 
####################################################### 
#                                                     # 
#                        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/T0060.inter 
CONANA-PAIR            ../CONANA/T0060.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0060.1gif_A.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0060.1fim.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 884 atoms, MODEL 897 atoms, 883 common with TARGET 
           Number of atoms possible to evaluate: 850 
 
 
 CA-RMS TARGET<->PARENT(1gif-A)	 1.091738 
 
 CA-RMS TARGET<->PARENT(1fim)	 1.538250 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    31.41           85.3   224    96.6   232     ARMSMC  
     WELL ORDERED  . . . . .    31.41           85.3   224    96.6   232     ARMSMC  
     NO INTER CONTACTS . . .    34.42           85.2   115    98.3   117     ARMSMC  
     SHIFTED CHAIN . . . . .    37.90           82.8   116    97.5   119     ARMSMC  
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSMC  
     SECONDARY STRUCTURE . .    14.72           94.9   117    99.2   118     ARMSMC  
     LARGE SHIFTS/INSERTIONS   127.04            0.0     2    40.0     5     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    36.35           83.3   138    95.2   145     ARMSMC  
     BURIED  . . . . . . . .    21.19           88.4    86    98.9    87     ARMSMC  
     CORE  . . . . . . . . .    29.15           86.0   222    97.8   227     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.60           51.6    91    95.8    95     ARMSSC1 
     WELL ORDERED  . . . . .    68.60           51.6    91    95.8    95     ARMSSC1 
     NO INTER CONTACTS . . .    59.67           57.4    47    97.9    48     ARMSSC1 
     RELIABLE SIDE CHAINS  .    69.84           48.8    84    95.5    88     ARMSSC1 
     CHANGED ANGLES  . . . .    88.64           31.7    41    93.2    44     ARMSSC1 
     SHIFTED CHAIN . . . . .    74.29           48.9    45    95.7    47     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SECONDARY STRUCTURE . .    71.45           51.9    52   100.0    52     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    74.57           48.1    52    94.5    55     ARMSSC1 
     BURIED  . . . . . . . .    59.73           56.4    39    97.5    40     ARMSSC1 
     CORE  . . . . . . . . .    68.60           51.6    91    97.8    93     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    56.90           56.7    67    95.7    70     ARMSSC2 
     WELL ORDERED  . . . . .    56.55           59.0    61    95.3    64     ARMSSC2 
     NO INTER CONTACTS . . .    62.56           51.4    37    97.4    38     ARMSSC2 
     RELIABLE SIDE CHAINS  .    49.36           59.6    47    95.9    49     ARMSSC2 
     CHANGED ANGLES  . . . .    62.31           53.5    43    95.6    45     ARMSSC2 
     SHIFTED CHAIN . . . . .    61.26           55.6    36    94.7    38     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SECONDARY STRUCTURE . .    60.24           55.0    40   100.0    40     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    52.55           55.3    38    95.0    40     ARMSSC2 
     BURIED  . . . . . . . .    62.15           58.6    29    96.7    30     ARMSSC2 
     CORE  . . . . . . . . .    56.90           56.7    67    98.5    68     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   101.16           13.0    23   100.0    23     ARMSSC3 
     WELL ORDERED  . . . . .   100.40            6.2    16   100.0    16     ARMSSC3 
     NO INTER CONTACTS . . .   105.14           15.4    13   100.0    13     ARMSSC3 
     RELIABLE SIDE CHAINS  .    98.66           15.0    20   100.0    20     ARMSSC3 
     CHANGED ANGLES  . . . .   101.40            9.5    21   100.0    21     ARMSSC3 
     SHIFTED CHAIN . . . . .    98.47           16.7    12   100.0    12     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    99.64            8.3    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    96.04           16.7    18   100.0    18     ARMSSC3 
     BURIED  . . . . . . . .   117.78            0.0     5   100.0     5     ARMSSC3 
     CORE  . . . . . . . . .   101.16           13.0    23   100.0    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.91           36.4    11   100.0    11     ARMSSC4 
     WELL ORDERED  . . . . .    91.65           28.6     7   100.0     7     ARMSSC4 
     NO INTER CONTACTS . . .    96.52           28.6     7   100.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .    80.91           36.4    11   100.0    11     ARMSSC4 
     CHANGED ANGLES  . . . .    80.91           36.4    11   100.0    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    72.44           33.3     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    75.73           33.3     6   100.0     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 . . . . . . . .    71.73           44.4     9   100.0     9     ARMSSC4 
     BURIED  . . . . . . . .   113.37            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .    80.91           36.4    11   100.0    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.32106     r(1,2) =  -0.22515     r(1,3) =   0.91991 
 r(2,1) =   0.68346     r(2,2) =   0.61731     r(2,3) =   0.38963 
 r(3,1) =  -0.65559     r(3,2) =   0.75381     r(3,3) =  -0.04431 
THE OFFSET VECTOR: 
 v(1) =  11.05039     v(2) =   4.34921     v(3) =  41.47708 
 
