 
####################################################### 
#                                                     # 
#                        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/T0009.inter 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp2.T0009.2cbp.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 837 atoms, MODEL 975 atoms, 828 common with TARGET 
           Number of atoms possible to evaluate: 115 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.80           53.8    26    12.1   214     ARMSMC  
     WELL ORDERED  . . . . .    33.40           64.7    17     9.4   181     ARMSMC  
     NO INTER CONTACTS . . .    68.80           53.8    26    15.9   164     ARMSMC  
     SHIFTED CHAIN . . . . .    87.50           50.0    14    12.7   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    27.33           50.0     8    10.0    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS    96.58           50.0     6    13.0    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    73.82           54.5    22    16.7   132     ARMSMC  
     BURIED  . . . . . . . .    28.18           50.0     4     4.9    82     ARMSMC  
     CORE  . . . . . . . . .    57.92           55.0    20    11.9   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.53           28.6    14    14.9    94     ARMSSC1 
     WELL ORDERED  . . . . .    92.79           50.0     6     9.5    63     ARMSSC1 
     NO INTER CONTACTS . . .    98.53           28.6    14    18.7    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    89.68           33.3    12    14.6    82     ARMSSC1 
     CHANGED ANGLES  . . . .    94.62           30.0    10    21.3    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    95.58           25.0     8    17.0    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .   109.88           25.0     4    11.1    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   110.28            0.0     4    19.0    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    93.52           33.3    12    20.7    58     ARMSSC1 
     BURIED  . . . . . . . .   124.42            0.0     2     5.6    36     ARMSSC1 
     CORE  . . . . . . . . .    93.41           40.0    10    13.7    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    85.58           22.2     9    14.8    61     ARMSSC2 
     WELL ORDERED  . . . . .    80.70           50.0     2     6.1    33     ARMSSC2 
     NO INTER CONTACTS . . .    85.58           22.2     9    17.6    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    81.54           25.0     8    19.0    42     ARMSSC2 
     CHANGED ANGLES  . . . .    93.20           16.7     6    15.0    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    63.27           25.0     4    14.8    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .   110.86            0.0     3    11.1    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    81.67            0.0     2    15.4    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    81.54           25.0     8    21.1    38     ARMSSC2 
     BURIED  . . . . . . . .   112.80            0.0     1     4.3    23     ARMSSC2 
     CORE  . . . . . . . . .    86.66           28.6     7    14.6    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    42.10           20.0     5    27.8    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     NO INTER CONTACTS . . .    42.10           20.0     5    29.4    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    42.10           20.0     5    38.5    13     ARMSSC3 
     CHANGED ANGLES  . . . .    42.10           20.0     5    29.4    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    36.78           33.3     3    30.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    49.01            0.0     2    20.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    44.94            0.0     2    50.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    42.10           20.0     5    31.2    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .    40.10           33.3     3    21.4    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   120.23            0.0     2    33.3     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     NO INTER CONTACTS . . .   120.23            0.0     2    40.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .   120.23            0.0     2    33.3     6     ARMSSC4 
     CHANGED ANGLES  . . . .   120.23            0.0     2    50.0     4     ARMSSC4 
     SHIFTED CHAIN . . . . .    53.02            0.0     1    33.3     3     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   161.55            0.0     1    33.3     3     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 . . . . . . . .   120.23            0.0     2    33.3     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .   120.23            0.0     2    33.3     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.61042     r(1,2) =  -0.05107     r(1,3) =  -0.79043 
 r(2,1) =   0.11772     r(2,2) =  -0.98099     r(2,3) =   0.15430 
 r(3,1) =  -0.78328     r(3,2) =  -0.18724     r(3,3) =  -0.59280 
THE OFFSET VECTOR: 
 v(1) =  -4.50776     v(2) =  27.17548     v(3) =  72.14999 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   2.05           (Number of atoms:    9) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    3.38         14    13.0   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2415                            CRMSCA  
     WELL ORDERED  . . . . .    2.52          9     9.9    91     CRMSCA  
     NO INTER CONTACTS . . .    3.38         14    16.9    83     CRMSCA  
     SHIFTED CHAIN . . . . .    3.84          8    14.3    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.62          4    10.0    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    5.06          4    16.7    24     CRMSCA  
     SURFACE . . . . . . . .    3.35         12    17.9    67     CRMSCA  
     BURIED  . . . . . . . .    3.58          2     4.9    41     CRMSCA  
     CORE  . . . . . . . . .    2.40         10    11.9    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.68         70    13.1   533     CRMSMC  
     WELL ORDERED  . . . . .    2.91         45    10.3   439     CRMSMC  
     NO INTER CONTACTS . . .    3.68         70    17.1   410     CRMSMC  
     SHIFTED CHAIN . . . . .    4.09         40    14.5   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.79         20    10.1   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    5.12         20    16.7   120     CRMSMC  
     SURFACE . . . . . . . .    3.66         60    18.1   332     CRMSMC  
     BURIED  . . . . . . . .    3.78         10     5.0   201     CRMSMC  
