 
####################################################### 
#                                                     # 
#                        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 1718 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 . . . . . . . . . .    42.89           84.2   196    85.2   230     ARMSMC  
     WELL ORDERED  . . . . .    44.31           83.7   178    86.0   207     ARMSMC  
     NO INTER CONTACTS . . .    39.96           85.9   142    86.6   164     ARMSMC  
     SHIFTED CHAIN . . . . .    47.34           82.2   118    77.6   152     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    37.31           85.6   118   100.0   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS   101.60           25.0    12    26.1    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    49.61           80.6   108    79.4   136     ARMSMC  
     BURIED  . . . . . . . .    32.81           88.6    88    93.6    94     ARMSMC  
     CORE  . . . . . . . . .    35.86           88.0   184   100.0   184     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.13           44.7    85    88.5    96     ARMSSC1 
     WELL ORDERED  . . . . .    89.39           42.6    68    91.9    74     ARMSSC1 
     NO INTER CONTACTS . . .    86.86           43.5    62    92.5    67     ARMSSC1 
     RELIABLE SIDE CHAINS  .    84.39           44.2    77    87.5    88     ARMSSC1 
     CHANGED ANGLES  . . . .    88.25           40.8    49    81.7    60     ARMSSC1 
     SHIFTED CHAIN . . . . .    87.30           41.2    51    82.3    62     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    94.38           34.0    50   100.0    50     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    53.61           66.7     6    35.3    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    83.25           42.6    47    82.5    57     ARMSSC1 
     BURIED  . . . . . . . .    87.40           47.4    38    97.4    39     ARMSSC1 
     CORE  . . . . . . . . .    87.06           43.0    79   100.0    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    70.56           55.2    67    89.3    75     ARMSSC2 
     WELL ORDERED  . . . . .    64.61           57.1    49    94.2    52     ARMSSC2 
     NO INTER CONTACTS . . .    68.34           57.4    47    94.0    50     ARMSSC2 
     RELIABLE SIDE CHAINS  .    65.48           62.5    48    88.9    54     ARMSSC2 
     CHANGED ANGLES  . . . .    73.81           51.1    47    85.5    55     ARMSSC2 
     SHIFTED CHAIN . . . . .    71.67           52.5    40    83.3    48     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    68.12           55.3    38   100.0    38     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    65.29           40.0     5    38.5    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    76.27           47.5    40    85.1    47     ARMSSC2 
     BURIED  . . . . . . . .    61.13           66.7    27    96.4    28     ARMSSC2 
     CORE  . . . . . . . . .    70.97           56.5    62   100.0    62     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.62           37.5    24    82.8    29     ARMSSC3 
     WELL ORDERED  . . . . .    79.25           41.7    12    92.3    13     ARMSSC3 
     NO INTER CONTACTS . . .    63.53           42.1    19    95.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    71.28           36.4    22    84.6    26     ARMSSC3 
     CHANGED ANGLES  . . . .    69.87           34.8    23    82.1    28     ARMSSC3 
     SHIFTED CHAIN . . . . .    64.21           35.3    17    77.3    22     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    70.39           41.2    17   100.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    43.63           50.0     2    28.6     7     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    66.55           33.3    18    78.3    23     ARMSSC3 
     BURIED  . . . . . . . .    74.46           50.0     6   100.0     6     ARMSSC3 
     CORE  . . . . . . . . .    70.45           36.4    22   100.0    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.82           40.0    10    76.9    13     ARMSSC4 
     WELL ORDERED  . . . . .    59.48           66.7     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .    71.36           57.1     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    84.82           40.0    10    76.9    13     ARMSSC4 
     CHANGED ANGLES  . . . .    89.38           33.3     9    75.0    12     ARMSSC4 