 Number of iteration 29                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.20           (Number of atoms:  106) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.38        113    96.6   117     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0122                            CRMSCA  
     WELL ORDERED  . . . . .    1.38        113    96.6   117     CRMSCA  
     NO INTER CONTACTS . . .    1.39         58    98.3    59     CRMSCA  
     SHIFTED CHAIN . . . . .    1.73         58    96.7    60     CRMSCA  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSCA  
     SECONDARY STRUCTURE . .    1.14         59   100.0    59     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    2.65          1    33.3     3     CRMSCA  
     SURFACE . . . . . . . .    1.42         70    95.9    73     CRMSCA  
     BURIED  . . . . . . . .    1.32         43    97.7    44     CRMSCA  
     CORE  . . . . . . . . .    1.37        112    98.2   114     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.42        555    96.4   576     CRMSMC  
     WELL ORDERED  . . . . .    1.42        555    96.4   576     CRMSMC  
     NO INTER CONTACTS . . .    1.40        284    97.9   290     CRMSMC  
     SHIFTED CHAIN . . . . .    1.73        283    96.6   293     CRMSMC  
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSMC  
     SECONDARY STRUCTURE . .    1.21        295   100.0   295     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    2.35          4    28.6    14     CRMSMC  
     SURFACE . . . . . . . .    1.44        340    95.5   356     CRMSMC  
     BURIED  . . . . . . . .    1.38        215    97.7   220     CRMSMC  
     CORE  . . . . . . . . .    1.41        551    98.0   562     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    2.59        399    95.9   416     CRMSSC  
     WELL ORDERED  . . . . .    2.57        372    95.6   389     CRMSSC  
     NO INTER CONTACTS . . .    2.44        201    98.5   204     CRMSSC  
     RELIABLE SIDE CHAINS  .    2.57        335    95.7   350     CRMSSC  
     CHANGED ANGLES  . . . .    3.27        194    94.6   205     CRMSSC  
     SECONDARY STRUCTURE . .    2.51        237   100.0   237     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    11     CRMSSC  
     SURFACE . . . . . . . .    2.80        233    94.3   247     CRMSSC  
     BURIED  . . . . . . . .    2.26        166    98.2   169     CRMSSC  
     CORE  . . . . . . . . .    2.59        399    98.5   405     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    2.04        850    96.2   884     CRMSALL 
     WELL ORDERED  . . . . .    2.02        823    96.0   857     CRMSALL 
     NO INTER CONTACTS . . .    1.95        432    98.2   440     CRMSALL 
     SHIFTED CHAIN . . . . .    2.17        430    95.8   449     CRMSALL 
     ALTERNATIVE PARENT  . .    0.00          0     0.0     0     CRMSALL 
     SECONDARY STRUCTURE . .    1.96        473   100.0   473     CRMSALL 
     LARGE SHIFTS/INSERTIONS    2.35          4    17.4    23     CRMSALL 
     SURFACE . . . . . . . .    2.16        512    95.0   539     CRMSALL 
     BURIED  . . . . . . . .    1.86        338    98.0   345     CRMSALL 
     CORE  . . . . . . . . .    2.04        846    98.3   861     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOPS cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOPS 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 . . . . . . . . . .    0.486      0.203       0.154    113    96.6   117     ERRCA  
     WELL ORDERED  . . . . .    0.486      0.203       0.154    113    96.6   117     ERRCA  
     NO INTER CONTACTS . . .    0.495      0.206       0.157     58    98.3    59     ERRCA  
     SHIFTED CHAIN . . . . .    0.647      0.213       0.115     58    96.7    60     ERRCA  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRCA  
     SECONDARY STRUCTURE . .    0.393      0.193       0.174     59   100.0    59     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.650      0.452       0.226      1    33.3     3     ERRCA  
