 
####################################################### 
#                                                     # 
#                        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 627 atoms, 612 common with TARGET 
           Number of atoms possible to evaluate: 482 
 
 
 CA-RMS TARGET<->PARENT(1dcp-E)	 1.412918 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    29.03           83.1   166    72.2   230     ARMSMC  
     WELL ORDERED  . . . . .    28.23           86.2   152    73.4   207     ARMSMC  
     NO INTER CONTACTS . . .    27.82           85.8   120    73.2   164     ARMSMC  
     SHIFTED CHAIN . . . . .    34.38           80.9    94    61.8   152     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    16.73           90.4   104    88.1   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    52.61            0.0     1     2.2    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    32.91           75.3    89    65.4   136     ARMSMC  
     BURIED  . . . . . . . .    23.77           92.2    77    81.9    94     ARMSMC  
     CORE  . . . . . . . . .    28.83           83.6   165    89.7   184     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    59.56           72.0    25    26.0    96     ARMSSC1 
     WELL ORDERED  . . . . .    47.49           84.2    19    25.7    74     ARMSSC1 
     NO INTER CONTACTS . . .    64.98           72.2    18    26.9    67     ARMSSC1 
     RELIABLE SIDE CHAINS  .    63.33           68.2    22    25.0    88     ARMSSC1 
     CHANGED ANGLES  . . . .    95.09           33.3     9    15.0    60     ARMSSC1 
     SHIFTED CHAIN . . . . .    84.10           50.0    10    16.1    62     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    58.81           75.0    12    24.0    50     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    70.42            0.0     1     5.9    17     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    71.58           50.0    12    21.1    57     ARMSSC1 
     BURIED  . . . . . . . .    45.74           92.3    13    33.3    39     ARMSSC1 
     CORE  . . . . . . . . .    59.07           75.0    24    30.4    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    52.72           65.0    20    26.7    75     ARMSSC2 
     WELL ORDERED  . . . . .    58.27           66.7    15    28.8    52     ARMSSC2 
     NO INTER CONTACTS . . .    53.34           69.2    13    26.0    50     ARMSSC2 
     RELIABLE SIDE CHAINS  .    41.83           69.2    13    24.1    54     ARMSSC2 
     CHANGED ANGLES  . . . .    71.92           42.9     7    12.7    55     ARMSSC2 
     SHIFTED CHAIN . . . . .    27.29           71.4     7    14.6    48     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    76.84           62.5     8    21.1    38     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    28.71          100.0     1     7.7    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    69.15           45.5    11    23.4    47     ARMSSC2 
     BURIED  . . . . . . . .    18.21           88.9     9    32.1    28     ARMSSC2 
     CORE  . . . . . . . . .    53.69           63.2    19    30.6    62     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    46.25           50.0     6    20.7    29     ARMSSC3 
     WELL ORDERED  . . . . .    59.75           33.3     3    23.1    13     ARMSSC3 
     NO INTER CONTACTS . . .    35.47           75.0     4    20.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    46.25           50.0     6    23.1    26     ARMSSC3 
     CHANGED ANGLES  . . . .    37.35           60.0     5    17.9    28     ARMSSC3 
     SHIFTED CHAIN . . . . .    26.59           66.7     3    13.6    22     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    59.75           33.3     3    17.6    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     7     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    49.11           40.0     5    21.7    23     ARMSSC3 
     BURIED  . . . . . . . .    27.79          100.0     1    16.7     6     ARMSSC3 
     CORE  . . . . . . . . .    46.25           50.0     6    27.3    22     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    97.11            0.0     3    23.1    13     ARMSSC4 
     WELL ORDERED  . . . . .    37.74            0.0     1    33.3     3     ARMSSC4 
     NO INTER CONTACTS . . .    57.95            0.0     2    28.6     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    97.11            0.0     3    23.1    13     ARMSSC4 
     CHANGED ANGLES  . . . .   107.24            0.0     2    16.7    12     ARMSSC4 
     SHIFTED CHAIN . . . . .   146.89            0.0     1     9.1    11     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    57.95            0.0     2    28.6     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     4     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   115.91            0.0     2    18.2    11     ARMSSC4 
     BURIED  . . . . . . . .    37.74            0.0     1    50.0     2     ARMSSC4 
     CORE  . . . . . . . . .    97.11            0.0     3    33.3     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.79192     r(1,2) =   0.54288     r(1,3) =   0.27954 
 r(2,1) =  -0.49569     r(2,2) =   0.30419     r(2,3) =   0.81348 
 r(3,1) =   0.35659     r(3,2) =  -0.78278     r(3,3) =   0.51000 
THE OFFSET VECTOR: 
 v(1) = -49.30497     v(2) =  11.06190     v(3) =  30.27963 
 
