############################################################### ############################################################### ############################################################### ### CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12## ############################################################### User: unknown Run date: 24/ 4/2013 Run time: 19:32:38 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up.$TEXT:Reference1: $$ Main reference $$ "REFMAC5 for the refinement of macromolecular crystal structures:" G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) Acta Crystallogr. D67, 355-367 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference2: $$ Secondary reference $$ "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 EU Validation contract: BIO2CT-92-0524 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- make check NONE Data line--- make hydrogen ALL hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO newligand continue Data line--- NCSR LOCAL Data line--- refi type REST resi MLKF meth CGMAT bref ISOT Data line--- ncyc 300 Data line--- weight MATRIX 0.005 Data line--- ridg dist sigma 0.05 Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0 Data line--- labin FP=F_sls SIGFP=SIGF_sls FREE=FreeR_flag Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM Data line--- NOHARVEST Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: tpp_tutorial_data.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: /xtal/Suites/CCP4/ccp4-6.3.0/lib/data/syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - 1dbi_ssm-AB.pdb Output coordinate file. Logical name - XYZOUT actual file name - refmac_prosmart.pdb Input reflection file. Logical name - HKLIN actual file name - tpp_tutorial_data.mtz Output reflection file. Logical name - HKLOUT actual file name - refmac_prosmart.mtz Cell from mtz : 113.450 128.930 100.500 90.000 90.000 90.000 Space group from mtz: number - 18; name - P 21 21 2 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /xtal/Suites/CCP4/ccp4-6.3.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /xtal/Suites/CCP4/ccp4-6.3.0/lib/data/monomers/ener_lib.cif Program will rely on residue and atom names. No checking If this option is used then monomers should be checked carefully before using Hydrogens will be restored in their riding positions Links between monomers will be checked. Only those links present in the coordinate file will be used All links to sugar will be analysed and used For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif Symmetry related links will be analysed and used Cis peptides will be found and used automatically Residual : Rice Maximum Likelihood for Fs **** Least-square scaling parameters **** Overall scale Overall B value Overall anisotropic B with tr(B) = 0.0 Constant bulk solvent in non protein region Probe radii for non-ions 1.200 Probe radii for ions 0.800 Shrinkage of the mask by 0.800 **** Map sharpening parameters and methods **** No map sharpening will be performed Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0091 Refinement of individual isotropic Bfactors Refinement resln : 42.6014 2.3500 Estimated number of reflections : 81119 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.0050 Refinement cycles : 300 Scaling type : Wilson using 1 Gaussian Estimation of D/Sigma in resolution bins using free set of reflns with experimental sigmas using free set of reflns with experimental sigmas Scaling and SigmaA resln: 42.6014 2.3500 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups WEIGHT= 1.00 Chiral centers Weight= 1.00 NON-BONDED CONTACTS Overall weight = 1.00 Sigma for simple VDW = 0.20 Sigma for VDW trhough torsion angle = 0.20 Sigma for HBOND = 0.20 Sigma for metal-ion = 0.20 Sigma for DUMMY and other atom = 0.30 Distance for donor-accepetor = vdw1+vdw2+(-0.30) Distance for acceptor - H = vdw1+ ( 0.10) VDW distance through torsion = vdw1+vdw2+(-0.30) Distance for DUMMY-others = vdw1+vdw2+(-0.70) TORSION ANGLES Weight= 1.00 THERMAL FACTORS