     SHIFTED CHAIN . . . . .    94.71           25.0     8    72.7    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    77.48           57.1     7   100.0     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   102.27            0.0     1    25.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    94.73           25.0     8    72.7    11     ARMSSC4 
     BURIED  . . . . . . . .     8.73          100.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    82.65           44.4     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.55250     r(1,2) =  -0.26626     r(1,3) =   0.78984 
 r(2,1) =   0.76053     r(2,2) =  -0.22673     r(2,3) =  -0.60843 
 r(3,1) =   0.34108     r(3,2) =   0.93686     r(3,3) =   0.07723 
THE OFFSET VECTOR: 
 v(1) = -16.60688     v(2) =  17.63923     v(3) = -32.31461 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.24           (Number of atoms:   90) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.65         99    85.3   116     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0267                            CRMSCA  
     WELL ORDERED  . . . . .    2.67         90    85.7   105     CRMSCA  
     NO INTER CONTACTS . . .    2.51         72    87.8    82     CRMSCA  
     SHIFTED CHAIN . . . . .    3.29         60    77.9    77     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.50         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    7.31          3   100.0     3     CRMSCA  
     LARGE SHIFTS/INSERTIONS    7.45          7    29.2    24     CRMSCA  
     SURFACE . . . . . . . .    2.95         55    79.7    69     CRMSCA  
     BURIED  . . . . . . . .    2.21         44    93.6    47     CRMSCA  
     CORE  . . . . . . . . .    1.82         92   100.0    92     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.70        489    85.3   573     CRMSMC  
     WELL ORDERED  . . . . .    2.65        445    85.6   520     CRMSMC  
     NO INTER CONTACTS . . .    2.60        358    88.0   407     CRMSMC  
     SHIFTED CHAIN . . . . .    3.32        296    77.9   380     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.59        293   100.0   293     CRMSMC  
     SHIFTED SS UNITS  . . .    7.32         15   100.0    15     CRMSMC  
     LARGE SHIFTS/INSERTIONS    7.53         34    28.8   118     CRMSMC  
     SURFACE . . . . . . . .    3.01        271    79.5   341     CRMSMC  
     BURIED  . . . . . . . .    2.25        218    94.0   232     CRMSMC  
     CORE  . . . . . . . . .    1.89        455   100.0   455     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.09        404    88.0   459     CRMSSC  
     WELL ORDERED  . . . . .    3.76        311    91.5   340     CRMSSC  
     NO INTER CONTACTS . . .    4.22        297    93.1   319     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.15        334    87.7   381     CRMSSC  
     CHANGED ANGLES  . . . .    5.06        209    84.3   248     CRMSSC  
     SECONDARY STRUCTURE . .    4.24        239   100.0   239     CRMSSC  
     LARGE SHIFTS/INSERTIONS    9.42         26    32.1    81     CRMSSC  
     SURFACE . . . . . . . .    4.36        220    81.5   270     CRMSSC  
     BURIED  . . . . . . . .    3.73        184    97.4   189     CRMSSC  
     CORE  . . . . . . . . .    3.42        378   100.0   378     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.44        800    86.7   923     CRMSALL 
     WELL ORDERED  . . . . .    3.21        673    88.1   764     CRMSALL 
     NO INTER CONTACTS . . .    3.47        585    90.4   647     CRMSALL 
     SHIFTED CHAIN . . . . .    4.14        476    79.5   599     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    3.48        475   100.0   475     CRMSALL 
     LARGE SHIFTS/INSERTIONS    8.45         54    30.5   177     CRMSALL 
     SURFACE . . . . . . . .    3.72        440    80.6   546     CRMSALL 
     BURIED  . . . . . . . .    3.07        360    95.5   377     CRMSALL 
     CORE  . . . . . . . . .    2.74        746   100.0   746     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.81      1     6.7    15       3-ALTQAHCEACRADAP-17   
 CA  LOOP  2     8.32      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     5.86      1    25.0     4     115-EGRK-118  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.63      5     6.7    75       3-ALTQAHCEACRADAP-17   
 MC  LOOP  2     8.38     24   100.0    24      38-VRDGI-42   
 MC  LOOP  3     6.48      5    26.3    19     115-EGRK-118  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     2.51      7     6.6   106       3-ALTQAHCEACRADAP-17   
 ALL LOOP  2     8.98     38   100.0    38      38-VRDGI-42   
