 
####################################################### 
#                                                     # 
#                        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: 793 
 
 
 CA-RMS TARGET<->PARENT(1dcp-E)	 1.412918 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    35.07           87.6   194    84.3   230     ARMSMC  
     WELL ORDERED  . . . . .    36.35           88.1   176    85.0   207     ARMSMC  
     NO INTER CONTACTS . . .    34.74           87.9   141    86.0   164     ARMSMC  
     SHIFTED CHAIN . . . . .    36.38           85.3   116    76.3   152     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    25.58           92.4   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    71.96           54.5    11    23.9    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    40.94           83.0   106    77.9   136     ARMSMC  
     BURIED  . . . . . . . .    26.30           93.2    88    93.6    94     ARMSMC  
     CORE  . . . . . . . . .    31.50           89.6   183    99.5   184     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.67           57.1    84    87.5    96     ARMSSC1 
     WELL ORDERED  . . . . .    72.13           61.2    67    90.5    74     ARMSSC1 
     NO INTER CONTACTS . . .    80.35           54.1    61    91.0    67     ARMSSC1 
     RELIABLE SIDE CHAINS  .    75.82           55.3    76    86.4    88     ARMSSC1 
     CHANGED ANGLES  . . . .    84.01           45.8    48    80.0    60     ARMSSC1 
     SHIFTED CHAIN . . . . .    75.61           54.0    50    80.6    62     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    76.82           56.0    50   100.0    50     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    29.18           80.0     5    29.4    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    73.52           52.2    46    80.7    57     ARMSSC1 
     BURIED  . . . . . . . .    76.04           63.2    38    97.4    39     ARMSSC1 
     CORE  . . . . . . . . .    76.65           55.7    79   100.0    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    72.31           60.6    66    88.0    75     ARMSSC2 
     WELL ORDERED  . . . . .    74.22           62.5    48    92.3    52     ARMSSC2 
     NO INTER CONTACTS . . .    73.54           60.9    46    92.0    50     ARMSSC2 
     RELIABLE SIDE CHAINS  .    65.39           66.0    47    87.0    54     ARMSSC2 
     CHANGED ANGLES  . . . .    84.47           50.0    46    83.6    55     ARMSSC2 
     SHIFTED CHAIN . . . . .    79.77           51.3    39    81.2    48     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    74.83           63.2    38   100.0    38     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    94.15           50.0     4    30.8    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    73.96           59.0    39    83.0    47     ARMSSC2 
     BURIED  . . . . . . . .    69.85           63.0    27    96.4    28     ARMSSC2 
     CORE  . . . . . . . . .    70.67           61.3    62   100.0    62     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.79           37.5    24    82.8    29     ARMSSC3 
     WELL ORDERED  . . . . .    66.42           50.0    12    92.3    13     ARMSSC3 
     NO INTER CONTACTS . . .    64.13           47.4    19    95.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    71.65           31.8    22    84.6    26     ARMSSC3 
     CHANGED ANGLES  . . . .    69.68           39.1    23    82.1    28     ARMSSC3 
     SHIFTED CHAIN . . . . .    67.73           35.3    17    77.3    22     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    70.61           35.3    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    20.22          100.0     2    28.6     7     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    66.86           33.3    18    78.3    23     ARMSSC3 
     BURIED  . . . . . . . .    74.26           50.0     6   100.0     6     ARMSSC3 
     CORE  . . . . . . . . .    71.59           31.8    22   100.0    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.04           50.0    10    76.9    13     ARMSSC4 
     WELL ORDERED  . . . . .    67.96           33.3     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    64.99           57.1     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    79.04           50.0    10    76.9    13     ARMSSC4 
     CHANGED ANGLES  . . . .    83.31           44.4     9    75.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    88.33           37.5     8    72.7    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    64.97           57.1     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    80.84            0.0     1    25.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    83.03           50.0     8    72.7    11     ARMSSC4 
     BURIED  . . . . . . . .    60.50           50.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    78.84           55.6     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.84564     r(1,2) =   0.09467     r(1,3) =  -0.52529 
 r(2,1) =   0.49090     r(2,2) =  -0.24843     r(2,3) =  -0.83504 
 r(3,1) =  -0.20956     r(3,2) =  -0.96401     r(3,3) =   0.16361 
THE OFFSET VECTOR: 
 v(1) =  50.43816     v(2) =  42.38695     v(3) =  66.31746 
 
