 
####################################################### 
#                                                     # 
#                        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/T0060.inter 
CONANA-PAIR            ../CONANA/T0060.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0060.1gif_A.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0060.1fim.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 884 atoms, MODEL 1648 atoms, 884 common with TARGET 
           Number of atoms possible to evaluate: 750 
 
 
 CA-RMS TARGET<->PARENT(1gif-A)	 1.091738 
 
 CA-RMS TARGET<->PARENT(1fim)	 1.538250 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    34.48           84.8   198    85.3   232     ARMSMC  
     WELL ORDERED  . . . . .    34.48           84.8   198    85.3   232     ARMSMC  
     NO INTER CONTACTS . . .    36.66           83.8   111    94.9   117     ARMSMC  
     SHIFTED CHAIN . . . . .    40.75           82.4   108    90.8   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    16.10           92.0   113    95.8   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS    87.47            0.0     2    40.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    41.97           80.9   115    79.3   145     ARMSMC  
     BURIED  . . . . . . . .    19.87           90.4    83    95.4    87     ARMSMC  
     CORE  . . . . . . . . .    33.51           85.7   196    86.3   227     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.63           63.8    80    84.2    95     ARMSSC1 
     WELL ORDERED  . . . . .    64.63           63.8    80    84.2    95     ARMSSC1 
     NO INTER CONTACTS . . .    59.61           64.4    45    93.8    48     ARMSSC1 
     RELIABLE SIDE CHAINS  .    64.54           63.5    74    84.1    88     ARMSSC1 
     CHANGED ANGLES  . . . .    87.91           41.2    34    77.3    44     ARMSSC1 
     SHIFTED CHAIN . . . . .    66.67           64.3    42    89.4    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    66.89           66.0    50    96.2    52     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    70.25           54.8    42    76.4    55     ARMSSC1 
     BURIED  . . . . . . . .    57.79           73.7    38    95.0    40     ARMSSC1 
     CORE  . . . . . . . . .    64.63           63.8    80    86.0    93     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.58           50.8    59    84.3    70     ARMSSC2 
     WELL ORDERED  . . . . .    64.74           54.7    53    82.8    64     ARMSSC2 
     NO INTER CONTACTS . . .    70.37           44.4    36    94.7    38     ARMSSC2 
     RELIABLE SIDE CHAINS  .    53.30           50.0    40    81.6    49     ARMSSC2 
     CHANGED ANGLES  . . . .    70.28           40.0    35    77.8    45     ARMSSC2 
     SHIFTED CHAIN . . . . .    74.89           42.4    33    86.8    38     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    60.19           57.9    38    95.0    40     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    56.57           45.2    31    77.5    40     ARMSSC2 
     BURIED  . . . . . . . .    72.42           57.1    28    93.3    30     ARMSSC2 
     CORE  . . . . . . . . .    64.58           50.8    59    86.8    68     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.25           36.8    19    82.6    23     ARMSSC3 
     WELL ORDERED  . . . . .    77.44           30.8    13    81.2    16     ARMSSC3 
     NO INTER CONTACTS . . .    95.16           36.4    11    84.6    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .    89.62           35.3    17    85.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .    90.10           29.4    17    81.0    21     ARMSSC3 
     SHIFTED CHAIN . . . . .    80.42           36.4    11    91.7    12     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    82.24           25.0    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    90.94           35.7    14    77.8    18     ARMSSC3 
     BURIED  . . . . . . . .    66.80           40.0     5   100.0     5     ARMSSC3 
     CORE  . . . . . . . . .    85.25           36.8    19    82.6    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    81.30           20.0    10    90.9    11     ARMSSC4 
     WELL ORDERED  . . . . .    94.93           16.7     6    85.7     7     ARMSSC4 
     NO INTER CONTACTS . . .    68.45           28.6     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    81.30           20.0    10    90.9    11     ARMSSC4 
     CHANGED ANGLES  . . . .    81.30           20.0    10    90.9    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    74.80           40.0     5    83.3     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    88.74           16.7     6   100.0     6     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    85.13           12.5     8    88.9     9     ARMSSC4 
     BURIED  . . . . . . . .    63.72           50.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    81.30           20.0    10    90.9    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.96787     r(1,2) =  -0.02713     r(1,3) =   0.24996 
 r(2,1) =  -0.21819     r(2,2) =   0.40338     r(2,3) =   0.88864 
 r(3,1) =  -0.12494     r(3,2) =  -0.91463     r(3,3) =   0.38450 
THE OFFSET VECTOR: 
 v(1) = -18.88059     v(2) = -43.09121     v(3) =  69.63264 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.05           (Number of atoms:   98) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.13        100    85.5   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0113                            CRMSCA  
     WELL ORDERED  . . . . .    1.13        100    85.5   117     CRMSCA  
     NO INTER CONTACTS . . .    1.06         56    94.9    59     CRMSCA  
     SHIFTED CHAIN . . . . .    1.42         54    90.0    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    0.97         57    96.6    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.54          1    33.3     3     CRMSCA  
     SURFACE . . . . . . . .    1.22         58    79.5    73     CRMSCA  
     BURIED  . . . . . . . .    0.99         42    95.5    44     CRMSCA  
     CORE  . . . . . . . . .    1.08         99    86.8   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.20        493    85.6   576     CRMSMC  
     WELL ORDERED  . . . . .    1.20        493    85.6   576     CRMSMC  
     NO INTER CONTACTS . . .    1.11        275    94.8   290     CRMSMC  
