 1.412918 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    31.00           88.8   196    85.2   230     ARMSMC  
     WELL ORDERED  . . . . .    31.37           89.3   178    86.0   207     ARMSMC  
     NO INTER CONTACTS . . .    35.12           85.9   142    86.6   164     ARMSMC  
     SHIFTED CHAIN . . . . .    28.87           89.8   118    77.6   152     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    24.77           93.2   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    57.14           66.7    12    26.1    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    36.86           88.9   108    79.4   136     ARMSMC  
     BURIED  . . . . . . . .    21.76           88.6    88    93.6    94     ARMSMC  
     CORE  . . . . . . . . .    28.48           90.2   184   100.0   184     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.19           50.6    85    88.5    96     ARMSSC1 
     WELL ORDERED  . . . . .    73.14           57.4    68    91.9    74     ARMSSC1 
     NO INTER CONTACTS . . .    81.09           48.4    62    92.5    67     ARMSSC1 
     RELIABLE SIDE CHAINS  .    74.76           53.2    77    87.5    88     ARMSSC1 
     CHANGED ANGLES  . . . .    85.70           38.8    49    81.7    60     ARMSSC1 
     SHIFTED CHAIN . . . . .    81.05           45.1    51    82.3    62     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    76.21           52.0    50   100.0    50     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    55.25           66.7     6    35.3    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    77.65           46.8    47    82.5    57     ARMSSC1 
     BURIED  . . . . . . . .    76.62           55.3    38    97.4    39     ARMSSC1 
     CORE  . . . . . . . . .    78.61           49.4    79   100.0    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.19           53.7    67    89.3    75     ARMSSC2 
     WELL ORDERED  . . . . .    69.87           57.1    49    94.2    52     ARMSSC2 
     NO INTER CONTACTS . . .    71.38           48.9    47    94.0    50     ARMSSC2 
     RELIABLE SIDE CHAINS  .    73.85           56.2    48    88.9    54     ARMSSC2 
     CHANGED ANGLES  . . . .    80.27           46.8    47    85.5    55     ARMSSC2 
     SHIFTED CHAIN . . . . .    78.92           45.0    40    83.3    48     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    78.18           55.3    38   100.0    38     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    50.41           60.0     5    38.5    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    80.17           50.0    40    85.1    47     ARMSSC2 
     BURIED  . . . . . . . .    67.15           59.3    27    96.4    28     ARMSSC2 
     CORE  . . . . . . . . .    76.84           53.2    62   100.0    62     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    92.14           41.7    24    82.8    29     ARMSSC3 
     WELL ORDERED  . . . . .    90.63           41.7    12    92.3    13     ARMSSC3 
     NO INTER CONTACTS . . .    83.03           52.6    19    95.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    83.76           45.5    22    84.6    26     ARMSSC3 
     CHANGED ANGLES  . . . .    92.65           43.5    23    82.1    28     ARMSSC3 
     SHIFTED CHAIN . . . . .    95.34           41.2    17    77.3    22     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    87.01           47.1    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    61.23           50.0     2    28.6     7     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    90.35           44.4    18    78.3    23     ARMSSC3 
     BURIED  . . . . . . . .    97.30           33.3     6   100.0     6     ARMSSC3 
     CORE  . . . . . . . . .    94.44           40.9    22   100.0    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.90           50.0    10    76.9    13     ARMSSC4 
     WELL ORDERED  . . . . .    46.42           66.7     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    71.20           42.9     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    73.90           50.0    10    76.9    13     ARMSSC4 
     CHANGED ANGLES  . . . .    77.89           44.4     9    75.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    82.56           37.5     8    72.7    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    78.60           42.9     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    79.95            0.0     1    25.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    82.56           37.5     8    72.7    11     ARMSSC4 
