 
####################################################### 
#                                                     # 
#                        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 939 atoms, 923 common with TARGET 
           Number of atoms possible to evaluate: 829 
 
 
 CA-RMS TARGET<->PARENT(1dcp-E)	 1.412918 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    41.71           78.9   204    88.7   230     ARMSMC  
     WELL ORDERED  . . . . .    41.29           81.4   183    88.4   207     ARMSMC  
     NO INTER CONTACTS . . .    43.01           81.0   147    89.6   164     ARMSMC  
     SHIFTED CHAIN . . . . .    42.22           75.4   126    82.9   152     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    29.90           88.1   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    74.93           45.0    20    43.5    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    46.41           71.7   113    83.1   136     ARMSMC  
     BURIED  . . . . . . . .    34.99           87.9    91    96.8    94     ARMSMC  
     CORE  . . . . . . . . .    36.31           82.6   184   100.0   184     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.14           49.4    87    90.6    96     ARMSSC1 
     WELL ORDERED  . . . . .    74.81           52.9    68    91.9    74     ARMSSC1 
     NO INTER CONTACTS . . .    76.67           51.6    62    92.5    67     ARMSSC1 
     RELIABLE SIDE CHAINS  .    78.36           49.4    79    89.8    88     ARMSSC1 
     CHANGED ANGLES  . . . .    85.08           41.2    51    85.0    60     ARMSSC1 
     SHIFTED CHAIN . . . . .    82.88           43.4    53    85.5    62     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    77.34           48.0    50   100.0    50     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   101.54           25.0     8    47.1    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    87.45           38.8    49    86.0    57     ARMSSC1 
     BURIED  . . . . . . . .    66.93           63.2    38    97.4    39     ARMSSC1 
     CORE  . . . . . . . . .    76.51           51.9    79   100.0    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.27           42.0    69    92.0    75     ARMSSC2 
     WELL ORDERED  . . . . .    83.36           42.9    49    94.2    52     ARMSSC2 
     NO INTER CONTACTS . . .    76.02           42.6    47    94.0    50     ARMSSC2 
     RELIABLE SIDE CHAINS  .    79.78           44.0    50    92.6    54     ARMSSC2 
     CHANGED ANGLES  . . . .    88.13           32.7    49    89.1    55     ARMSSC2 
     SHIFTED CHAIN . . . . .    83.56           38.1    42    87.5    48     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    86.11           42.1    38   100.0    38     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    81.89           42.9     7    53.8    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    86.98           38.1    42    89.4    47     ARMSSC2 
     BURIED  . . . . . . . .    71.47           48.1    27    96.4    28     ARMSSC2 
     CORE  . . . . . . . . .    81.20           41.9    62   100.0    62     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.30           34.6    26    89.7    29     ARMSSC3 
     WELL ORDERED  . . . . .    76.10           33.3    12    92.3    13     ARMSSC3 
     NO INTER CONTACTS . . .    71.91           36.8    19    95.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    76.93           33.3    24    92.3    26     ARMSSC3 
     CHANGED ANGLES  . . . .    73.77           36.0    25    89.3    28     ARMSSC3 
     SHIFTED CHAIN . . . . .    69.26           36.8    19    86.4    22     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    75.15           35.3    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    22.85           75.0     4    57.1     7     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    75.00           30.0    20    87.0    23     ARMSSC3 
     BURIED  . . . . . . . .    71.92           50.0     6   100.0     6     ARMSSC3 
     CORE  . . . . . . . . .    80.19           27.3    22   100.0    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.48           41.7    12    92.3    13     ARMSSC4 
     WELL ORDERED  . . . . .    24.01           66.7     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    74.50           42.9     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    74.48           41.7    12    92.3    13     ARMSSC4 
     CHANGED ANGLES  . . . .    77.79           36.4    11    91.7    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    81.56           30.0    10    90.9    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    64.69           57.1     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    85.89            0.0     3    75.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    81.55           30.0    10    90.9    11     ARMSSC4 
     BURIED  . . . . . . . .     5.48          100.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    70.27           55.6     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.66563     r(1,2) =   0.32878     r(1,3) =  -0.66996 
 r(2,1) =   0.33419     r(2,2) =  -0.67137     r(2,3) =  -0.66150 
 r(3,1) =  -0.66728     r(3,2) =  -0.66420     r(3,3) =   0.33701 
THE OFFSET VECTOR: 
 v(1) =  46.23341     v(2) =  53.66996     v(3) =  71.62515 
 
