 
####################################################### 
#                                                     # 
#                        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: 156 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   108.55           25.0    36    16.8   214     ARMSMC  
     WELL ORDERED  . . . . .   113.27           18.2    33    18.2   181     ARMSMC  
     NO INTER CONTACTS . . .   111.86           23.1    26    15.9   164     ARMSMC  
     SHIFTED CHAIN . . . . .   107.16           26.3    19    17.3   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .   110.93           22.2    18    22.5    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS   100.93           42.9     7    15.2    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    95.36           42.9    21    15.9   132     ARMSMC  
     BURIED  . . . . . . . .   124.68            0.0    15    18.3    82     ARMSMC  
     CORE  . . . . . . . . .   110.31           20.7    29    17.3   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    98.52           27.8    18    19.1    94     ARMSSC1 
     WELL ORDERED  . . . . .    90.69           30.0    10    15.9    63     ARMSSC1 
     NO INTER CONTACTS . . .   102.27           30.8    13    17.3    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .   103.33           25.0    16    19.5    82     ARMSSC1 
     CHANGED ANGLES  . . . .   107.97           14.3     7    14.9    47     ARMSSC1 
     SHIFTED CHAIN . . . . .   102.30           20.0    10    21.3    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    98.78           25.0     8    22.2    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   106.52           25.0     4    19.0    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    98.86           30.0    10    17.2    58     ARMSSC1 
     BURIED  . . . . . . . .    98.08           25.0     8    22.2    36     ARMSSC1 
     CORE  . . . . . . . . .    96.11           28.6    14    19.2    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    94.41           23.1    13    21.3    61     ARMSSC2 
     WELL ORDERED  . . . . .    86.51           33.3     6    18.2    33     ARMSSC2 
     NO INTER CONTACTS . . .    81.86           33.3     9    17.6    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    64.08           37.5     8    19.0    42     ARMSSC2 
     CHANGED ANGLES  . . . .   102.20           10.0    10    25.0    40     ARMSSC2 
     SHIFTED CHAIN . . . . .   104.61           28.6     7    25.9    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    78.68           42.9     7    25.9    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS   141.46            0.0     2    15.4    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    93.56           25.0     8    21.1    38     ARMSSC2 
     BURIED  . . . . . . . .    95.76           20.0     5    21.7    23     ARMSSC2 
     CORE  . . . . . . . . .    83.04           27.3    11    22.9    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    37.34           60.0     5    27.8    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     NO INTER CONTACTS . . .    37.34           60.0     5    29.4    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    33.56           75.0     4    30.8    13     ARMSSC3 
     CHANGED ANGLES  . . . .    37.34           60.0     5    29.4    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    46.14           33.3     3    30.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    29.07           75.0     4    40.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    59.94            0.0     1    25.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    40.67           50.0     4    25.0    16     ARMSSC3 
     BURIED  . . . . . . . .    18.83          100.0     1    50.0     2     ARMSSC3 
     CORE  . . . . . . . . .    29.07           75.0     4    28.6    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    15.14          100.0     1    16.7     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     NO INTER CONTACTS . . .    15.14          100.0     1    20.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .    15.14          100.0     1    16.7     6     ARMSSC4 
     CHANGED ANGLES  . . . .    15.14          100.0     1    25.0     4     ARMSSC4 
     SHIFTED CHAIN . . . . .    15.14          100.0     1    33.3     3     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    15.14          100.0     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 . . . . . . . .    15.14          100.0     1    16.7     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    15.14          100.0     1    16.7     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.65624     r(1,2) =   0.52368     r(1,3) =   0.54323 
 r(2,1) =   0.73214     r(2,2) =   0.26776     r(2,3) =   0.62632 
 r(3,1) =   0.18254     r(3,2) =   0.80874     r(3,3) =  -0.55912 
THE OFFSET VECTOR: 
 v(1) =  72.08915     v(2) =  26.85824     v(3) =  47.80343 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.47           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.84         19    17.6   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3074                            CRMSCA  
     WELL ORDERED  . . . . .    5.87         17    18.7    91     CRMSCA  
     NO INTER CONTACTS . . .    6.28         13    15.7    83     CRMSCA  
     SHIFTED CHAIN . . . . .    5.96         10    17.9    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    4.74          9    22.5    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.19          4    16.7    24     CRMSCA  
     SURFACE . . . . . . . .    5.32         11    16.4    67     CRMSCA  
     BURIED  . . . . . . . .    6.49          8    19.5    41     CRMSCA  
     CORE  . . . . . . . . .    5.74         15    17.9    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.00         95    17.8   533     CRMSMC  
     WELL ORDERED  . . . . .    5.94         82    18.7   439     CRMSMC  
     NO INTER CONTACTS . . .    6.33         65    15.9   410     CRMSMC  
     SHIFTED CHAIN . . . . .    6.12         50    18.1   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    4.84         45    22.6   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.48         20    16.7   120     CRMSMC  
     SURFACE . . . . . . . .    5.53         55    16.6   332     CRMSMC  