     BURIED  . . . . . . . .     5.99          100.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    73.19           55.6     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.42967     r(1,2) =  -0.75950     r(1,3) =   0.48841 
 r(2,1) =  -0.77344     r(2,2) =  -0.03041     r(2,3) =   0.63314 
 r(3,1) =  -0.46601     r(3,2) =  -0.64980     r(3,3) =  -0.60050 
THE OFFSET VECTOR: 
 v(1) =  -1.28761     v(2) =   1.36649     v(3) = 111.56172 
 
 Number of iteration 29                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.18           (Number of atoms:   87) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.49         99    85.3   116     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0252                            CRMSCA  
     WELL ORDERED  . . . . .    2.54         90    85.7   105     CRMSCA  
     NO INTER CONTACTS . . .    2.46         72    87.8    82     CRMSCA  
     SHIFTED CHAIN . . . . .    2.60         60    77.9    77     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.36         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    1.45          3   100.0     3     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.36          7    29.2    24     CRMSCA  
     SURFACE . . . . . . . .    3.07         55    79.7    69     CRMSCA  
     BURIED  . . . . . . . .    1.49         44    93.6    47     CRMSCA  
     CORE  . . . . . . . . .    1.90         92   100.0    92     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.56        489    85.3   573     CRMSMC  
     WELL ORDERED  . . . . .    2.51        445    85.6   520     CRMSMC  
     NO INTER CONTACTS . . .    2.54        358    88.0   407     CRMSMC  
     SHIFTED CHAIN . . . . .    2.67        296    77.9   380     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.42        293   100.0   293     CRMSMC  
     SHIFTED SS UNITS  . . .    1.43         15   100.0    15     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.53         34    28.8   118     CRMSMC  
     SURFACE . . . . . . . .    3.16        271    79.5   341     CRMSMC  
     BURIED  . . . . . . . .    1.51        218    94.0   232     CRMSMC  
     CORE  . . . . . . . . .    1.96        455   100.0   455     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.80        404    88.0   459     CRMSSC  
     WELL ORDERED  . . . . .    3.33        311    91.5   340     CRMSSC  
     NO INTER CONTACTS . . .    3.94        297    93.1   319     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.95        334    87.7   381     CRMSSC  
     CHANGED ANGLES  . . . .    4.30        209    84.3   248     CRMSSC  
     SECONDARY STRUCTURE . .    3.41        239   100.0   239     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.93         26    32.1    81     CRMSSC  
     SURFACE . . . . . . . .    4.35        220    81.5   270     CRMSSC  
     BURIED  . . . . . . . .    3.01        184    97.4   189     CRMSSC  
     CORE  . . . . . . . . .    3.34        378   100.0   378     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.22        800    86.7   923     CRMSALL 
     WELL ORDERED  . . . . .    2.92        673    88.1   764     CRMSALL 
     NO INTER CONTACTS . . .    3.29        585    90.4   647     CRMSALL 
     SHIFTED CHAIN . . . . .    3.35        476    79.5   599     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    2.95        475   100.0   475     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.15         54    30.5   177     CRMSALL 
     SURFACE . . . . . . . .    3.76        440    80.6   546     CRMSALL 
     BURIED  . . . . . . . .    2.39        360    95.5   377     CRMSALL 
     CORE  . . . . . . . . .    2.72        746   100.0   746     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.64      1     6.7    15       3-ALTQAHCEACRADAP-17   
 CA  LOOP  2     7.09      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     5.01      1    25.0     4     115-EGRK-118  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.47      5     6.7    75       3-ALTQAHCEACRADAP-17   
 MC  LOOP  2     7.16     24   100.0    24      38-VRDGI-42   
 MC  LOOP  3     6.14      5    26.3    19     115-EGRK-118  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.59      7     6.6   106       3-ALTQAHCEACRADAP-17   
 ALL LOOP  2     7.61     38   100.0    38      38-VRDGI-42   
 ALL LOOP  3     7.56      9    27.3    33     115-EGRK-118  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     1.49      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     1.68     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     3.15     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 . . . . . . . . . .    1.235      0.414       0.211     99    85.3   116     ERRCA  