Weight= 1.00 Main chain bond (1-2 neighbour) 1.5A**2 Main chain angle (1-3 neighbour) 2.0A**2 Side chain bond 3.0A**2 Side chain angle 4.5A**2 NCS will defined automatically and applied **** Alignment parameters **** Alignment leve 80.000% Aligment cut 2.000A Iterative aligment N **** Local NCS parameters **** Maximum distance 4.2000A Maximum difference of distances 1.0000A Geman-Mcclure parameter 0.1000 Weights sigx = 0.0500 if dist1+dist2<8.0 sigx = 0.0500*sqrt((dist1+dist2)/8.0) if dist1+dist2>=8.0 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.00A Thermal parameters 0.00A**2 Occupancy parameters 0.00 Restraints on changes of interatomic distances is appplied **** Distance shift penlty parameters **** Sigma: 0.0500 Maximum distance 4.2000 Monitoring style is "MEDIUM". Complete information will be printed out in the first and last cycle. In all other cycles minimum information will be printed out Sigma cutoffs for printing out outliers If deviation of restraint parameter > alpha*sigma then information will be printed out Distance outliers 10.000 Angle outliers 10.000 Torsion outliers 10.000 Chiral volume outliers 10.000 Plane outliers 10.000 Non-bonding outliers 10.000 B value outliers 10.000 --------------------------------------------------------------- Input file :1dbi_ssm-AB.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.39 _lib_update 06/11/12 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 11462 with complete description : 11462 NUMBER OF MODIFICATIONS : 53 NUMBER OF LINKS : 66 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /xtal/Suites/CCP4/ccp4-6.3.0/lib/data/atomsf.lib Number of atoms : 4062 Number of residues : 542 Number of chains : 2 I am reading library. Please wait. mon_lib.cif WARNING : link:SS is found dist = 2.035 ideal_dist= 2.031 ch:AA res: 137 CYS at:SG .->AA res: 139 CYS at:SG . WARNING : link:SS is found dist = 2.035 ideal_dist= 2.031 ch:BB res: 137 CYS at:SG .->BB res: 139 CYS at:SG . -------------------------------- --- title of input coord file --- PDB_code:1DBI PDB_name:HYDROLASE PDB_date:02-NOV-99 -------------------------------- ATTENTION: atom:CG GLN 9 AA is missing in the structure ATTENTION: atom:CD GLN 9 AA is missing in the structure ATTENTION: atom:OE1 GLN 9 AA is missing in the structure ATTENTION: atom:NE2 GLN 9 AA is missing in the structure ATTENTION: atom:CG ASP 106 AA is missing in the structure ATTENTION: atom:OD1 ASP 106 AA is missing in the structure ATTENTION: atom:OD2 ASP 106 AA is missing in the structure ATTENTION: atom:CG ARG 107 AA is missing in the structure ATTENTION: atom:CD ARG 107 AA is missing in the structure ATTENTION: atom:NE ARG 107 AA is missing in the structure ATTENTION: atom:CZ ARG 107 AA is missing in the structure ATTENTION: atom:NH1 ARG 107 AA is missing in the structure ATTENTION: atom:NH2 ARG 107 AA is missing in the structure ATTENTION: atom:CG ASN 108 AA is missing in the structure ATTENTION: atom:OD1 ASN 108 AA is missing in the structure ATTENTION: atom:ND2 ASN 108 AA is missing in the structure ATTENTION: atom:CG GLN 9 BB is missing in the structure ATTENTION: atom:CD GLN 9 BB is missing in the structure ATTENTION: atom:OE1 GLN 9 BB is missing in the structure ATTENTION: atom:NE2 GLN 9 BB is missing in the structure ... and more ... Number of chains : 2 Total number of monomers : 542 Number of atoms : 7972 Number of missing atoms : 32 Number of rebuilt atoms : 3848 Number of unknown atoms : 0 Number of deleted atoms : 0 ********* Alignment results ********* ----------------------------------------------------------------------------------------------------------------------- : Ncsr group : Chain 1 : Chain 2 : No of aligned : Score : RMS : Ave(RmsLoc) : ----------------------------------------------------------------------------------------------------------------------- : 1 : A( 1 - 280 ) : B( 1 - 280 ) : 271 : 1.0000 : 0.2221 : 0.0642 : ----------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------- **** Assign all residues to one of