     CORE  . . . . . . . . .    2.91         50    12.1   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    6.80         59    14.6   405     CRMSSC  
     WELL ORDERED  . . . . .    6.05         20     7.3   274     CRMSSC  
     NO INTER CONTACTS . . .    6.80         59    18.0   327     CRMSSC  
     RELIABLE SIDE CHAINS  .    6.77         53    16.4   323     CRMSSC  
     CHANGED ANGLES  . . . .    7.53         37    20.1   184     CRMSSC  
     SECONDARY STRUCTURE . .    5.86         19    10.8   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.79         17    20.5    83     CRMSSC  
     SURFACE . . . . . . . .    6.78         52    22.2   234     CRMSSC  
     BURIED  . . . . . . . .    6.92          7     4.1   171     CRMSSC  
     CORE  . . . . . . . . .    6.80         42    13.0   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.40        115    13.7   837     CRMSALL 
     WELL ORDERED  . . . . .    4.09         57     9.0   635     CRMSALL 
     NO INTER CONTACTS . . .    5.40        115    17.5   659     CRMSALL 
     SHIFTED CHAIN . . . . .    5.93         65    15.6   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    4.58         35    10.4   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    5.96         33    18.4   179     CRMSALL 
     SURFACE . . . . . . . .    5.42        100    19.9   502     CRMSALL 
     BURIED  . . . . . . . .    5.25         15     4.5   335     CRMSALL 
     CORE  . . . . . . . . .    5.15         82    12.5   658     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     8      16-PSSPNFYS-23   
 CA  LOOP  2     5.67      3    37.5     8      63-VNSDNDVE-70   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    40      16-PSSPNFYS-23   
 MC  LOOP  2     5.68     15    37.5    40      63-VNSDNDVE-70   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    63      16-PSSPNFYS-23   
 ALL LOOP  2     6.73     24    39.3    61      63-VNSDNDVE-70   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 CA  LOOP  2     0.42      3    37.5     8      63-VNSDNDVE-70   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 MC  LOOP  2     2.21     15    37.5    40      63-VNSDNDVE-70   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 ALL LOOP  2     3.28     24    39.3    61      63-VNSDNDVE-70   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.018      1.000       0.500     14    13.0   108     ERRCA  
     WELL ORDERED  . . . . .    2.421      1.000       0.500      9     9.9    91     ERRCA  
     NO INTER CONTACTS . . .    3.018      1.000       0.500     14    16.9    83     ERRCA  
     SHIFTED CHAIN . . . . .    3.379      1.000       0.500      8    14.3    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    2.454      1.000       0.500      4    10.0    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.835      1.000       0.500      4    16.7    24     ERRCA  
     SURFACE . . . . . . . .    2.928      1.000       0.500     12    17.9    67     ERRCA  
     BURIED  . . . . . . . .    3.559      1.000       0.500      2     4.9    41     ERRCA  
     CORE  . . . . . . . . .    2.291      1.000       0.500     10    11.9    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.248      1.000       0.500     70    13.1   533     ERRMC  
     WELL ORDERED  . . . . .    2.624      1.000       0.500     45    10.3   439     ERRMC  
     NO INTER CONTACTS . . .    3.248      1.000       0.500     70    17.1   410     ERRMC  
     SHIFTED CHAIN . . . . .    3.605      1.000       0.500     40    14.5   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    2.530      1.000       0.500     20    10.1   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.776      1.000       0.500     20    16.7   120     ERRMC  
     SURFACE . . . . . . . .    3.192      1.000       0.500     60    18.1   332     ERRMC  
     BURIED  . . . . . . . .    3.581      1.000       0.500     10     5.0   201     ERRMC  
     CORE  . . . . . . . . .    2.636      1.000       0.500     50    12.1   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.168      1.000       0.500     59    14.6   405     ERRSC  
     WELL ORDERED  . . . . .    5.385      1.000       0.500     20     7.3   274     ERRSC  
     NO INTER CONTACTS . . .    6.168      1.000       0.500     59    18.0   327     ERRSC  
     RELIABLE SIDE CHAINS  .    6.091      1.000       0.500     53    16.4   323     ERRSC  
     CHANGED ANGLES  . . . .    6.866      1.000       0.500     37    20.1   184     ERRSC  
     SHIFTED CHAIN . . . . .    6.720      1.000       0.500     33    17.1   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    5.437      1.000       0.500     19    10.8   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.256      1.000       0.500     17    20.5    83     ERRSC  
     SURFACE . . . . . . . .    6.087      1.000       0.500     52    22.2   234     ERRSC  
     BURIED  . . . . . . . .    6.767      1.000       0.500      7     4.1   171     ERRSC  
     CORE  . . . . . . . . .    6.132      1.000       0.500     42    13.0   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.589      1.000       0.500    115    13.7   837     ERRALL 
     WELL ORDERED  . . . . .    3.346      1.000       0.500     57     9.0   635     ERRALL 
     NO INTER CONTACTS . . .    4.589      1.000       0.500    115    17.5   659     ERRALL 
     SHIFTED CHAIN . . . . .    5.051      1.000       0.500     65    15.6   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    3.923      1.000       0.500     35    10.4   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.464      1.000       0.500     33    18.4   179     ERRALL 
     SURFACE . . . . . . . .    4.558      1.000       0.500    100    19.9   502     ERRALL 
     BURIED  . . . . . . . .    4.791      1.000       0.500     15     4.5   335     ERRALL 
     CORE  . . . . . . . . .    4.236      1.000       0.500     82    12.5   658     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)         0         4         9        12        14      14     108   DISTCA 
CA  (P)      0.00      3.70      8.33     11.11     12.96             108   DISTCA 
CA  (RMS)    0.00      1.71      2.05      2.70      3.38                   DISTCA 
 
ALL (N)         3        19        39        75       109     115     837   DISTALL 
ALL (P)      0.36      2.27      4.66      8.96     13.02             837   DISTALL 
ALL (RMS)    0.82      1.43      2.02      3.10      4.75                   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)          84            10             4          RMSLSI 
CA  (P)       77.78          9.26          3.70          RMSLSI 
CA  (RMS)      1.02          2.40          5.06          RMSLSI 
 
 
 
END of the results output 