 Number of iteration 34                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.29           (Number of atoms:   88) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.44         98    84.5   116     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0249                            CRMSCA  
     WELL ORDERED  . . . . .    2.48         89    84.8   105     CRMSCA  
     NO INTER CONTACTS . . .    2.39         71    86.6    82     CRMSCA  
     SHIFTED CHAIN . . . . .    2.53         59    76.6    77     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.36         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    1.44          3   100.0     3     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.35          6    25.0    24     CRMSCA  
     SURFACE . . . . . . . .    3.01         54    78.3    69     CRMSCA  
     BURIED  . . . . . . . .    1.44         44    93.6    47     CRMSCA  
     CORE  . . . . . . . . .    1.92         92   100.0    92     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.49        484    84.5   573     CRMSMC  
     WELL ORDERED  . . . . .    2.48        440    84.6   520     CRMSMC  
     NO INTER CONTACTS . . .    2.42        353    86.7   407     CRMSMC  
     SHIFTED CHAIN . . . . .    2.60        291    76.6   380     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.42        293   100.0   293     CRMSMC  
     SHIFTED SS UNITS  . . .    1.44         15   100.0    15     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.42         29    24.6   118     CRMSMC  
     SURFACE . . . . . . . .    3.09        266    78.0   341     CRMSMC  
     BURIED  . . . . . . . .    1.46        218    94.0   232     CRMSMC  
     CORE  . . . . . . . . .    1.99        455   100.0   455     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.63        401    87.4   459     CRMSSC  
     WELL ORDERED  . . . . .    3.43        308    90.6   340     CRMSSC  
     NO INTER CONTACTS . . .    3.77        294    92.2   319     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.76        331    86.9   381     CRMSSC  
     CHANGED ANGLES  . . . .    3.78        207    83.5   248     CRMSSC  
     SECONDARY STRUCTURE . .    3.22        239   100.0   239     CRMSSC  
     LARGE SHIFTS/INSERTIONS    7.54         23    28.4    81     CRMSSC  
     SURFACE . . . . . . . .    3.97        217    80.4   270     CRMSSC  
     BURIED  . . . . . . . .    3.18        184    97.4   189     CRMSSC  
     CORE  . . . . . . . . .    3.24        378   100.0   378     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.09        793    85.9   923     CRMSALL 
     WELL ORDERED  . . . . .    2.95        666    87.2   764     CRMSALL 
     NO INTER CONTACTS . . .    3.15        578    89.3   647     CRMSALL 
     SHIFTED CHAIN . . . . .    3.13        469    78.3   599     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    2.84        475   100.0   475     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.92         47    26.6   177     CRMSALL 
     SURFACE . . . . . . . .    3.52        433    79.3   546     CRMSALL 
     BURIED  . . . . . . . .    2.48        360    95.5   377     CRMSALL 
     CORE  . . . . . . . . .    2.68        746   100.0   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     6.76      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     3.61      1    25.0     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     6.83     24   100.0    24      38-VRDGI-42   
 MC  LOOP  3     3.85      5    26.3    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     7.41     38   100.0    38      38-VRDGI-42   
 ALL LOOP  3     4.20      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     1.82      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     1.86     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     2.66     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 . . . . . . . . . .   20.277      0.772       0.793     98    84.5   116     ERRCA  
     WELL ORDERED  . . . . .   16.818      0.756       0.779     89    84.8   105     ERRCA  
     NO INTER CONTACTS . . .   20.838      0.794       0.813     71    86.6    82     ERRCA  
