 
####################################################### 
#                                                     # 
#                        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/T0058.inter 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0058.1akz.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0058.1udh.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 1784 atoms, MODEL 989 atoms, 973 common with TARGET 
           Number of atoms possible to evaluate: 828 
 
 
 CA-RMS TARGET<->PARENT(1akz)	 1.191923 
 
 CA-RMS TARGET<->PARENT(1udh)	 1.648171 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.48           50.5   402    89.7   448     ARMSMC  
     WELL ORDERED  . . . . .    78.92           50.9   399    89.7   445     ARMSMC  
     NO INTER CONTACTS . . .    78.24           51.8   282    89.5   315     ARMSMC  
     SHIFTED CHAIN . . . . .    84.06           46.5   114    85.1   134     ARMSMC  
     ALTERNATIVE PARENT  . .    46.90           25.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    67.79           61.7   154    97.5   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS    91.24           36.4    22   100.0    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    80.03           48.7   191    83.8   228     ARMSMC  
     BURIED  . . . . . . . .    78.98           52.1   211    95.9   220     ARMSMC  
     CORE  . . . . . . . . .    78.75           51.3   380    89.2   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   190     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   176     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   173     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    58     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    58     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    97     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    93     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   148     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   132     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   102     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    74     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    80     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    68     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    33     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    32     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     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 . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.13095     r(1,2) =   0.11876     r(1,3) =   0.98425 
 r(2,1) =  -0.68982     r(2,2) =  -0.72397     r(2,3) =  -0.00442 
 r(3,1) =   0.71204     r(3,2) =  -0.67953     r(3,3) =   0.17673 
THE OFFSET VECTOR: 
 v(1) =   5.16374     v(2) =  56.05721     v(3) =  19.97446 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.64           (Number of atoms:    7) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   21.79        207    92.0   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1053                            CRMSCA  
     WELL ORDERED  . . . . .   21.75        206    92.0   224     CRMSCA  
     NO INTER CONTACTS . . .   20.17        145    91.8   158     CRMSCA  
     SHIFTED CHAIN . . . . .   24.15         59    86.8    68     CRMSCA  
     ALTERNATIVE PARENT  . .   32.94          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .   21.30         78    98.7    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS   28.21         12   100.0    12     CRMSCA  
     SURFACE . . . . . . . .   24.69         99    86.1   115     CRMSCA  
     BURIED  . . . . . . . .   18.74        108    98.2   110     CRMSCA  
     CORE  . . . . . . . . .   21.33        195    91.5   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   21.81        828    74.8  1107     CRMSMC  
     WELL ORDERED  . . . . .   21.76        820    74.9  1095     CRMSMC  
     NO INTER CONTACTS . . .   20.20        580    74.6   778     CRMSMC  
     SHIFTED CHAIN . . . . .   24.38        236    70.7   334     CRMSMC  
     ALTERNATIVE PARENT  . .   32.95          8    80.0    10     CRMSMC  
     SECONDARY STRUCTURE . .   21.38        312    79.2   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS   28.44         48    81.4    59     CRMSMC  
     SURFACE . . . . . . . .   24.67        396    70.0   566     CRMSMC  
     BURIED  . . . . . . . .   18.82        432    79.9   541     CRMSMC  
     CORE  . . . . . . . . .   21.34        780    74.4  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   884     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   816     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   704     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   328     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    36     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   448     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   436     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   21.81        828    46.4  1784     CRMSALL 
     WELL ORDERED  . . . . .   21.76        820    48.0  1708     CRMSALL 
     NO INTER CONTACTS . . .   20.20        580    46.0  1262     CRMSALL 
     SHIFTED CHAIN . . . . .   24.38        236    44.5   530     CRMSALL 