the chains **** -------------------------------------------------------------------------------- The program will use local ncs restraints I.e. corresonding distances between ncs related molecules will be restrained. Covalent bonds and angles will not be included in these restraints. ---------------------------------------------------------------------------------------------- loop_ _atom_type_symbol _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669 -------------------------------------------------------------------------------- External restraints group : 1 External restraints file :input_keywords Fail if one of the atoms involved in the restraints is missing in the pdb file Use restraints for all defined atoms Ignore restraints if abs(dmod-drest) > 50.000000 *sigma Ignore retraints if input dist > 1.00000003E+32 Weight scale sigmas : 500.00000 Weight min sigma : 0.0000000 Weight max sigma : 100.00000 GM parameter : 0.10000000 Number of distances : 23442 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- --------------------------------------- Standard External All Bonds: 7862 23442 31304 Angles: 14170 0 14170 Chirals: 644 0 644 Planes: 1324 0 1324 Torsions: 3220 0 3220 --------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 3167 Number of all reflections 62056 -------------------------------------------------------------------------------- Number of reflections in file 62056 Number of reflections read 62056 CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 36 ALA CA . - A 132 ASN N . mod.= 4.897 id.= 4.899 dev= 0.002 sig.= 0.000 A 36 ALA C . - A 132 ASN N . mod.= 4.030 id.= 4.032 dev= 0.002 sig.= 0.000 A 37 VAL C . - A 100 LEU C . mod.= 5.304 id.= 5.306 dev= 0.002 sig.= 0.000 A 39 ASP N . - A 102 VAL N . mod.= 5.397 id.= 5.399 dev= 0.002 sig.= 0.000 A 62 ASN N . - A 63 ASP CA . mod.= 4.338 id.= 4.340 dev= 0.002 sig.= 0.000 A 62 ASN CA . - A 63 ASP CA . mod.= 3.782 id.= 3.784 dev= 0.002 sig.= 0.000 A 75 HIS CA . - A 78 GLY C . mod.= 5.913 id.= 5.915 dev= 0.002 sig.= 0.000 A 77 ALA N . - A 77 ALA O . mod.= 3.499 id.= 3.501 dev= 0.002 sig.= 0.000 A 77 ALA N . - A 79 ILE C . mod.= 5.741 id.= 5.743 dev= 0.002 sig.= 0.000 A 77 ALA N . - A 80 ALA CA . mod.= 5.744 id.= 5.747 dev= 0.002 sig.= 0.000 A 77 ALA CA . - A 79 ILE C . mod.= 5.601 id.= 5.603 dev= 0.002 sig.= 0.000 A 120 ILE N . - A 121 ILE CA . mod.= 4.216 id.= 4.218 dev= 0.002 sig.= 0.000 A 120 ILE CA . - A 121 ILE CA . mod.= 3.828 id.= 3.830 dev= 0.002 sig.= 0.000 A 131 ILE N . - A 132 ASN C . mod.= 5.814 id.= 5.816 dev= 0.002 sig.= 0.000 A 138 ASP C . - A 139 CYS C . mod.= 3.065 id.= 3.067 dev= 0.002 sig.= 0.000 A 138 ASP C . - A 140 HIS C . mod.= 5.997 id.= 5.999 dev= 0.002 sig.= 0.000 A 138 ASP O . - A 140 HIS C . mod.= 5.796 id.= 5.798 dev= 0.002 sig.= 0.000 A 148 VAL O . - A 151 ALA N . mod.= 3.230 id.= 3.232 dev= 0.002 sig.= 0.000 A 150 TYR N . - A 153 ASN CA . mod.= 5.486 id.= 5.488 dev= 0.002 sig.= 0.000 A 178 ASN O . - A 180 ILE CA . mod.= 5.607 id.= 5.609 dev= 0.002 sig.= 0.000 A 229 SER O . - A 233 ALA C . mod.= 5.154 id.= 5.157 dev= 0.002 sig.= 0.000 A 232 VAL N . - A 234 GLY C . mod.= 5.578 id.= 5.580 dev= 0.002 sig.= 0.000 A 239 LEU O . - A 243 GLY O . mod.= 5.818 id.= 5.820 dev= 0.002 sig.= 0.000 A 247 ILE CA . - A 250 ARG C . mod.= 5.798 id.= 5.800 dev= 0.002 sig.= 0.000 A 248 GLU N . - A 250 ARG C . mod.= 5.605 id.= 5.607 dev= 0.002 sig.= 0.000 A 273 ASN C . - A 275 TYR O . mod.= 5.774 id.= 5.776 dev= 0.002 sig.= 0.000 B 5 ASP O . - B 88 THR C . mod.= 5.921 id.= 5.924 dev= 0.002 sig.= 0.000 B 6 THR N . - B 88 THR C . mod.= 4.113 id.= 4.115 dev= 0.002 sig.= 0.000 B 6 THR N . - B 90 ILE CA . mod.= 5.637 id.= 5.640 dev= 0.002 sig.= 0.000 B 8 TYR CA . - B 10 GLY CA . mod.= 5.811 id.= 5.813 dev= 0.002 sig.= 0.000 B 8 TYR C . - B 10 GLY CA . mod.= 4.693 id.= 4.696 dev= 0.002 sig.= 0.000 B 9 GLN CA . - B 10 GLY CA . mod.= 3.753 id.= 3.755 dev= 0.002 sig.= 0.000 B 57 TYR CA . - B 58 ASP O . mod.= 4.991 id.= 4.993 dev= 0.002 sig.= 0.000 B 76 VAL O . - B 79 ILE O . mod.