 Number of iteration 31                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.22           (Number of atoms:   87) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.79         98    84.5   116     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0285                            CRMSCA  
     WELL ORDERED  . . . . .    2.76         89    84.8   105     CRMSCA  
     NO INTER CONTACTS . . .    2.57         71    86.6    82     CRMSCA  
     SHIFTED CHAIN . . . . .    3.52         59    76.6    77     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.46         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    5.96          3   100.0     3     CRMSCA  
     LARGE SHIFTS/INSERTIONS    8.33          6    25.0    24     CRMSCA  
     SURFACE . . . . . . . .    3.25         54    78.3    69     CRMSCA  
     BURIED  . . . . . . . .    2.09         44    93.6    47     CRMSCA  
     CORE  . . . . . . . . .    1.94         92   100.0    92     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.10        387    67.5   573     CRMSMC  
     WELL ORDERED  . . . . .    1.94        354    68.1   520     CRMSMC  
     NO INTER CONTACTS . . .    2.11        284    69.8   407     CRMSMC  
     SHIFTED CHAIN . . . . .    2.67        217    57.1   380     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.59        233    79.5   293     CRMSMC  
     SHIFTED SS UNITS  . . .    5.96          3    20.0    15     CRMSMC  
     LARGE SHIFTS/INSERTIONS    8.30         13    11.0   118     CRMSMC  
     SURFACE . . . . . . . .    2.58        207    60.7   341     CRMSMC  
     BURIED  . . . . . . . .    1.37        180    77.6   232     CRMSMC  
     CORE  . . . . . . . . .    1.48        374    82.2   455     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    3.16        123    26.8   459     CRMSSC  
     WELL ORDERED  . . . . .    1.43         97    28.5   340     CRMSSC  
     NO INTER CONTACTS . . .    3.61         87    27.3   319     CRMSSC  
     RELIABLE SIDE CHAINS  .    3.48         97    25.5   381     CRMSSC  
     CHANGED ANGLES  . . . .    5.57         30    12.1   248     CRMSSC  
     SECONDARY STRUCTURE . .    1.75         59    24.7   239     CRMSSC  
     LARGE SHIFTS/INSERTIONS   14.38          4     4.9    81     CRMSSC  
     SURFACE . . . . . . . .    4.48         58    21.5   270     CRMSSC  
     BURIED  . . . . . . . .    1.00         65    34.4   189     CRMSSC  
     CORE  . . . . . . . . .    1.84        119    31.5   378     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.39        482    52.2   923     CRMSALL 
     WELL ORDERED  . . . . .    1.88        427    55.9   764     CRMSALL 
     NO INTER CONTACTS . . .    2.52        350    54.1   647     CRMSALL 
     SHIFTED CHAIN . . . . .    3.12        251    41.9   599     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.65        277    58.3   475     CRMSALL 
     LARGE SHIFTS/INSERTIONS    9.96         16     9.0   177     CRMSALL 
     SURFACE . . . . . . . .    3.06        253    46.3   546     CRMSALL 
     BURIED  . . . . . . . .    1.31        229    60.7   377     CRMSALL 
     CORE  . . . . . . . . .    1.58        466    62.5   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     8.76      5   100.0     5      38-VRDGI-42   
 CA  LOOP  3     5.78      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     9.26      9    37.5    24      38-VRDGI-42   
 MC  LOOP  3     5.57      4    21.1    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    11.04     12    31.6    38      38-VRDGI-42   
 ALL LOOP  3     5.57      4    12.1    33     115-EGRK-118  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     2.81      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     2.68      9    37.5    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     3.65     12    31.6    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 . . . . . . . . . .    1.528      0.360       0.398     98    84.5   116     ERRCA  
     WELL ORDERED  . . . . .    1.547      0.368       0.412     89    84.8   105     ERRCA  
