 
####################################################### 
#                                                     # 
#                        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: 117 
 
 
 CA-RMS TARGET<->PARENT(2cbp)	 1.470937 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.10           61.5    26    12.1   214     ARMSMC  
     WELL ORDERED  . . . . .    69.10           61.5    26    14.4   181     ARMSMC  
     NO INTER CONTACTS . . .    76.44           57.1    21    12.8   164     ARMSMC  
     SHIFTED CHAIN . . . . .    96.29           33.3     6     5.5   110     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    64.58           62.5     8    10.0    80     ARMSMC  
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    46     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    40.06           66.7    12     9.1   132     ARMSMC  
     BURIED  . . . . . . . .    86.56           57.1    14    17.1    82     ARMSMC  
     CORE  . . . . . . . . .    69.10           61.5    26    15.5   168     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    75.13           61.5    13    13.8    94     ARMSSC1 
     WELL ORDERED  . . . . .    75.13           61.5    13    20.6    63     ARMSSC1 
     NO INTER CONTACTS . . .    85.29           50.0    10    13.3    75     ARMSSC1 
     RELIABLE SIDE CHAINS  .    70.62           66.7    12    14.6    82     ARMSSC1 
     CHANGED ANGLES  . . . .    84.06           50.0     2     4.3    47     ARMSSC1 
     SHIFTED CHAIN . . . . .    68.70           66.7     3     6.4    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .   105.71           25.0     4    11.1    36     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    21     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    66.95           71.4     7    12.1    58     ARMSSC1 
     BURIED  . . . . . . . .    83.66           50.0     6    16.7    36     ARMSSC1 
     CORE  . . . . . . . . .    75.13           61.5    13    17.8    73     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    51.70           70.0    10    16.4    61     ARMSSC2 
     WELL ORDERED  . . . . .    51.70           70.0    10    30.3    33     ARMSSC2 
     NO INTER CONTACTS . . .    56.29           75.0     8    15.7    51     ARMSSC2 
     RELIABLE SIDE CHAINS  .    20.35           75.0     8    19.0    42     ARMSSC2 
     CHANGED ANGLES  . . . .     5.31          100.0     1     2.5    40     ARMSSC2 
     SHIFTED CHAIN . . . . .    23.72           50.0     2     7.4    27     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    10.25          100.0     3    11.1    27     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    13     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    70.49           60.0     5    13.2    38     ARMSSC2 
     BURIED  . . . . . . . .    19.39           80.0     5    21.7    23     ARMSSC2 
     CORE  . . . . . . . . .    51.70           70.0    10    20.8    48     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    67.01           66.7     3    16.7    18     ARMSSC3 
     WELL ORDERED  . . . . .   114.50            0.0     1    33.3     3     ARMSSC3 
     NO INTER CONTACTS . . .    82.04           50.0     2    11.8    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    13.47          100.0     2    15.4    13     ARMSSC3 
     CHANGED ANGLES  . . . .    81.00           50.0     2    11.8    17     ARMSSC3 
     SHIFTED CHAIN . . . . .    18.73          100.0     1    10.0    10     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .   114.50            0.0     1    10.0    10     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     4     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    67.01           66.7     3    18.8    16     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
     CORE  . . . . . . . . .    67.01           66.7     3    21.4    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.34           50.0     2    33.3     6     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     NO INTER CONTACTS . . .     1.21          100.0     1    20.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .    74.34           50.0     2    33.3     6     ARMSSC4 
     CHANGED ANGLES  . . . .     1.21          100.0     1    25.0     4     ARMSSC4 
     SHIFTED CHAIN . . . . .     1.21          100.0     1    33.3     3     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     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 . . . . . . . .    74.34           50.0     2    33.3     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    74.34           50.0     2    33.3     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.35948     r(1,2) =   0.89545     r(1,3) =   0.26256 
 r(2,1) =  -0.34744     r(2,2) =   0.38957     r(2,3) =  -0.85295 
 r(3,1) =  -0.86606     r(3,2) =   0.21540     r(3,3) =   0.45116 
THE OFFSET VECTOR: 
 v(1) =  14.19938     v(2) = -10.07542     v(3) =  79.65945 
 