 Number of iteration 35                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.28           (Number of atoms:   88) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.90        103    88.8   116     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0282                            CRMSCA  
     WELL ORDERED  . . . . .    2.81         93    88.6   105     CRMSCA  
     NO INTER CONTACTS . . .    2.62         74    90.2    82     CRMSCA  
     SHIFTED CHAIN . . . . .    3.19         64    83.1    77     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.43         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    1.44          3   100.0     3     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.88         11    45.8    24     CRMSCA  
     SURFACE . . . . . . . .    3.51         57    82.6    69     CRMSCA  
     BURIED  . . . . . . . .    1.89         46    97.9    47     CRMSCA  
     CORE  . . . . . . . . .    1.94         92   100.0    92     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.99        508    88.7   573     CRMSMC  
     WELL ORDERED  . . . . .    2.84        459    88.3   520     CRMSMC  
     NO INTER CONTACTS . . .    2.72        367    90.2   407     CRMSMC  
     SHIFTED CHAIN . . . . .    3.30        315    82.9   380     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.52        293   100.0   293     CRMSMC  
     SHIFTED SS UNITS  . . .    1.43         15   100.0    15     CRMSMC  
     LARGE SHIFTS/INSERTIONS    7.11         53    44.9   118     CRMSMC  
     SURFACE . . . . . . . .    3.62        281    82.4   341     CRMSMC  
     BURIED  . . . . . . . .    1.95        227    97.8   232     CRMSMC  
     CORE  . . . . . . . . .    2.03        455   100.0   455     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.31        417    90.8   459     CRMSSC  
     WELL ORDERED  . . . . .    3.67        313    92.1   340     CRMSSC  
     NO INTER CONTACTS . . .    3.94        298    93.4   319     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.53        347    91.1   381     CRMSSC  
     CHANGED ANGLES  . . . .    4.84        219    88.3   248     CRMSSC  
     SECONDARY STRUCTURE . .    3.49        239   100.0   239     CRMSSC  
     LARGE SHIFTS/INSERTIONS   10.11         39    48.1    81     CRMSSC  
     SURFACE . . . . . . . .    5.12        232    85.9   270     CRMSSC  
     BURIED  . . . . . . . .    2.99        185    97.9   189     CRMSSC  
     CORE  . . . . . . . . .    3.15        378   100.0   378     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.69        829    89.8   923     CRMSALL 
     WELL ORDERED  . . . . .    3.25        687    89.9   764     CRMSALL 
     NO INTER CONTACTS . . .    3.36        594    91.8   647     CRMSALL 
     SHIFTED CHAIN . . . . .    4.02        505    84.3   599     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    3.04        475   100.0   475     CRMSALL 
     LARGE SHIFTS/INSERTIONS    8.57         83    46.9   177     CRMSALL 
     SURFACE . . . . . . . .    4.40        460    84.2   546     CRMSALL 
     BURIED  . . . . . . . .    2.53        369    97.9   377     CRMSALL 
     CORE  . . . . . . . . .    2.64        746   100.0   746     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.82      2    13.3    15       3-ALTQAHCEACRADAP-17   
 CA  LOOP  2     7.41      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     7.58      4   100.0     4     115-EGRK-118  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.19     10    13.3    75       3-ALTQAHCEACRADAP-17   
 MC  LOOP  2     7.54     24   100.0    24      38-VRDGI-42   
 MC  LOOP  3     7.97     19   100.0    19     115-EGRK-118  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.23     12    11.3   106       3-ALTQAHCEACRADAP-17   
 ALL LOOP  2     8.52     38   100.0    38      38-VRDGI-42   
 ALL LOOP  3     9.86     33   100.0    33     115-EGRK-118  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     1.55      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     0.64      4   100.0     4     115-EGRK-118  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     1.85     24   100.0    24      38-VRDGI-42   
 MC  LOOP  3     1.95     19   100.0    19     115-EGRK-118  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     3.77     38   100.0    38      38-VRDGI-42   