     WELL ORDERED  . . . . .    1.251      0.414       0.211     90    85.7   105     ERRCA  
     NO INTER CONTACTS . . .    1.197      0.405       0.207     72    87.8    82     ERRCA  
     SHIFTED CHAIN . . . . .    1.427      0.492       0.246     60    77.9    77     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.105      0.382       0.197     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.402      0.818       0.409      7    29.2    24     ERRCA  
     SURFACE . . . . . . . .    1.677      0.479       0.244     55    79.7    69     ERRCA  
     BURIED  . . . . . . . .    0.682      0.334       0.169     44    93.6    47     ERRCA  
     CORE  . . . . . . . . .    0.918      0.384       0.196     92   100.0    92     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.270      0.421       0.215    489    85.3   573     ERRMC  
     WELL ORDERED  . . . . .    1.246      0.416       0.213    445    85.6   520     ERRMC  
     NO INTER CONTACTS . . .    1.240      0.412       0.212    358    88.0   407     ERRMC  
     SHIFTED CHAIN . . . . .    1.449      0.486       0.243    296    77.9   380     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.137      0.388       0.200    293   100.0   293     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.515      0.814       0.407     34    28.8   118     ERRMC  
     SURFACE . . . . . . . .    1.733      0.486       0.249    271    79.5   341     ERRMC  
     BURIED  . . . . . . . .    0.694      0.339       0.172    218    94.0   232     ERRMC  
     CORE  . . . . . . . . .    0.952      0.391       0.201    455   100.0   455     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.345      0.565       0.290    404    88.0   459     ERRSC  
     WELL ORDERED  . . . . .    2.017      0.536       0.277    311    91.5   340     ERRSC  
     NO INTER CONTACTS . . .    2.412      0.563       0.291    297    93.1   319     ERRSC  
     RELIABLE SIDE CHAINS  .    2.434      0.565       0.289    334    87.7   381     ERRSC  
     CHANGED ANGLES  . . . .    2.952      0.646       0.326    209    84.3   248     ERRSC  
     SHIFTED CHAIN . . . . .    2.600      0.621       0.310    236    81.1   291     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    2.143      0.549       0.281    239   100.0   239     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.135      0.781       0.390     26    32.1    81     ERRSC  
     SURFACE . . . . . . . .    2.884      0.636       0.321    220    81.5   270     ERRSC  
     BURIED  . . . . . . . .    1.701      0.481       0.252    184    97.4   189     ERRSC  
     CORE  . . . . . . . . .    2.085      0.551       0.283    378   100.0   378     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.794      0.490       0.250    800    86.7   923     ERRALL 
     WELL ORDERED  . . . . .    1.596      0.468       0.240    673    88.1   764     ERRALL 
     NO INTER CONTACTS . . .    1.813      0.485       0.249    585    90.4   647     ERRALL 
     SHIFTED CHAIN . . . . .    1.998      0.550       0.275    476    79.5   599     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.630      0.464       0.237    475   100.0   475     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.748      0.797       0.399     54    30.5   177     ERRALL 
     SURFACE . . . . . . . .    2.277      0.555       0.281    440    80.6   546     ERRALL 
     BURIED  . . . . . . . .    1.203      0.411       0.212    360    95.5   377     ERRALL 
     CORE  . . . . . . . . .    1.507      0.468       0.239    746   100.0   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)        34        85        88        90        98      99     116   DISTCA 
CA  (P)     29.31     73.28     75.86     77.59     84.48             116   DISTCA 
CA  (RMS)    0.75      1.15      1.21      1.35      2.29                   DISTCA 
 
ALL (N)       222       551       628       701       792     800     923   DISTALL 
ALL (P)     24.05     59.70     68.04     75.95     85.81             923   DISTALL 
ALL (RMS)    0.76      1.18      1.40      1.83      2.97                   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            92             7          RMSLSI 
CA  (P)       79.31         79.31          6.03          RMSLSI 
CA  (RMS)      1.19          1.90          6.36          RMSLSI 
 
 
 
END of the results output 