     SHIFTED CHAIN . . . . .   25.026      0.762       0.782     59    76.6    77     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .   10.874      0.705       0.732     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS   33.285      0.683       0.732      6    25.0    24     ERRCA  
     SURFACE . . . . . . . .   24.901      0.744       0.767     54    78.3    69     ERRCA  
     BURIED  . . . . . . . .   14.603      0.806       0.825     44    93.6    47     ERRCA  
     CORE  . . . . . . . . .   19.429      0.778       0.797     92   100.0    92     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   22.207      0.796       0.810    484    84.5   573     ERRMC  
     WELL ORDERED  . . . . .   18.843      0.783       0.799    440    84.6   520     ERRMC  
     NO INTER CONTACTS . . .   22.825      0.811       0.823    353    86.7   407     ERRMC  
     SHIFTED CHAIN . . . . .   26.525      0.783       0.799    291    76.6   380     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .   13.413      0.744       0.761    293   100.0   293     ERRMC  
     LARGE SHIFTS/INSERTIONS   35.846      0.704       0.748     29    24.6   118     ERRMC  
     SURFACE . . . . . . . .   26.536      0.780       0.795    266    78.0   341     ERRMC  
     BURIED  . . . . . . . .   16.925      0.815       0.829    218    94.0   232     ERRMC  
     CORE  . . . . . . . . .   21.338      0.802       0.814    455   100.0   455     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   18.082      0.872       0.667    401    87.4   459     ERRSC  
     WELL ORDERED  . . . . .   13.995      0.849       0.667    308    90.6   340     ERRSC  
     NO INTER CONTACTS . . .   18.328      0.882       0.657    294    92.2   319     ERRSC  
     RELIABLE SIDE CHAINS  .   18.826      0.871       0.676    331    86.9   381     ERRSC  
     CHANGED ANGLES  . . . .   15.531      0.924       0.592    207    83.5   248     ERRSC  
     SHIFTED CHAIN . . . . .   21.356      0.872       0.657    233    80.1   291     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .   12.405      0.831       0.637    239   100.0   239     ERRSC  
     LARGE SHIFTS/INSERTIONS   19.321      0.902       0.591     23    28.4    81     ERRSC  
     SURFACE . . . . . . . .   24.386      0.881       0.680    217    80.4   270     ERRSC  
     BURIED  . . . . . . . .   10.648      0.862       0.652    184    97.4   189     ERRSC  
     CORE  . . . . . . . . .   18.007      0.870       0.672    378   100.0   378     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   20.061      0.837       0.741    793    85.9   923     ERRALL 
     WELL ORDERED  . . . . .   16.628      0.816       0.741    666    87.2   764     ERRALL 
     NO INTER CONTACTS . . .   20.521      0.850       0.742    578    89.3   647     ERRALL 
     SHIFTED CHAIN . . . . .   23.886      0.832       0.733    469    78.3   599     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .   12.865      0.790       0.702    475   100.0   475     ERRALL 
     LARGE SHIFTS/INSERTIONS   27.305      0.801       0.671     47    26.6   177     ERRALL 
     SURFACE . . . . . . . .   25.236      0.832       0.740    433    79.3   546     ERRALL 
     BURIED  . . . . . . . .   13.838      0.843       0.743    360    95.5   377     ERRALL 
     CORE  . . . . . . . . .   19.605      0.839       0.746    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)        35        82        88        91        98      98     116   DISTCA 
CA  (P)     30.17     70.69     75.86     78.45     84.48             116   DISTCA 
CA  (RMS)    0.79      1.20      1.29      1.49      2.44                   DISTCA 
 
ALL (N)       213       537       636       711       784     793     923   DISTALL 
ALL (P)     23.08     58.18     68.91     77.03     84.94             923   DISTALL 
ALL (RMS)    0.78      1.20      1.46      1.88      2.80                   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             6          RMSLSI 
CA  (P)       79.31         79.31          5.17          RMSLSI 
CA  (RMS)      1.19          1.92          6.35          RMSLSI 
 
 
 
END of the results output 