     ALTERNATIVE PARENT  . .   32.95          8    61.5    13     CRMSALL 
     SECONDARY STRUCTURE . .   21.38        312    47.5   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS   28.44         48    57.1    84     CRMSALL 
     SURFACE . . . . . . . .   24.67        396    43.6   908     CRMSALL 
     BURIED  . . . . . . . .   18.82        432    49.3   876     CRMSALL 
     CORE  . . . . . . . . .   21.34        780    45.9  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    31.41      8   100.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    31.81     32    80.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    31.81     32    55.2    58     222-PVLPAESE-229  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.81      8   100.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.70     32    80.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.70     32    55.2    58     222-PVLPAESE-229  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   19.113      1.000       0.500    207    92.0   225     ERRCA  
     WELL ORDERED  . . . . .   19.064      1.000       0.500    206    92.0   224     ERRCA  
     NO INTER CONTACTS . . .   17.657      1.000       0.500    145    91.8   158     ERRCA  
     SHIFTED CHAIN . . . . .   21.656      1.000       0.500     59    86.8    68     ERRCA  
     ALTERNATIVE PARENT  . .   31.371      1.000       0.500      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .   19.294      1.000       0.500     78    98.7    79     ERRCA  
     LARGE SHIFTS/INSERTIONS   26.707      1.000       0.500     12   100.0    12     ERRCA  
     SURFACE . . . . . . . .   22.030      1.000       0.500     99    86.1   115     ERRCA  
     BURIED  . . . . . . . .   16.440      1.000       0.500    108    98.2   110     ERRCA  
     CORE  . . . . . . . . .   18.646      1.000       0.500    195    91.5   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   19.144      1.000       0.500    828    74.8  1107     ERRMC  
     WELL ORDERED  . . . . .   19.081      1.000       0.500    820    74.9  1095     ERRMC  
     NO INTER CONTACTS . . .   17.685      1.000       0.500    580    74.6   778     ERRMC  
     SHIFTED CHAIN . . . . .   21.862      1.000       0.500    236    70.7   334     ERRMC  
     ALTERNATIVE PARENT  . .   31.545      1.000       0.500      8    80.0    10     ERRMC  
     SECONDARY STRUCTURE . .   19.403      1.000       0.500    312    79.2   394     ERRMC  
     LARGE SHIFTS/INSERTIONS   26.797      1.000       0.500     48    81.4    59     ERRMC  
     SURFACE . . . . . . . .   22.010      1.000       0.500    396    70.0   566     ERRMC  
     BURIED  . . . . . . . .   16.518      1.000       0.500    432    79.9   541     ERRMC  
     CORE  . . . . . . . . .   18.673      1.000       0.500    780    74.4  1048     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   884     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   816     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   630     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   704     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   328     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   258     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     5     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    36     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   448     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   436     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .   19.144      1.000       0.500    828    46.4  1784     ERRALL 
     WELL ORDERED  . . . . .   19.081      1.000       0.500    820    48.0  1708     ERRALL 
     NO INTER CONTACTS . . .   17.685      1.000       0.500    580    46.0  1262     ERRALL 
     SHIFTED CHAIN . . . . .   21.862      1.000       0.500    236    44.5   530     ERRALL 
     ALTERNATIVE PARENT  . .   31.545      1.000       0.500      8    61.5    13     ERRALL 
     SECONDARY STRUCTURE . .   19.403      1.000       0.500    312    47.5   657     ERRALL 
     LARGE SHIFTS/INSERTIONS   26.797      1.000       0.500     48    57.1    84     ERRALL 
     SURFACE . . . . . . . .   22.010      1.000       0.500    396    43.6   908     ERRALL 
     BURIED  . . . . . . . .   16.518      1.000       0.500    432    49.3   876     ERRALL 
     CORE  . . . . . . . . .   18.673      1.000       0.500    780    45.9  1700     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)         1         5         7        13        43     207     225   DISTCA 
CA  (P)      0.44      2.22      3.11      5.78     19.11             225   DISTCA 
CA  (RMS)    0.57      1.28      1.64      3.16      7.06                   DISTCA 
 
ALL (N)         4        17        27        43       170     828    1784   DISTALL 
ALL (P)      0.22      0.95      1.51      2.41      9.53            1784   DISTALL 
ALL (RMS)    0.74      1.37      1.89      2.87      6.97                   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)         213           195            12          RMSLSI 
CA  (P)       94.67         86.67          5.33          RMSLSI 
CA  (RMS)      0.91         21.33         28.21          RMSLSI 
 
 
 
END of the results output 