 ALL LOOP  3     2.94     33   100.0    33     115-EGRK-118  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.572      0.526       0.264    103    88.8   116     ERRCA  
     WELL ORDERED  . . . . .    1.502      0.511       0.257     93    88.6   105     ERRCA  
     NO INTER CONTACTS . . .    1.410      0.509       0.255     74    90.2    82     ERRCA  
     SHIFTED CHAIN . . . . .    1.863      0.586       0.293     64    83.1    77     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.232      0.480       0.241     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.867      0.837       0.418     11    45.8    24     ERRCA  
     SURFACE . . . . . . . .    2.027      0.561       0.281     57    82.6    69     ERRCA  
     BURIED  . . . . . . . .    1.007      0.482       0.243     46    97.9    47     ERRCA  
     CORE  . . . . . . . . .    1.058      0.489       0.245     92   100.0    92     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.628      0.532       0.268    508    88.7   573     ERRMC  
     WELL ORDERED  . . . . .    1.530      0.517       0.261    459    88.3   520     ERRMC  
     NO INTER CONTACTS . . .    1.465      0.513       0.259    367    90.2   407     ERRMC  
     SHIFTED CHAIN . . . . .    1.921      0.588       0.295    315    82.9   380     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.283      0.484       0.242    293   100.0   293     ERRMC  
     LARGE SHIFTS/INSERTIONS    6.027      0.825       0.413     53    44.9   118     ERRMC  
     SURFACE . . . . . . . .    2.123      0.574       0.289    281    82.4   341     ERRMC  
     BURIED  . . . . . . . .    1.015      0.479       0.243    227    97.8   232     ERRMC  
     CORE  . . . . . . . . .    1.115      0.497       0.252    455   100.0   455     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.647      0.628       0.315    417    90.8   459     ERRSC  
     WELL ORDERED  . . . . .    2.264      0.609       0.306    313    92.1   340     ERRSC  
     NO INTER CONTACTS . . .    2.429      0.611       0.307    298    93.4   319     ERRSC  
     RELIABLE SIDE CHAINS  .    2.768      0.621       0.312    347    91.1   381     ERRSC  
     CHANGED ANGLES  . . . .    3.151      0.660       0.330    219    88.3   248     ERRSC  
     SHIFTED CHAIN . . . . .    2.976      0.664       0.333    249    85.6   291     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    2.198      0.607       0.303    239   100.0   239     ERRSC  
     LARGE SHIFTS/INSERTIONS    8.921      0.877       0.438     39    48.1    81     ERRSC  
     SURFACE . . . . . . . .    3.402      0.686       0.344    232    85.9   270     ERRSC  
     BURIED  . . . . . . . .    1.699      0.556       0.280    185    97.9   189     ERRSC  
     CORE  . . . . . . . . .    1.999      0.603       0.303    378   100.0   378     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.119      0.578       0.291    829    89.8   923     ERRALL 
     WELL ORDERED  . . . . .    1.857      0.557       0.281    687    89.9   764     ERRALL 
     NO INTER CONTACTS . . .    1.926      0.560       0.281    594    91.8   647     ERRALL 
     SHIFTED CHAIN . . . . .    2.413      0.622       0.312    505    84.3   599     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.727      0.544       0.272    475   100.0   475     ERRALL 
     LARGE SHIFTS/INSERTIONS    7.281      0.846       0.423     83    46.9   177     ERRALL 
     SURFACE . . . . . . . .    2.730      0.627       0.315    460    84.2   546     ERRALL 
     BURIED  . . . . . . . .    1.357      0.517       0.261    369    97.9   377     ERRALL 
     CORE  . . . . . . . . .    1.545      0.549       0.276    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        92       102     103     116   DISTCA 
CA  (P)     30.17     70.69     75.86     79.31     87.93             116   DISTCA 
CA  (RMS)    0.77      1.19      1.28      1.50      2.73                   DISTCA 
 
ALL (N)       214       545       633       716       805     829     923   DISTALL 
ALL (P)     23.19     59.05     68.58     77.57     87.22             923   DISTALL 
ALL (RMS)    0.78      1.24      1.46      1.89      3.06                   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            11          RMSLSI 
CA  (P)       79.31         79.31          9.48          RMSLSI 
CA  (RMS)      1.19          1.94          6.88          RMSLSI 
 
 
 
END of the results output 