     NO INTER CONTACTS . . .    1.547      0.379       0.424     71    86.6    82     ERRCA  
     SHIFTED CHAIN . . . . .    1.614      0.299       0.309     59    76.6    77     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.508      0.382       0.440     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.712      0.392       0.197      6    25.0    24     ERRCA  
     SURFACE . . . . . . . .    1.658      0.341       0.360     54    78.3    69     ERRCA  
     BURIED  . . . . . . . .    1.368      0.383       0.445     44    93.6    47     ERRCA  
     CORE  . . . . . . . . .    1.321      0.357       0.412     92   100.0    92     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.317      0.351       0.395    387    67.5   573     ERRMC  
     WELL ORDERED  . . . . .    1.312      0.361       0.412    354    68.1   520     ERRMC  
     NO INTER CONTACTS . . .    1.377      0.369       0.421    284    69.8   407     ERRMC  
     SHIFTED CHAIN . . . . .    1.361      0.300       0.324    217    57.1   380     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.322      0.381       0.449    233    79.5   293     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.326      0.478       0.239     13    11.0   118     ERRMC  
     SURFACE . . . . . . . .    1.414      0.332       0.354    207    60.7   341     ERRMC  
     BURIED  . . . . . . . .    1.207      0.374       0.443    180    77.6   232     ERRMC  
     CORE  . . . . . . . . .    1.178      0.347       0.401    374    82.2   455     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.239      0.300       0.288    123    26.8   459     ERRSC  
     WELL ORDERED  . . . . .    0.754      0.286       0.311     97    28.5   340     ERRSC  
     NO INTER CONTACTS . . .    1.521      0.340       0.332     87    27.3   319     ERRSC  
     RELIABLE SIDE CHAINS  .    1.363      0.303       0.281     97    25.5   381     ERRSC  
     CHANGED ANGLES  . . . .    2.586      0.349       0.237     30    12.1   248     ERRSC  
     SHIFTED CHAIN . . . . .    1.987      0.279       0.191     45    15.5   291     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    0.892      0.288       0.306     59    24.7   239     ERRSC  
     LARGE SHIFTS/INSERTIONS   12.621      0.788       0.394      4     4.9    81     ERRSC  
     SURFACE . . . . . . . .    1.707      0.248       0.155     58    21.5   270     ERRSC  
     BURIED  . . . . . . . .    0.823      0.346       0.407     65    34.4   189     ERRSC  
     CORE  . . . . . . . . .    0.857      0.283       0.285    119    31.5   378     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.308      0.341       0.373    482    52.2   923     ERRALL 
     WELL ORDERED  . . . . .    1.216      0.348       0.394    427    55.9   764     ERRALL 
     NO INTER CONTACTS . . .    1.415      0.364       0.403    350    54.1   647     ERRALL 
     SHIFTED CHAIN . . . . .    1.462      0.298       0.306    251    41.9   599     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.254      0.365       0.423    277    58.3   475     ERRALL 
     LARGE SHIFTS/INSERTIONS    6.857      0.539       0.269     16     9.0   177     ERRALL 
     SURFACE . . . . . . . .    1.477      0.316       0.316    253    46.3   546     ERRALL 
     BURIED  . . . . . . . .    1.122      0.368       0.436    229    60.7   377     ERRALL 
     CORE  . . . . . . . . .    1.118      0.334       0.377    466    62.5   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)        37        82        88        89        96      98     116   DISTCA 
CA  (P)     31.90     70.69     75.86     76.72     82.76             116   DISTCA 
CA  (RMS)    0.79      1.12      1.24      1.29      2.41                   DISTCA 
 
ALL (N)       185       409       448       462       476     482     923   DISTALL 
ALL (P)     20.04     44.31     48.54     50.05     51.57             923   DISTALL 
ALL (RMS)    0.75      1.11      1.27      1.42      1.90                   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          1.94          8.33          RMSLSI 
 
 
 
END of the results output 
