 
####################################################### 
#                                                     # 
#                        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/T0073.inter 
CONANA-PAIR            ../CONANA/T0073.pair 
# 
NUMBER-OF-PARENTS      1 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0073.1cos.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 358 atoms, MODEL 337 atoms, 336 common with TARGET 
           Number of atoms possible to evaluate: 24 
 
 
 CA-RMS TARGET<->PARENT(1cos)	 1.128383 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.78           30.0    10    10.6    94     ARMSMC  
     WELL ORDERED  . . . . .    84.78           30.0    10    10.6    94     ARMSMC  
     NO INTER CONTACTS . . .    90.76           20.0     5    26.3    19     ARMSMC  
     SHIFTED CHAIN . . . . .    90.34           20.0     5    10.9    46     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    78.83           40.0     5     6.1    82     ARMSMC  
     LARGE SHIFTS/INSERTIONS    26.59           50.0     2    11.8    17     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    84.78           30.0    10    11.5    87     ARMSMC  
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSMC  
     CORE  . . . . . . . . .    93.85           25.0     8    10.4    77     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    37     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    37     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     6     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    37     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    27     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    17     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     7     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    34     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    30     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    32     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    29     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     5     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    19     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    13     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    29     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    29     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    26     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    15     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     3     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    15     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    17     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    16     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     1     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     8     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0     7     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     7     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.95241     r(1,2) =   0.15106     r(1,3) =   0.26475 
 r(2,1) =   0.29985     r(2,2) =   0.62039     r(2,3) =   0.72471 
 r(3,1) =  -0.05477     r(3,2) =   0.76961     r(3,3) =  -0.63616 
THE OFFSET VECTOR: 
 v(1) =  23.03064     v(2) =  16.85804     v(3) = -11.67064 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   2.71           (Number of atoms:    6) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.71          6    12.5    48     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4518                            CRMSCA  
     WELL ORDERED  . . . . .    2.71          6    12.5    48     CRMSCA  
     NO INTER CONTACTS . . .    3.26          3    30.0    10     CRMSCA  
     SHIFTED CHAIN . . . . .    3.18          3    12.5    24     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    2.14          3     7.3    41     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    1.84          1    11.1     9     CRMSCA  
     SURFACE . . . . . . . .    2.71          6    13.6    44     CRMSCA  
     BURIED  . . . . . . . .    0.00          0     0.0     4     CRMSCA  
     CORE  . . . . . . . . .    2.85          5    12.8    39     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.75         24    10.1   237     CRMSMC  
     WELL ORDERED  . . . . .    2.75         24    10.1   237     CRMSMC  
     NO INTER CONTACTS . . .    2.84         12    25.5    47     CRMSMC  
     SHIFTED CHAIN . . . . .    2.72         12    10.3   117     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    2.79         12     5.9   205     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    1.54          4     9.3    43     CRMSMC  
     SURFACE . . . . . . . .    2.75         24    11.0   219     CRMSMC  
     BURIED  . . . . . . . .    0.00          0     0.0    18     CRMSMC  
     CORE  . . . . . . . . .    2.94         20    10.3   194     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   167     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   156     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0    26     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   137     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   100     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   146     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    33     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   155     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    12     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   134     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.75         24     6.7   358     CRMSALL 
     WELL ORDERED  . . . . .    2.75         24     6.9   347     CRMSALL 
     NO INTER CONTACTS . . .    2.84         12    18.5    65     CRMSALL 
     SHIFTED CHAIN . . . . .    2.72         12     7.0   171     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    2.79         12     3.9   310     CRMSALL 
     LARGE SHIFTS/INSERTIONS    1.54          4     5.9    68     CRMSALL 
     SURFACE . . . . . . . .    2.75         24     7.3   331     CRMSALL 
     BURIED  . . . . . . . .    0.00          0     0.0    27     CRMSALL 
     CORE  . . . . . . . . .    2.94         20     6.9   290     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     0.00      0     0.0     8      41-SKLQALKG-48   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     0.00      0     0.0    38      41-SKLQALKG-48   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     0.00      0     0.0    57      41-SKLQALKG-48   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 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 . . . . . . . . . .    2.515      1.000       0.500      6    12.5    48     ERRCA  
     WELL ORDERED  . . . . .    2.515      1.000       0.500      6    12.5    48     ERRCA  
     NO INTER CONTACTS . . .    3.076      1.000       0.500      3    30.0    10     ERRCA  
     SHIFTED CHAIN . . . . .    2.953      1.000       0.500      3    12.5    24     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    2.077      1.000       0.500      3     7.3    41     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.844      1.000       0.500      1    11.1     9     ERRCA  
     SURFACE . . . . . . . .    2.515      1.000       0.500      6    13.6    44     ERRCA  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0     4     ERRCA  
     CORE  . . . . . . . . .    2.649      1.000       0.500      5    12.8    39     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.436      1.000       0.500     24    10.1   237     ERRMC  
     WELL ORDERED  . . . . .    2.436      1.000       0.500     24    10.1   237     ERRMC  
     NO INTER CONTACTS . . .    2.554      1.000       0.500     12    25.5    47     ERRMC  
     SHIFTED CHAIN . . . . .    2.396      1.000       0.500     12    10.3   117     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    2.475      1.000       0.500     12     5.9   205     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.471      1.000       0.500      4     9.3    43     ERRMC  
     SURFACE . . . . . . . .    2.436      1.000       0.500     24    11.0   219     ERRMC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    18     ERRMC  
     CORE  . . . . . . . . .    2.629      1.000       0.500     20    10.3   194     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   167     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   156     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0    26     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   137     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   100     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0    76     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   146     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    33     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   155     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    12     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   134     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.436      1.000       0.500     24     6.7   358     ERRALL 
     WELL ORDERED  . . . . .    2.436      1.000       0.500     24     6.9   347     ERRALL 
     NO INTER CONTACTS . . .    2.554      1.000       0.500     12    18.5    65     ERRALL 
     SHIFTED CHAIN . . . . .    2.396      1.000       0.500     12     7.0   171     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    2.475      1.000       0.500     12     3.9   310     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.471      1.000       0.500      4     5.9    68     ERRALL 
     SURFACE . . . . . . . .    2.436      1.000       0.500     24     7.3   331     ERRALL 
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    27     ERRALL 
     CORE  . . . . . . . . .    2.629      1.000       0.500     20     6.9   290     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         5         6         6       6      48   DISTCA 
CA  (P)      0.00      4.17     10.42     12.50     12.50              48   DISTCA 
CA  (RMS)    0.00      1.63      2.15      2.71      2.71                   DISTCA 
 
ALL (N)         3        11        17        23        24      24     358   DISTALL 
ALL (P)      0.84      3.07      4.75      6.42      6.70             358   DISTALL 
ALL (RMS)    0.76      1.38      1.91      2.57      2.75                   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)          39             5             1          RMSLSI 
CA  (P)       81.25         10.42          2.08          RMSLSI 
CA  (RMS)      1.02          2.85          1.84          RMSLSI 
 
 
 
END of the results output 