= 5.181 id.= 5.184 dev= 0.002 sig.= 0.000 B 80 ALA CA . - B 230 PRO C . mod.= 4.223 id.= 4.225 dev= 0.002 sig.= 0.000 B 80 ALA CA . - B 231 HIS CA . mod.= 5.630 id.= 5.632 dev= 0.002 sig.= 0.000 B 81 ALA O . - B 94 ALA C . mod.= 5.595 id.= 5.597 dev= 0.002 sig.= 0.000 B 118 ASP CA . - B 122 TYR N . mod.= 5.164 id.= 5.166 dev= 0.002 sig.= 0.000 B 163 GLY O . - B 165 ASN CA . mod.= 5.199 id.= 5.201 dev= 0.002 sig.= 0.000 B 164 ASN N . - B 165 ASN CA . mod.= 4.797 id.= 4.799 dev= 0.002 sig.= 0.000 B 164 ASN CA . - B 165 ASN O . mod.= 4.690 id.= 4.692 dev= 0.002 sig.= 0.000 B 207 GLY O . - B 223 SER O . mod.= 4.694 id.= 4.696 dev= 0.002 sig.= 0.000 B 229 SER C . - B 234 GLY N . mod.= 5.972 id.= 5.974 dev= 0.002 sig.= 0.000 B 229 SER O . - B 234 GLY N . mod.= 5.166 id.= 5.168 dev= 0.002 sig.= 0.000 B 230 PRO CA . - B 233 ALA C . mod.= 5.128 id.= 5.130 dev= 0.002 sig.= 0.000 B 230 PRO CA . - B 234 GLY N . mod.= 4.714 id.= 4.716 dev= 0.002 sig.= 0.000 B 232 VAL N . - B 234 GLY C . mod.= 5.578 id.= 5.580 dev= 0.002 sig.= 0.000 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 31 SER HB2 - A 31 SER OG B mod.= 78.71 id.= 109.00 dev= 30.290 sig.= 3.000 A 31 SER HB3 - A 31 SER OG B mod.= 33.62 id.= 109.00 dev= 75.376 sig.= 3.000 A 143 THR HB - A 143 THR CG2 B mod.= 19.35 id.= 108.00 dev= 88.654 sig.= 3.000 B 31 SER HB2 - B 31 SER OG B mod.= 78.80 id.= 109.00 dev= 30.198 sig.= 3.000 B 31 SER HB3 - B 31 SER OG B mod.= 33.58 id.= 109.00 dev= 75.425 sig.= 3.000 B 143 THR HB - B 143 THR CG2 B mod.= 19.46 id.= 108.00 dev= 88.536 sig.= 3.000 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 192 216 180 Maximuum H,K,L : 49 55 43 Minimum acceptable grid spacing: 123 140 109 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 192 216 180 Maximuum H,K,L : 49 55 43 Minimum acceptable grid spacing: 123 140 109 fast hessian tabulation Weight matrix 4.99999989E-03 Actual weight 559.46674 is applied to the X-ray term Norm of X_ray positional gradient 209. Norm of Geom. positional gradient 56.5 Norm of X_ray B-factor gradient 341. Norm of Geom. B-factor gradient 774. Product of X_ray and Geom posit. gradients -0.522E+07 Cosine of angle between them -0.019 Product of X_ray and Geom B-fact gradients 0.596E+08 Cosine of angle between them 0.029 Residuals: XRAY= 0.1875E+09 GEOM= 0.7715E+05 TOTAL= 0.1876E+09 function value 1.87584656E+08 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 4146 0.014 0.020 Bond distances: others 3716 0.000 0.020 External distances: refined atoms 23442 0.001 0.010 Bond angles : refined atoms 5674 1.799 1.925 Bond angles : others 8496 4.516 3.001 Torsion angles, period 1. refined 538 3.685 5.000 Torsion angles, period 2. refined 190 32.629 25.158 Torsion angles, period 3. refined 580 14.633 15.000 Torsion angles, period 3. others 4 10.779 15.000 Torsion angles, period 4. refined 14 20.269 15.000 Chiral centres: refined atoms 644 0.157 0.200 Planar groups: refined atoms 4920 0.014 0.020 Planar groups: others 970 0.020 0.020 VDW repulsions: refined_atoms 583 0.102 0.200 VDW repulsions.others 3315 0.243 0.200 VDW; torsion: refined_atoms 2045 0.180 0.200 VDW; torsion.others 1999 0.130 0.200 HBOND: refined_atoms 78 0.083 0.200 M. chain bond B values: refined atoms 2164 3.323 1.222 M. chain bond B values: others 2163 3.308 1.222 M. chain angle B values: refined atoms 2698 4.146 1.766 M. chain angle B values: others 2699 4.151 1.766 S. chain bond B values: refined atoms 1982 6.088 1.537 S. chain bond B values: others 1982 6.088 1.537 S. chain angle B values: refined atoms 2976 6.948 2.115 S. chain angle B values: others 2976 6.947 2.115 Long range B values: refined atoms 35119 5.636 13.390 Long range B values: others 35117 5.636 13.390 ncsr local: group 1 16805 0.041 0.050 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.992, B = 42.918 Partial structure 1: scale = 0.374, B = 76.309 Overall anisotropic scale factors B11 = -0.35 B22 = 5.94 B33 = -5.60 B12 = 0.00 B13 = -0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1.