     SHIFTED CHAIN . . . . .    1.49        264    90.1   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.00        285    96.6   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.78          4    28.6    14     CRMSMC  
     SURFACE . . . . . . . .    1.28        283    79.5   356     CRMSMC  
     BURIED  . . . . . . . .    1.08        210    95.5   220     CRMSMC  
     CORE  . . . . . . . . .    1.15        489    87.0   562     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.15        350    84.1   416     CRMSSC  
     WELL ORDERED  . . . . .    2.11        325    83.5   389     CRMSSC  
     NO INTER CONTACTS . . .    2.18        193    94.6   204     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.15        292    83.4   350     CRMSSC  
     CHANGED ANGLES  . . . .    2.79        160    78.0   205     CRMSSC  
     SECONDARY STRUCTURE . .    2.24        230    97.0   237     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    11     CRMSSC  
     SURFACE . . . . . . . .    2.46        189    76.5   247     CRMSSC  
     BURIED  . . . . . . . .    1.70        161    95.3   169     CRMSSC  
     CORE  . . . . . . . . .    2.15        350    86.4   405     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.70        750    84.8   884     CRMSALL 
     WELL ORDERED  . . . . .    1.66        725    84.6   857     CRMSALL 
     NO INTER CONTACTS . . .    1.69        417    94.8   440     CRMSALL 
     SHIFTED CHAIN . . . . .    1.82        401    89.3   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.73        458    96.8   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS    3.78          4    17.4    23     CRMSALL 
     SURFACE . . . . . . . .    1.90        421    78.1   539     CRMSALL 
     BURIED  . . . . . . . .    1.42        329    95.4   345     CRMSALL 
     CORE  . . . . . . . . .    1.69        746    86.6   861     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS 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 . . . . . . . . . .    1.116      0.397       0.454    100    85.5   117     ERRCA  
     WELL ORDERED  . . . . .    1.116      0.397       0.454    100    85.5   117     ERRCA  
     NO INTER CONTACTS . . .    1.067      0.374       0.434     56    94.9    59     ERRCA  
     SHIFTED CHAIN . . . . .    0.861      0.259       0.301     54    90.0    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    1.216      0.439       0.502     57    96.6    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.853      0.137       0.068      1    33.3     3     ERRCA  
     SURFACE . . . . . . . .    1.132      0.387       0.451     58    79.5    73     ERRCA  
     BURIED  . . . . . . . .    1.094      0.410       0.459     42    95.5    44     ERRCA  
     CORE  . . . . . . . . .    1.118      0.399       0.458     99    86.8   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.102      0.384       0.439    493    85.6   576     ERRMC  
     WELL ORDERED  . . . . .    1.102      0.384       0.439    493    85.6   576     ERRMC  
     NO INTER CONTACTS . . .    1.050      0.364       0.423    275    94.8   290     ERRMC  
     SHIFTED CHAIN . . . . .    0.889      0.264       0.302    264    90.1   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    1.186      0.420       0.485    285    96.6   295     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.123      0.162       0.083      4    28.6    14     ERRMC  
     SURFACE . . . . . . . .    1.120      0.375       0.435    283    79.5   356     ERRMC  
     BURIED  . . . . . . . .    1.077      0.395       0.444    210    95.5   220     ERRMC  
     CORE  . . . . . . . . .    1.102      0.385       0.442    489    87.0   562     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.083      0.310       0.310    350    84.1   416     ERRSC  
     WELL ORDERED  . . . . .    1.117      0.324       0.328    325    83.5   389     ERRSC  
     NO INTER CONTACTS . . .    1.030      0.286       0.283    193    94.6   204     ERRSC  
     RELIABLE SIDE CHAINS  .    1.102      0.316       0.320    292    83.4   350     ERRSC  
     CHANGED ANGLES  . . . .    1.113      0.247       0.198    160    78.0   205     ERRSC  
     SHIFTED CHAIN . . . . .    0.920      0.238       0.227    185    88.5   209     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    1.155      0.322       0.320    230    97.0   237     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    11     ERRSC  
     SURFACE . . . . . . . .    1.086      0.271       0.261    189    76.5   247     ERRSC  
     BURIED  . . . . . . . .    1.080      0.356       0.367    161    95.3   169     ERRSC  
     CORE  . . . . . . . . .    1.083      0.310       0.310    350    86.4   405     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.097      0.351       0.381    750    84.8   884     ERRALL 
     WELL ORDERED  . . . . .    1.112      0.358       0.392    725    84.6   857     ERRALL 
     NO INTER CONTACTS . . .    1.041      0.329       0.361    417    94.8   440     ERRALL 
     SHIFTED CHAIN . . . . .    0.908      0.253       0.271    401    89.3   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    1.176      0.373       0.405    458    96.8   473     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.123      0.162       0.083      4    17.4    23     ERRALL 
     SURFACE . . . . . . . .    1.114      0.332       0.361    421    78.1   539     ERRALL 
     BURIED  . . . . . . . .    1.075      0.375       0.407    329    95.4   345     ERRALL 
     CORE  . . . . . . . . .    1.096      0.352       0.383    746    86.6   861     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)        53        96        99       100       100     100     117   DISTCA 
CA  (P)     45.30     82.05     84.62     85.47     85.47             117   DISTCA 
CA  (RMS)    0.63      1.01      1.08      1.13      1.13                   DISTCA 
 
ALL (N)       314       629       702       739       750     750     884   DISTALL 
ALL (P)     35.52     71.15     79.41     83.60     84.84             884   DISTALL 
ALL (RMS)    0.65      1.08      1.29      1.52      1.70                   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)         114            99             1          RMSLSI 
CA  (P)       97.44         84.62          0.85          RMSLSI 
CA  (RMS)      1.09          1.08          3.54          RMSLSI 
 
 
 
END of the results output 