     BURIED  . . . . . . . .    6.58         40    19.9   201     CRMSMC  
     CORE  . . . . . . . . .    5.86         75    18.2   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.55         80    19.8   405     CRMSSC  
     WELL ORDERED  . . . . .    8.78         49    17.9   274     CRMSSC  
     NO INTER CONTACTS . . .    8.28         55    16.8   327     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.15         60    18.6   323     CRMSSC  
     CHANGED ANGLES  . . . .    8.20         38    20.7   184     CRMSSC  
     SECONDARY STRUCTURE . .    6.96         39    22.2   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.81         15    18.1    83     CRMSSC  
     SURFACE . . . . . . . .    7.99         46    19.7   234     CRMSSC  
     BURIED  . . . . . . . .    9.26         34    19.9   171     CRMSSC  
     CORE  . . . . . . . . .    8.49         65    20.2   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.30        156    18.6   837     CRMSALL 
     WELL ORDERED  . . . . .    7.14        116    18.3   635     CRMSALL 
     NO INTER CONTACTS . . .    7.27        107    16.2   659     CRMSALL 
     SHIFTED CHAIN . . . . .    7.35         87    20.9   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    5.97         75    22.3   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.48         31    17.3   179     CRMSALL 
     SURFACE . . . . . . . .    6.77         90    17.9   502     CRMSALL 
     BURIED  . . . . . . . .    7.97         66    19.7   335     CRMSALL 
     CORE  . . . . . . . . .    7.26        125    19.0   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     2.92      2    25.0     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     3.73     10    25.0    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     3.86     15    24.6    61      63-VNSDNDVE-70   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 WARNING! LOOP  2 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 . . . . . . . . . .    4.796      1.000       0.500     19    17.6   108     ERRCA  
     WELL ORDERED  . . . . .    4.734      1.000       0.500     17    18.7    91     ERRCA  
     NO INTER CONTACTS . . .    5.375      1.000       0.500     13    15.7    83     ERRCA  
     SHIFTED CHAIN . . . . .    5.232      1.000       0.500     10    17.9    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    3.713      1.000       0.500      9    22.5    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.450      1.000       0.500      4    16.7    24     ERRCA  
     SURFACE . . . . . . . .    4.324      1.000       0.500     11    16.4    67     ERRCA  
     BURIED  . . . . . . . .    5.445      1.000       0.500      8    19.5    41     ERRCA  
     CORE  . . . . . . . . .    4.622      1.000       0.500     15    17.9    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.023      1.000       0.500     95    17.8   533     ERRMC  
     WELL ORDERED  . . . . .    4.872      1.000       0.500     82    18.7   439     ERRMC  
     NO INTER CONTACTS . . .    5.451      1.000       0.500     65    15.9   410     ERRMC  
     SHIFTED CHAIN . . . . .    5.367      1.000       0.500     50    18.1   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    3.911      1.000       0.500     45    22.6   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.772      1.000       0.500     20    16.7   120     ERRMC  
     SURFACE . . . . . . . .    4.616      1.000       0.500     55    16.6   332     ERRMC  
     BURIED  . . . . . . . .    5.583      1.000       0.500     40    19.9   201     ERRMC  
     CORE  . . . . . . . . .    4.823      1.000       0.500     75    18.2   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.703      1.000       0.500     80    19.8   405     ERRSC  
     WELL ORDERED  . . . . .    7.900      1.000       0.500     49    17.9   274     ERRSC  
     NO INTER CONTACTS . . .    7.558      1.000       0.500     55    16.8   327     ERRSC  
     RELIABLE SIDE CHAINS  .    7.364      1.000       0.500     60    18.6   323     ERRSC  
     CHANGED ANGLES  . . . .    7.522      1.000       0.500     38    20.7   184     ERRSC  
     SHIFTED CHAIN . . . . .    7.883      1.000       0.500     47    24.4   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    6.206      1.000       0.500     39    22.2   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    7.971      1.000       0.500     15    18.1    83     ERRSC  
     SURFACE . . . . . . . .    7.257      1.000       0.500     46    19.7   234     ERRSC  
     BURIED  . . . . . . . .    8.306      1.000       0.500     34    19.9   171     ERRSC  
     CORE  . . . . . . . . .    7.641      1.000       0.500     65    20.2   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.251      1.000       0.500    156    18.6   837     ERRALL 
     WELL ORDERED  . . . . .    5.984      1.000       0.500    116    18.3   635     ERRALL 
     NO INTER CONTACTS . . .    6.398      1.000       0.500    107    16.2   659     ERRALL 
     SHIFTED CHAIN . . . . .    6.579      1.000       0.500     87    20.9   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    5.015      1.000       0.500     75    22.3   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    6.627      1.000       0.500     31    17.3   179     ERRALL 
     SURFACE . . . . . . . .    5.805      1.000       0.500     90    17.9   502     ERRALL 
     BURIED  . . . . . . . .    6.858      1.000       0.500     66    19.7   335     ERRALL 
     CORE  . . . . . . . . .    6.157      1.000       0.500    125    19.0   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)         2         6         8        11        17      19     108   DISTCA 
CA  (P)      1.85      5.56      7.41     10.19     15.74             108   DISTCA 
CA  (RMS)    0.63      1.32      1.73      2.45      5.11                   DISTCA 
 
ALL (N)         6        24        42        67       127     156     837   DISTALL 
ALL (P)      0.72      2.87      5.02      8.00     15.17             837   DISTALL 
ALL (RMS)    0.72      1.47      1.99      2.93      5.67                   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            15             4          RMSLSI 
CA  (P)       77.78         13.89          3.70          RMSLSI 
CA  (RMS)      1.02          5.74          6.19          RMSLSI 
 
 
 
END of the results output 