 Number of iteration 23                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.89           (Number of atoms:    4) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.74         14    13.0   108     CRMSCA  
     CRN = ALL/NP  . . . . .    0.6244                            CRMSCA  
     WELL ORDERED  . . . . .    8.74         14    15.4    91     CRMSCA  
     NO INTER CONTACTS . . .    7.36         11    13.3    83     CRMSCA  
     SHIFTED CHAIN . . . . .   11.66          4     7.1    56     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    5.15          4    10.0    40     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    24     CRMSCA  
     SURFACE . . . . . . . .    9.75          7    10.4    67     CRMSCA  
     BURIED  . . . . . . . .    7.60          7    17.1    41     CRMSCA  
     CORE  . . . . . . . . .    8.74         14    16.7    84     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.06         69    12.9   533     CRMSMC  
     WELL ORDERED  . . . . .    9.06         69    15.7   439     CRMSMC  
     NO INTER CONTACTS . . .    7.60         54    13.2   410     CRMSMC  
     SHIFTED CHAIN . . . . .   12.17         19     6.9   276     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    5.36         20    10.1   199     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   120     CRMSMC  
     SURFACE . . . . . . . .   10.06         35    10.5   332     CRMSMC  
     BURIED  . . . . . . . .    7.90         34    16.9   201     CRMSMC  
     CORE  . . . . . . . . .    9.06         69    16.7   413     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   10.30         61    15.1   405     CRMSSC  
     WELL ORDERED  . . . . .   10.33         54    19.7   274     CRMSSC  
     NO INTER CONTACTS . . .    9.89         48    14.7   327     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.56         53    16.4   323     CRMSSC  
     CHANGED ANGLES  . . . .   12.01         13     7.1   184     CRMSSC  
     SECONDARY STRUCTURE . .    6.71         18    10.2   176     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    83     CRMSSC  
     SURFACE . . . . . . . .   10.00         30    12.8   234     CRMSSC  
     BURIED  . . . . . . . .   10.58         31    18.1   171     CRMSSC  
     CORE  . . . . . . . . .   10.30         61    18.9   322     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.64        117    14.0   837     CRMSALL 
     WELL ORDERED  . . . . .    9.61        110    17.3   635     CRMSALL 
     NO INTER CONTACTS . . .    8.78         92    14.0   659     CRMSALL 
     SHIFTED CHAIN . . . . .   13.06         27     6.5   417     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    6.04         34    10.1   336     CRMSALL 
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0   179     CRMSALL 
     SURFACE . . . . . . . .    9.99         58    11.6   502     CRMSALL 
     BURIED  . . . . . . . .    9.27         59    17.6   335     CRMSALL 
     CORE  . . . . . . . . .    9.64        117    17.8   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     0.00      0     0.0     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     0.00      0     0.0    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     0.00      0     0.0    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 . . . . . . . . . .    6.833      1.000       0.500     14    13.0   108     ERRCA  
     WELL ORDERED  . . . . .    6.833      1.000       0.500     14    15.4    91     ERRCA  
     NO INTER CONTACTS . . .    6.200      1.000       0.500     11    13.3    83     ERRCA  
     SHIFTED CHAIN . . . . .    9.142      1.000       0.500      4     7.1    56     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    4.714      1.000       0.500      4    10.0    40     ERRCA  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    24     ERRCA  
     SURFACE . . . . . . . .    7.476      1.000       0.500      7    10.4    67     ERRCA  
     BURIED  . . . . . . . .    6.190      1.000       0.500      7    17.1    41     ERRCA  
     CORE  . . . . . . . . .    6.833      1.000       0.500     14    16.7    84     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.051      1.000       0.500     69    12.9   533     ERRMC  
     WELL ORDERED  . . . . .    7.051      1.000       0.500     69    15.7   439     ERRMC  
     NO INTER CONTACTS . . .    6.319      1.000       0.500     54    13.2   410     ERRMC  
     SHIFTED CHAIN . . . . .    9.475      1.000       0.500     19     6.9   276     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    4.874      1.000       0.500     20    10.1   199     ERRMC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   120     ERRMC  
     SURFACE . . . . . . . .    7.791      1.000       0.500     35    10.5   332     ERRMC  
     BURIED  . . . . . . . .    6.290      1.000       0.500     34    16.9   201     ERRMC  
     CORE  . . . . . . . . .    7.051      1.000       0.500     69    16.7   413     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.665      1.000       0.500     61    15.1   405     ERRSC  
     WELL ORDERED  . . . . .    8.569      1.000       0.500     54    19.7   274     ERRSC  
     NO INTER CONTACTS . . .    8.460      1.000       0.500     48    14.7   327     ERRSC  
     RELIABLE SIDE CHAINS  .    8.833      1.000       0.500     53    16.4   323     ERRSC  
     CHANGED ANGLES  . . . .   10.386      1.000       0.500     13     7.1   184     ERRSC  
     SHIFTED CHAIN . . . . .   13.865      1.000       0.500     11     5.7   193     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    5.635      1.000       0.500     18    10.2   176     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    83     ERRSC  
     SURFACE . . . . . . . .    8.207      1.000       0.500     30    12.8   234     ERRSC  
     BURIED  . . . . . . . .    9.108      1.000       0.500     31    18.1   171     ERRSC  
     CORE  . . . . . . . . .    8.665      1.000       0.500     61    18.9   322     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.793      1.000       0.500    117    14.0   837     ERRALL 
     WELL ORDERED  . . . . .    7.691      1.000       0.500    110    17.3   635     ERRALL 
     NO INTER CONTACTS . . .    7.337      1.000       0.500     92    14.0   659     ERRALL 
     SHIFTED CHAIN . . . . .   10.878      1.000       0.500     27     6.5   417     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    5.270      1.000       0.500     34    10.1   336     ERRALL 
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0   179     ERRALL 
     SURFACE . . . . . . . .    7.971      1.000       0.500     58    11.6   502     ERRALL 
     BURIED  . . . . . . . .    7.618      1.000       0.500     59    17.6   335     ERRALL 
     CORE  . . . . . . . . .    7.793      1.000       0.500    117    17.8   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         2         4         6        12      14     108   DISTCA 
CA  (P)      0.00      1.85      3.70      5.56     11.11             108   DISTCA 
CA  (RMS)    0.00      1.54      1.89      2.95      5.54                   DISTCA 
 
ALL (N)         2        11        22        44        89     117     837   DISTALL 
ALL (P)      0.24      1.31      2.63      5.26     10.63             837   DISTALL 
ALL (RMS)    0.80      1.39      2.00      3.22      5.60                   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            14             0          RMSLSI 
CA  (P)       77.78         12.96          0.00          RMSLSI 
CA  (RMS)      1.02          8.74          0.00          RMSLSI 
 
 
 
END of the results output 