 ALL LOOP  3     9.08      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     2.58      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     3.12     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     3.89     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 . . . . . . . . . .    2.217      0.409       0.422     99    85.3   116     ERRCA  
     WELL ORDERED  . . . . .    2.269      0.415       0.429     90    85.7   105     ERRCA  
     NO INTER CONTACTS . . .    2.086      0.401       0.414     72    87.8    82     ERRCA  
     SHIFTED CHAIN . . . . .    2.355      0.366       0.355     60    77.9    77     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    2.277      0.434       0.460     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.699      0.406       0.248      7    29.2    24     ERRCA  
     SURFACE . . . . . . . .    2.155      0.373       0.372     55    79.7    69     ERRCA  
     BURIED  . . . . . . . .    2.294      0.454       0.484     44    93.6    47     ERRCA  
     CORE  . . . . . . . . .    2.028      0.409       0.435     92   100.0    92     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.218      0.408       0.421    489    85.3   573     ERRMC  
     WELL ORDERED  . . . . .    2.258      0.414       0.429    445    85.6   520     ERRMC  
     NO INTER CONTACTS . . .    2.086      0.396       0.411    358    88.0   407     ERRMC  
     SHIFTED CHAIN . . . . .    2.362      0.373       0.364    296    77.9   380     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    2.297      0.434       0.451    293   100.0   293     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.689      0.423       0.268     34    28.8   118     ERRMC  
     SURFACE . . . . . . . .    2.148      0.371       0.370    271    79.5   341     ERRMC  
     BURIED  . . . . . . . .    2.305      0.453       0.484    218    94.0   232     ERRMC  
     CORE  . . . . . . . . .    2.033      0.406       0.432    455   100.0   455     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.272      0.347       0.340    404    88.0   459     ERRSC  
     WELL ORDERED  . . . . .    2.210      0.358       0.362    311    91.5   340     ERRSC  
     NO INTER CONTACTS . . .    2.232      0.343       0.328    297    93.1   319     ERRSC  
     RELIABLE SIDE CHAINS  .    2.391      0.361       0.357    334    87.7   381     ERRSC  
     CHANGED ANGLES  . . . .    2.546      0.311       0.291    209    84.3   248     ERRSC  
     SHIFTED CHAIN . . . . .    2.632      0.338       0.306    236    81.1   291     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    2.418      0.370       0.357    239   100.0   239     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.977      0.446       0.301     26    32.1    81     ERRSC  
     SURFACE . . . . . . . .    2.290      0.322       0.295    220    81.5   270     ERRSC  
     BURIED  . . . . . . . .    2.252      0.378       0.394    184    97.4   189     ERRSC  
     CORE  . . . . . . . . .    2.018      0.341       0.343    378   100.0   378     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.246      0.380       0.383    800    86.7   923     ERRALL 
     WELL ORDERED  . . . . .    2.242      0.390       0.400    673    88.1   764     ERRALL 
     NO INTER CONTACTS . . .    2.159      0.372       0.373    585    90.4   647     ERRALL 
     SHIFTED CHAIN . . . . .    2.498      0.358       0.338    476    79.5   599     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    2.350      0.403       0.406    475   100.0   475     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.340      0.443       0.292     54    30.5   177     ERRALL 
     SURFACE . . . . . . . .    2.226      0.350       0.336    440    80.6   546     ERRALL 
     BURIED  . . . . . . . .    2.271      0.416       0.439    360    95.5   377     ERRALL 
     CORE  . . . . . . . . .    2.022      0.375       0.389    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        86        91        92        96      99     116   DISTCA 
CA  (P)     30.17     74.14     78.45     79.31     82.76             116   DISTCA 
CA  (RMS)    0.73      1.18      1.26      1.31      1.98                   DISTCA 
 
ALL (N)       213       550       635       726       770     800     923   DISTALL 
ALL (P)     23.08     59.59     68.80     78.66     83.42             923   DISTALL 
ALL (RMS)    0.75      1.21      1.43      1.91      2.50                   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          1.82          7.45          RMSLSI 
 
 
 
END of the results output 