     SURFACE . . . . . . . .    0.462      0.181       0.126     70    95.9    73     ERRCA  
     BURIED  . . . . . . . .    0.524      0.237       0.199     43    97.7    44     ERRCA  
     CORE  . . . . . . . . .    0.476      0.200       0.153    112    98.2   114     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.500      0.204       0.150    555    96.4   576     ERRMC  
     WELL ORDERED  . . . . .    0.500      0.204       0.150    555    96.4   576     ERRMC  
     NO INTER CONTACTS . . .    0.502      0.208       0.156    284    97.9   290     ERRMC  
     SHIFTED CHAIN . . . . .    0.655      0.215       0.115    283    96.6   293     ERRMC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRMC  
     SECONDARY STRUCTURE . .    0.404      0.189       0.163    295   100.0   295     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.341      0.399       0.200      4    28.6    14     ERRMC  
     SURFACE . . . . . . . .    0.476      0.186       0.124    340    95.5   356     ERRMC  
     BURIED  . . . . . . . .    0.538      0.232       0.191    215    97.7   220     ERRMC  
     CORE  . . . . . . . . .    0.494      0.202       0.149    551    98.0   562     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    1.216      0.313       0.180    399    95.9   416     ERRSC  
     WELL ORDERED  . . . . .    1.190      0.306       0.177    372    95.6   389     ERRSC  
     NO INTER CONTACTS . . .    1.150      0.310       0.183    201    98.5   204     ERRSC  
     RELIABLE SIDE CHAINS  .    1.179      0.303       0.175    335    95.7   350     ERRSC  
     CHANGED ANGLES  . . . .    1.800      0.394       0.208    194    94.6   205     ERRSC  
     SHIFTED CHAIN . . . . .    1.292      0.327       0.175    198    94.7   209     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRSC  
     SECONDARY STRUCTURE . .    1.185      0.305       0.177    237   100.0   237     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    11     ERRSC  
     SURFACE . . . . . . . .    1.355      0.331       0.185    233    94.3   247     ERRSC  
     BURIED  . . . . . . . .    1.021      0.287       0.172    166    98.2   169     ERRSC  
     CORE  . . . . . . . . .    1.216      0.313       0.180    399    98.5   405     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.830      0.253       0.164    850    96.2   884     ERRALL 
     WELL ORDERED  . . . . .    0.806      0.249       0.162    823    96.0   857     ERRALL 
     NO INTER CONTACTS . . .    0.798      0.253       0.167    432    98.2   440     ERRALL 
     SHIFTED CHAIN . . . . .    0.939      0.264       0.141    430    95.8   449     ERRALL 
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     0     ERRALL 
     SECONDARY STRUCTURE . .    0.791      0.248       0.173    473   100.0   473     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.341      0.399       0.200      4    17.4    23     ERRALL 
     SURFACE . . . . . . . .    0.869      0.250       0.150    512    95.0   539     ERRALL 
     BURIED  . . . . . . . .    0.770      0.259       0.184    338    98.0   345     ERRALL 
     CORE  . . . . . . . . .    0.828      0.253       0.164    846    98.3   861     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)        49        99       112       113       113     113     117   DISTCA 
CA  (P)     41.88     84.62     95.73     96.58     96.58             117   DISTCA 
CA  (RMS)    0.71      1.08      1.34      1.38      1.38                   DISTCA 
 
ALL (N)       275       637       771       829       849     850     884   DISTALL 
ALL (P)     31.11     72.06     87.22     93.78     96.04             884   DISTALL 
ALL (RMS)    0.72      1.17      1.49      1.75      2.01                   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)         114           112             1          RMSLSI 
CA  (P)       97.44         95.73          0.85          RMSLSI 
CA  (RMS)      1.09          1.37          2.65          RMSLSI 
 
 
 
END of the results output 
